diff options
| author | Brendan Fabeny <bf@FreeBSD.org> | 2013-05-28 15:15:05 +0000 |
|---|---|---|
| committer | Brendan Fabeny <bf@FreeBSD.org> | 2013-05-28 15:15:05 +0000 |
| commit | e80e13199698384004812ef82084507a63c6db49 (patch) | |
| tree | 415589d9c68c0b0770aa00cfd4495ce30df83a29 | |
| parent | e84a004d0c124695b02bb3d3ffe2b62c2bbc29f8 (diff) | |
| download | ports-e80e13199698384004812ef82084507a63c6db49.tar.gz ports-e80e13199698384004812ef82084507a63c6db49.zip | |
Notes
140 files changed, 3529 insertions, 740 deletions
diff --git a/astro/R-cran-maptools/Makefile b/astro/R-cran-maptools/Makefile index c2b107ca476d..4b50bc1ed029 100644 --- a/astro/R-cran-maptools/Makefile +++ b/astro/R-cran-maptools/Makefile @@ -3,7 +3,7 @@ PORTNAME= maptools DISTVERSION= 0.8-23 -PORTREVISION= 1 +PORTREVISION= 2 CATEGORIES= astro DISTNAME= ${PORTNAME}_${DISTVERSION} diff --git a/converters/R-cran-RJSONIO/Makefile b/converters/R-cran-RJSONIO/Makefile index 884040359649..7df67e84d56d 100644 --- a/converters/R-cran-RJSONIO/Makefile +++ b/converters/R-cran-RJSONIO/Makefile @@ -3,6 +3,7 @@ PORTNAME= RJSONIO DISTVERSION= 1.0-3 +PORTREVISION= 1 CATEGORIES= converters DISTNAME= ${PORTNAME}_${DISTVERSION} diff --git a/converters/R-cran-rjson/Makefile b/converters/R-cran-rjson/Makefile index 34942d97655d..84ac02bbcbbb 100644 --- a/converters/R-cran-rjson/Makefile +++ b/converters/R-cran-rjson/Makefile @@ -3,7 +3,7 @@ PORTNAME= rjson PORTVERSION= 0.2.12 -PORTREVISION= 1 +PORTREVISION= 2 CATEGORIES= converters DISTNAME= ${PORTNAME}_${PORTVERSION} diff --git a/databases/R-cran-DBI/Makefile b/databases/R-cran-DBI/Makefile index 24dd06e884d0..7371e6950f66 100644 --- a/databases/R-cran-DBI/Makefile +++ b/databases/R-cran-DBI/Makefile @@ -3,6 +3,7 @@ PORTNAME= DBI DISTVERSION= 0.2-7 +PORTREVISION= 1 CATEGORIES= databases DISTNAME= ${PORTNAME}_${DISTVERSION} diff --git a/databases/R-cran-RMySQL/Makefile b/databases/R-cran-RMySQL/Makefile index aeb34b4f2f55..84e0a1a4a306 100644 --- a/databases/R-cran-RMySQL/Makefile +++ b/databases/R-cran-RMySQL/Makefile @@ -3,7 +3,7 @@ PORTNAME= RMySQL DISTVERSION= 0.9-3 -PORTREVISION= 5 +PORTREVISION= 6 CATEGORIES= databases DISTNAME= ${PORTNAME}_${DISTVERSION} diff --git a/databases/R-cran-RSQLite.extfuns/Makefile b/databases/R-cran-RSQLite.extfuns/Makefile index c96643b6778d..1416bb51e049 100644 --- a/databases/R-cran-RSQLite.extfuns/Makefile +++ b/databases/R-cran-RSQLite.extfuns/Makefile @@ -3,7 +3,7 @@ PORTNAME= RSQLite.extfuns PORTVERSION= 0.0.1 -PORTREVISION= 2 +PORTREVISION= 3 CATEGORIES= databases DISTNAME= ${PORTNAME}_${PORTVERSION} diff --git a/databases/R-cran-RSQLite/Makefile b/databases/R-cran-RSQLite/Makefile index afd94537dc45..fb508f2738ff 100644 --- a/databases/R-cran-RSQLite/Makefile +++ b/databases/R-cran-RSQLite/Makefile @@ -3,7 +3,7 @@ PORTNAME= RSQLite PORTVERSION= 0.11.2 -PORTREVISION= 2 +PORTREVISION= 3 CATEGORIES= databases DISTNAME= ${PORTNAME}_${PORTVERSION} diff --git a/databases/R-cran-sqldf/Makefile b/databases/R-cran-sqldf/Makefile index c5ba5674201c..e2a228058bb8 100644 --- a/databases/R-cran-sqldf/Makefile +++ b/databases/R-cran-sqldf/Makefile @@ -3,7 +3,7 @@ PORTNAME= sqldf DISTVERSION= 0.4-6.4 -PORTREVISION= 2 +PORTREVISION= 3 CATEGORIES= databases DISTNAME= ${PORTNAME}_${DISTVERSION} diff --git a/devel/R-cran-Defaults/Makefile b/devel/R-cran-Defaults/Makefile index 3c8cb2cc3503..3ba2e3b471da 100644 --- a/devel/R-cran-Defaults/Makefile +++ b/devel/R-cran-Defaults/Makefile @@ -3,7 +3,7 @@ PORTNAME= Defaults DISTVERSION= 1.1-1 -PORTREVISION= 4 +PORTREVISION= 5 CATEGORIES= devel DISTNAME= ${PORTNAME}_${DISTVERSION} diff --git a/devel/R-cran-Hmisc/Makefile b/devel/R-cran-Hmisc/Makefile index cef55f26e7d9..2fb08587ff30 100644 --- a/devel/R-cran-Hmisc/Makefile +++ b/devel/R-cran-Hmisc/Makefile @@ -2,7 +2,7 @@ PORTNAME= Hmisc DISTVERSION= 3.10-1 -PORTREVISION= 2 +PORTREVISION= 3 CATEGORIES= devel DISTNAME= ${PORTNAME}_${DISTVERSION} diff --git a/devel/R-cran-RUnit/Makefile b/devel/R-cran-RUnit/Makefile index 0e8bf7cff68b..025853052a52 100644 --- a/devel/R-cran-RUnit/Makefile +++ b/devel/R-cran-RUnit/Makefile @@ -3,7 +3,7 @@ PORTNAME= RUnit PORTVERSION= 0.4.26 -PORTREVISION= 2 +PORTREVISION= 3 CATEGORIES= devel DISTNAME= ${PORTNAME}_${PORTVERSION} diff --git a/devel/R-cran-Rcpp/Makefile b/devel/R-cran-Rcpp/Makefile index db74124b6e96..5c5130eea6e5 100644 --- a/devel/R-cran-Rcpp/Makefile +++ b/devel/R-cran-Rcpp/Makefile @@ -3,6 +3,7 @@ PORTNAME= Rcpp PORTVERSION= 0.10.3 +PORTREVISION= 1 CATEGORIES= devel DISTNAME= ${PORTNAME}_${PORTVERSION} diff --git a/devel/R-cran-bitops/Makefile b/devel/R-cran-bitops/Makefile index 8611b45b3d9b..8fc5b8c7325d 100644 --- a/devel/R-cran-bitops/Makefile +++ b/devel/R-cran-bitops/Makefile @@ -3,7 +3,7 @@ PORTNAME= bitops DISTVERSION= 1.0-5 -PORTREVISION= 2 +PORTREVISION= 3 CATEGORIES= devel DISTNAME= ${PORTNAME}_${DISTVERSION} diff --git a/devel/R-cran-caTools/Makefile b/devel/R-cran-caTools/Makefile index 064e1d0966a1..23dc52b4a1ae 100644 --- a/devel/R-cran-caTools/Makefile +++ b/devel/R-cran-caTools/Makefile @@ -3,6 +3,7 @@ PORTNAME= caTools PORTVERSION= 1.14 +PORTREVISION= 1 CATEGORIES= devel DISTNAME= ${PORTNAME}_${PORTVERSION} diff --git a/devel/R-cran-caret/Makefile b/devel/R-cran-caret/Makefile index b958555eaeab..1f5fd37df542 100644 --- a/devel/R-cran-caret/Makefile +++ b/devel/R-cran-caret/Makefile @@ -3,6 +3,7 @@ PORTNAME= caret DISTVERSION= 5.16-04 +PORTREVISION= 1 CATEGORIES= devel DISTNAME= ${PORTNAME}_${DISTVERSION} diff --git a/devel/R-cran-chron/Makefile b/devel/R-cran-chron/Makefile index cf9372b01c97..3eb0b56849c8 100644 --- a/devel/R-cran-chron/Makefile +++ b/devel/R-cran-chron/Makefile @@ -3,7 +3,7 @@ PORTNAME= chron DISTVERSION= 2.3-43 -PORTREVISION= 2 +PORTREVISION= 3 CATEGORIES= devel DISTNAME= ${PORTNAME}_${DISTVERSION} diff --git a/devel/R-cran-foreach/Makefile b/devel/R-cran-foreach/Makefile index c07d2befa35f..8d7bc98e7dea 100644 --- a/devel/R-cran-foreach/Makefile +++ b/devel/R-cran-foreach/Makefile @@ -3,7 +3,7 @@ PORTNAME= foreach PORTVERSION= 1.4.0 -PORTREVISION= 4 +PORTREVISION= 5 CATEGORIES= devel DISTNAME= ${PORTNAME}_${PORTVERSION} diff --git a/devel/R-cran-gbm/Makefile b/devel/R-cran-gbm/Makefile index 117bff254673..6075388effb0 100644 --- a/devel/R-cran-gbm/Makefile +++ b/devel/R-cran-gbm/Makefile @@ -2,7 +2,7 @@ PORTNAME= gbm DISTVERSION= 2.0-8 -PORTREVISION= 1 +PORTREVISION= 2 CATEGORIES= devel DISTNAME= ${PORTNAME}_${DISTVERSION} diff --git a/devel/R-cran-gdata/Makefile b/devel/R-cran-gdata/Makefile index 6add9c776f18..fbd3b05e0f70 100644 --- a/devel/R-cran-gdata/Makefile +++ b/devel/R-cran-gdata/Makefile @@ -3,6 +3,7 @@ PORTNAME= gdata PORTVERSION= 2.12.0.2 +PORTREVISION= 1 CATEGORIES= devel DISTNAME= ${PORTNAME}_${PORTVERSION} diff --git a/devel/R-cran-glmnet/Makefile b/devel/R-cran-glmnet/Makefile index 1a126cfbd301..ac5059d9d17f 100644 --- a/devel/R-cran-glmnet/Makefile +++ b/devel/R-cran-glmnet/Makefile @@ -2,7 +2,7 @@ PORTNAME= glmnet DISTVERSION= 1.8-5 -PORTREVISION= 1 +PORTREVISION= 2 CATEGORIES= devel DISTNAME= ${PORTNAME}_${DISTVERSION} diff --git a/devel/R-cran-gsubfn/Makefile b/devel/R-cran-gsubfn/Makefile index b25d121c397e..3a05f75e302d 100644 --- a/devel/R-cran-gsubfn/Makefile +++ b/devel/R-cran-gsubfn/Makefile @@ -3,7 +3,7 @@ PORTNAME= gsubfn DISTVERSION= 0.6-5 -PORTREVISION= 1 +PORTREVISION= 2 CATEGORIES= devel DISTNAME= ${PORTNAME}_${DISTVERSION} diff --git a/devel/R-cran-gtools/Makefile b/devel/R-cran-gtools/Makefile index 7b254334f5f7..8caf2271ef5d 100644 --- a/devel/R-cran-gtools/Makefile +++ b/devel/R-cran-gtools/Makefile @@ -3,6 +3,7 @@ PORTNAME= gtools PORTVERSION= 2.7.1 +PORTREVISION= 1 CATEGORIES= devel DISTNAME= ${PORTNAME}_${PORTVERSION} diff --git a/devel/R-cran-iterators/Makefile b/devel/R-cran-iterators/Makefile index da417b705c9a..3eec9dea4f74 100644 --- a/devel/R-cran-iterators/Makefile +++ b/devel/R-cran-iterators/Makefile @@ -3,7 +3,7 @@ PORTNAME= iterators PORTVERSION= 1.0.6 -PORTREVISION= 4 +PORTREVISION= 5 CATEGORIES= devel DISTNAME= ${PORTNAME}_${PORTVERSION} diff --git a/devel/R-cran-itertools/Makefile b/devel/R-cran-itertools/Makefile index 2b799496660d..ba5a2c3570a0 100644 --- a/devel/R-cran-itertools/Makefile +++ b/devel/R-cran-itertools/Makefile @@ -3,7 +3,7 @@ PORTNAME= itertools DISTVERSION= 0.1-1 -PORTREVISION= 8 +PORTREVISION= 9 CATEGORIES= devel DISTNAME= ${PORTNAME}_${DISTVERSION} diff --git a/devel/R-cran-memoise/Makefile b/devel/R-cran-memoise/Makefile index 8facacad9764..7df86643414a 100644 --- a/devel/R-cran-memoise/Makefile +++ b/devel/R-cran-memoise/Makefile @@ -3,7 +3,7 @@ PORTNAME= memoise PORTVERSION= 0.1 -PORTREVISION= 4 +PORTREVISION= 5 CATEGORIES= devel DISTNAME= ${PORTNAME}_${PORTVERSION} diff --git a/devel/R-cran-plyr/Makefile b/devel/R-cran-plyr/Makefile index 94adad557e68..0294daee4b1f 100644 --- a/devel/R-cran-plyr/Makefile +++ b/devel/R-cran-plyr/Makefile @@ -3,7 +3,7 @@ PORTNAME= plyr PORTVERSION= 1.8 -PORTREVISION= 2 +PORTREVISION= 3 CATEGORIES= devel DISTNAME= ${PORTNAME}_${DISTVERSION} diff --git a/devel/R-cran-proto/Makefile b/devel/R-cran-proto/Makefile index 796747747c63..c3ff7bad1351 100644 --- a/devel/R-cran-proto/Makefile +++ b/devel/R-cran-proto/Makefile @@ -3,7 +3,7 @@ PORTNAME= proto DISTVERSION= 0.3-10 -PORTREVISION= 2 +PORTREVISION= 3 CATEGORIES= devel DISTNAME= ${PORTNAME}_${DISTVERSION} diff --git a/devel/R-cran-randomForest/Makefile b/devel/R-cran-randomForest/Makefile index ba9bfa052fd8..033b7de7f042 100644 --- a/devel/R-cran-randomForest/Makefile +++ b/devel/R-cran-randomForest/Makefile @@ -2,7 +2,7 @@ PORTNAME= randomForest DISTVERSION= 4.6-7 -PORTREVISION= 1 +PORTREVISION= 2 CATEGORIES= devel DISTNAME= ${PORTNAME}_${DISTVERSION} diff --git a/devel/R-cran-reshape/Makefile b/devel/R-cran-reshape/Makefile index 16345e3a7857..7ed18c1e36d9 100644 --- a/devel/R-cran-reshape/Makefile +++ b/devel/R-cran-reshape/Makefile @@ -3,7 +3,7 @@ PORTNAME= reshape PORTVERSION= 0.8.4 -PORTREVISION= 8 +PORTREVISION= 9 CATEGORIES= devel DISTNAME= ${PORTNAME}_${PORTVERSION} diff --git a/devel/R-cran-reshape2/Makefile b/devel/R-cran-reshape2/Makefile index dc912895bd19..a2ac444172fc 100644 --- a/devel/R-cran-reshape2/Makefile +++ b/devel/R-cran-reshape2/Makefile @@ -3,7 +3,7 @@ PORTNAME= reshape2 PORTVERSION= 1.2.2 -PORTREVISION= 2 +PORTREVISION= 3 CATEGORIES= devel DISTNAME= ${PORTNAME}_${PORTVERSION} diff --git a/finance/R-cran-PerformanceAnalytics/Makefile b/finance/R-cran-PerformanceAnalytics/Makefile index 402936e9146a..dca4a82c2316 100644 --- a/finance/R-cran-PerformanceAnalytics/Makefile +++ b/finance/R-cran-PerformanceAnalytics/Makefile @@ -3,7 +3,7 @@ PORTNAME= PerformanceAnalytics PORTVERSION= 1.1.0 -PORTREVISION= 1 +PORTREVISION= 2 CATEGORIES= finance DISTNAME= ${PORTNAME}_${PORTVERSION} diff --git a/finance/R-cran-RFinanceYJ/Makefile b/finance/R-cran-RFinanceYJ/Makefile index a7ad19d0e00e..d1c247d7f54d 100644 --- a/finance/R-cran-RFinanceYJ/Makefile +++ b/finance/R-cran-RFinanceYJ/Makefile @@ -3,7 +3,7 @@ PORTNAME= RFinanceYJ PORTVERSION= 0.1.6 -PORTREVISION= 8 +PORTREVISION= 9 CATEGORIES= finance DISTNAME= ${PORTNAME}_${PORTVERSION} diff --git a/finance/R-cran-TTR/Makefile b/finance/R-cran-TTR/Makefile index f6e5435ebcfe..ea8eefabcf15 100644 --- a/finance/R-cran-TTR/Makefile +++ b/finance/R-cran-TTR/Makefile @@ -3,6 +3,7 @@ PORTNAME= TTR DISTVERSION= 0.22-0 +PORTREVISION= 1 CATEGORIES= finance DISTNAME= ${PORTNAME}_${DISTVERSION} diff --git a/finance/R-cran-ccgarch/Makefile b/finance/R-cran-ccgarch/Makefile index 4d46c5c5f46d..94c0c59b40e3 100644 --- a/finance/R-cran-ccgarch/Makefile +++ b/finance/R-cran-ccgarch/Makefile @@ -3,7 +3,7 @@ PORTNAME= ccgarch DISTVERSION= 0.2.0-2 -PORTREVISION= 1 +PORTREVISION= 2 CATEGORIES= finance DISTNAME= ${PORTNAME}_${DISTVERSION} diff --git a/finance/R-cran-fBasics/Makefile b/finance/R-cran-fBasics/Makefile index 8a7dd7138eba..cf7d84ee6102 100644 --- a/finance/R-cran-fBasics/Makefile +++ b/finance/R-cran-fBasics/Makefile @@ -3,6 +3,7 @@ PORTNAME= fBasics PORTVERSION= 3010.86 +PORTREVISION= 1 CATEGORIES= finance DISTNAME= ${PORTNAME}_${PORTVERSION} diff --git a/finance/R-cran-fGarch/Makefile b/finance/R-cran-fGarch/Makefile index e8da598c5e2b..283dd32f275b 100644 --- a/finance/R-cran-fGarch/Makefile +++ b/finance/R-cran-fGarch/Makefile @@ -3,6 +3,7 @@ PORTNAME= fGarch PORTVERSION= 3010.82 +PORTREVISION= 1 CATEGORIES= finance DISTNAME= ${PORTNAME}_${PORTVERSION} diff --git a/finance/R-cran-gmm/Makefile b/finance/R-cran-gmm/Makefile index d8986f7d9095..5b580aa725d2 100644 --- a/finance/R-cran-gmm/Makefile +++ b/finance/R-cran-gmm/Makefile @@ -3,7 +3,7 @@ PORTNAME= gmm DISTVERSION= 1.4-5 -PORTREVISION= 1 +PORTREVISION= 2 CATEGORIES= finance DISTNAME= ${PORTNAME}_${DISTVERSION} diff --git a/finance/R-cran-lmtest/Makefile b/finance/R-cran-lmtest/Makefile index c0caa116fb3f..baf2d2f89ab3 100644 --- a/finance/R-cran-lmtest/Makefile +++ b/finance/R-cran-lmtest/Makefile @@ -3,6 +3,7 @@ PORTNAME= lmtest DISTVERSION= 0.9-31 +PORTREVISION= 1 CATEGORIES= finance DISTNAME= ${PORTNAME}_${DISTVERSION} diff --git a/finance/R-cran-plm/Makefile b/finance/R-cran-plm/Makefile index fb0dae0a1cb9..b13292ed2243 100644 --- a/finance/R-cran-plm/Makefile +++ b/finance/R-cran-plm/Makefile @@ -3,7 +3,7 @@ PORTNAME= plm DISTVERSION= 1.3-1 -PORTREVISION= 2 +PORTREVISION= 3 CATEGORIES= finance DISTNAME= ${PORTNAME}_${DISTVERSION} diff --git a/finance/R-cran-quantmod/Makefile b/finance/R-cran-quantmod/Makefile index 9e8b99ae89ce..b0eb7111fe2f 100644 --- a/finance/R-cran-quantmod/Makefile +++ b/finance/R-cran-quantmod/Makefile @@ -3,7 +3,7 @@ PORTNAME= quantmod DISTVERSION= 0.4-0 -PORTREVISION= 1 +PORTREVISION= 2 CATEGORIES= finance DISTNAME= ${PORTNAME}_${DISTVERSION} diff --git a/finance/R-cran-strucchange/Makefile b/finance/R-cran-strucchange/Makefile index 42d114655501..9edf0485354c 100644 --- a/finance/R-cran-strucchange/Makefile +++ b/finance/R-cran-strucchange/Makefile @@ -3,7 +3,7 @@ PORTNAME= strucchange DISTVERSION= 1.4-7 -PORTREVISION= 3 +PORTREVISION= 4 CATEGORIES= finance DISTNAME= ${PORTNAME}_${DISTVERSION} diff --git a/finance/R-cran-timeDate/Makefile b/finance/R-cran-timeDate/Makefile index 13c0b1058394..73cecdb8ae35 100644 --- a/finance/R-cran-timeDate/Makefile +++ b/finance/R-cran-timeDate/Makefile @@ -3,6 +3,7 @@ PORTNAME= timeDate PORTVERSION= 3010.98 +PORTREVISION= 1 CATEGORIES= finance DISTNAME= ${PORTNAME}_${PORTVERSION} diff --git a/finance/R-cran-timeSeries/Makefile b/finance/R-cran-timeSeries/Makefile index fce61278492d..b0eda17b7cec 100644 --- a/finance/R-cran-timeSeries/Makefile +++ b/finance/R-cran-timeSeries/Makefile @@ -3,6 +3,7 @@ PORTNAME= timeSeries PORTVERSION= 3010.97 +PORTREVISION= 1 CATEGORIES= finance DISTNAME= ${PORTNAME}_${PORTVERSION} diff --git a/finance/R-cran-tseries/Makefile b/finance/R-cran-tseries/Makefile index b9fdfa9f0594..d18ce046dd4c 100644 --- a/finance/R-cran-tseries/Makefile +++ b/finance/R-cran-tseries/Makefile @@ -3,6 +3,7 @@ PORTNAME= tseries DISTVERSION= 0.10-32 +PORTREVISION= 1 CATEGORIES= finance DISTNAME= ${PORTNAME}_${DISTVERSION} diff --git a/finance/R-cran-urca/Makefile b/finance/R-cran-urca/Makefile index 23a3fe9164de..a728ec538aa8 100644 --- a/finance/R-cran-urca/Makefile +++ b/finance/R-cran-urca/Makefile @@ -3,7 +3,7 @@ PORTNAME= urca DISTVERSION= 1.2-7 -PORTREVISION= 2 +PORTREVISION= 3 CATEGORIES= finance DISTNAME= ${PORTNAME}_${DISTVERSION} diff --git a/finance/R-cran-vars/Makefile b/finance/R-cran-vars/Makefile index 1f245a698d04..7d1774c1cfd1 100644 --- a/finance/R-cran-vars/Makefile +++ b/finance/R-cran-vars/Makefile @@ -3,7 +3,7 @@ PORTNAME= vars DISTVERSION= 1.5-0 -PORTREVISION= 2 +PORTREVISION= 3 CATEGORIES= finance DISTNAME= ${PORTNAME}_${DISTVERSION} diff --git a/ftp/R-cran-RCurl/Makefile b/ftp/R-cran-RCurl/Makefile index dabf58ba9f00..52cadf3eb9ac 100644 --- a/ftp/R-cran-RCurl/Makefile +++ b/ftp/R-cran-RCurl/Makefile @@ -3,6 +3,7 @@ PORTNAME= RCurl DISTVERSION= 1.95-4.1 +PORTREVISION= 1 CATEGORIES= ftp DISTNAME= ${PORTNAME}_${DISTVERSION} diff --git a/graphics/R-cran-GDD/Makefile b/graphics/R-cran-GDD/Makefile index 7db00ea987d4..698ec7f4d5ae 100644 --- a/graphics/R-cran-GDD/Makefile +++ b/graphics/R-cran-GDD/Makefile @@ -3,7 +3,7 @@ PORTNAME= GDD DISTVERSION= 0.1-13.1 -PORTREVISION= 3 +PORTREVISION= 4 CATEGORIES= graphics DISTNAME= ${PORTNAME}_${DISTVERSION} diff --git a/graphics/R-cran-RColorBrewer/Makefile b/graphics/R-cran-RColorBrewer/Makefile index 7a2da12ef710..f96a5313afef 100644 --- a/graphics/R-cran-RColorBrewer/Makefile +++ b/graphics/R-cran-RColorBrewer/Makefile @@ -3,7 +3,7 @@ PORTNAME= RColorBrewer DISTVERSION= 1.0-5 -PORTREVISION= 8 +PORTREVISION= 9 CATEGORIES= graphics DISTNAME= ${PORTNAME}_${DISTVERSION} diff --git a/graphics/R-cran-colorspace/Makefile b/graphics/R-cran-colorspace/Makefile index 5283555b56c1..a9c7ba2fe896 100644 --- a/graphics/R-cran-colorspace/Makefile +++ b/graphics/R-cran-colorspace/Makefile @@ -3,6 +3,7 @@ PORTNAME= colorspace DISTVERSION= 1.2-2 +PORTREVISION= 1 CATEGORIES= graphics DISTNAME= ${PORTNAME}_${DISTVERSION} diff --git a/graphics/R-cran-diagram/Makefile b/graphics/R-cran-diagram/Makefile index bac2ac0214cd..3d804a326a40 100644 --- a/graphics/R-cran-diagram/Makefile +++ b/graphics/R-cran-diagram/Makefile @@ -3,6 +3,7 @@ PORTNAME= diagram PORTVERSION= 1.6.1 +PORTREVISION= 1 CATEGORIES= graphics DISTNAME= ${PORTNAME}_${PORTVERSION} diff --git a/graphics/R-cran-dichromat/Makefile b/graphics/R-cran-dichromat/Makefile index d4a7aa18c003..2e39126f3da3 100644 --- a/graphics/R-cran-dichromat/Makefile +++ b/graphics/R-cran-dichromat/Makefile @@ -3,7 +3,7 @@ PORTNAME= dichromat DISTVERSION= 2.0-0 -PORTREVISION= 1 +PORTREVISION= 2 CATEGORIES= graphics DISTNAME= ${PORTNAME}_${DISTVERSION} diff --git a/graphics/R-cran-ggplot2/Makefile b/graphics/R-cran-ggplot2/Makefile index 936a9b06b883..cb0d5a62ac48 100644 --- a/graphics/R-cran-ggplot2/Makefile +++ b/graphics/R-cran-ggplot2/Makefile @@ -2,7 +2,7 @@ PORTNAME= ggplot2 PORTVERSION= 0.9.3.1 -PORTREVISION= 1 +PORTREVISION= 2 CATEGORIES= graphics DISTNAME= ${PORTNAME}_${PORTVERSION} diff --git a/graphics/R-cran-munsell/Makefile b/graphics/R-cran-munsell/Makefile index 024a69af3412..a9904776640d 100644 --- a/graphics/R-cran-munsell/Makefile +++ b/graphics/R-cran-munsell/Makefile @@ -3,7 +3,7 @@ PORTNAME= munsell PORTVERSION= 0.4 -PORTREVISION= 2 +PORTREVISION= 3 CATEGORIES= graphics DISTNAME= ${PORTNAME}_${PORTVERSION} diff --git a/graphics/R-cran-pixmap/Makefile b/graphics/R-cran-pixmap/Makefile index cba7b82e5357..2c1b64f6851d 100644 --- a/graphics/R-cran-pixmap/Makefile +++ b/graphics/R-cran-pixmap/Makefile @@ -3,7 +3,7 @@ PORTNAME= pixmap DISTVERSION= 0.4-11 -PORTREVISION= 5 +PORTREVISION= 6 CATEGORIES= graphics DISTNAME= ${PORTNAME}_${DISTVERSION} diff --git a/graphics/R-cran-png/Makefile b/graphics/R-cran-png/Makefile index 9848b9d9e583..0df0d36bee44 100644 --- a/graphics/R-cran-png/Makefile +++ b/graphics/R-cran-png/Makefile @@ -3,7 +3,7 @@ PORTNAME= png DISTVERSION= 0.1-4 -PORTREVISION= 2 +PORTREVISION= 3 CATEGORIES= graphics DISTNAME= ${PORTNAME}_${DISTVERSION} diff --git a/graphics/R-cran-rgdal/Makefile b/graphics/R-cran-rgdal/Makefile index b079b001a387..94275144fe4e 100644 --- a/graphics/R-cran-rgdal/Makefile +++ b/graphics/R-cran-rgdal/Makefile @@ -3,6 +3,7 @@ PORTNAME= rgdal DISTVERSION= 0.8-9 +PORTREVISION= 1 CATEGORIES= graphics DISTNAME= ${PORTNAME}_${DISTVERSION} diff --git a/graphics/R-cran-rtiff/Makefile b/graphics/R-cran-rtiff/Makefile index 368e3457f397..6f17a28546f9 100644 --- a/graphics/R-cran-rtiff/Makefile +++ b/graphics/R-cran-rtiff/Makefile @@ -3,7 +3,7 @@ PORTNAME= rtiff PORTVERSION= 1.4.2 -PORTREVISION= 1 +PORTREVISION= 2 CATEGORIES= graphics DISTNAME= ${PORTNAME}_${PORTVERSION} diff --git a/graphics/R-cran-scales/Makefile b/graphics/R-cran-scales/Makefile index 32f29e60fa51..8130cd773ad0 100644 --- a/graphics/R-cran-scales/Makefile +++ b/graphics/R-cran-scales/Makefile @@ -2,7 +2,7 @@ PORTNAME= scales PORTVERSION= 0.2.3 -PORTREVISION= 2 +PORTREVISION= 3 CATEGORIES= graphics DISTNAME= ${PORTNAME}_${PORTVERSION} diff --git a/graphics/R-cran-shape/Makefile b/graphics/R-cran-shape/Makefile index 3e60aac8e027..d5473160f511 100644 --- a/graphics/R-cran-shape/Makefile +++ b/graphics/R-cran-shape/Makefile @@ -3,7 +3,7 @@ PORTNAME= shape PORTVERSION= 1.4.0 -PORTREVISION= 2 +PORTREVISION= 3 CATEGORIES= graphics DISTNAME= ${PORTNAME}_${PORTVERSION} diff --git a/math/R-cran-ChangeAnomalyDetection/Makefile b/math/R-cran-ChangeAnomalyDetection/Makefile index 8da221ac33eb..055bb161e2e0 100644 --- a/math/R-cran-ChangeAnomalyDetection/Makefile +++ b/math/R-cran-ChangeAnomalyDetection/Makefile @@ -3,6 +3,7 @@ PORTNAME= ChangeAnomalyDetection PORTVERSION= 0.1.0 +PORTREVISION= 1 CATEGORIES= math DISTNAME= ${PORTNAME}_${PORTVERSION} diff --git a/math/R-cran-Formula/Makefile b/math/R-cran-Formula/Makefile index 277cbbde125d..613f85976656 100644 --- a/math/R-cran-Formula/Makefile +++ b/math/R-cran-Formula/Makefile @@ -3,6 +3,7 @@ PORTNAME= Formula DISTVERSION= 1.1-1 +PORTREVISION= 1 CATEGORIES= math DISTNAME= ${PORTNAME}_${DISTVERSION} diff --git a/math/R-cran-KFAS/Makefile b/math/R-cran-KFAS/Makefile index c3d452f3d62d..4d016b2bdb0c 100644 --- a/math/R-cran-KFAS/Makefile +++ b/math/R-cran-KFAS/Makefile @@ -3,7 +3,7 @@ PORTNAME= KFAS PORTVERSION= 0.9.11 -PORTREVISION= 2 +PORTREVISION= 3 CATEGORIES= math DISTNAME= ${PORTNAME}_${PORTVERSION} diff --git a/math/R-cran-LearnBayes/Makefile b/math/R-cran-LearnBayes/Makefile index f04c0c123954..635292c8393a 100644 --- a/math/R-cran-LearnBayes/Makefile +++ b/math/R-cran-LearnBayes/Makefile @@ -3,7 +3,7 @@ PORTNAME= LearnBayes PORTVERSION= 2.12 -PORTREVISION= 2 +PORTREVISION= 3 CATEGORIES= math DISTNAME= ${PORTNAME}_${PORTVERSION} diff --git a/math/R-cran-MCMCpack/Makefile b/math/R-cran-MCMCpack/Makefile index 253ba8f10985..171053d64962 100644 --- a/math/R-cran-MCMCpack/Makefile +++ b/math/R-cran-MCMCpack/Makefile @@ -3,6 +3,7 @@ PORTNAME= MCMCpack DISTVERSION= 1.3-3 +PORTREVISION= 1 CATEGORIES= math DISTNAME= ${PORTNAME}_${DISTVERSION} diff --git a/math/R-cran-RHmm/Makefile b/math/R-cran-RHmm/Makefile index 8241e85f0f8d..9c3efa176a10 100644 --- a/math/R-cran-RHmm/Makefile +++ b/math/R-cran-RHmm/Makefile @@ -3,6 +3,7 @@ PORTNAME= RHmm PORTVERSION= 2.0.3 +PORTREVISION= 1 CATEGORIES= math DISTNAME= ${PORTNAME}_${PORTVERSION} diff --git a/math/R-cran-RSvgDevice/Makefile b/math/R-cran-RSvgDevice/Makefile index 69a84dee5713..7f7b16442bc3 100644 --- a/math/R-cran-RSvgDevice/Makefile +++ b/math/R-cran-RSvgDevice/Makefile @@ -3,7 +3,7 @@ PORTNAME= RSvgDevice PORTVERSION= 0.6.4.2 -PORTREVISION= 1 +PORTREVISION= 2 CATEGORIES= math DISTNAME= ${PORTNAME}_${PORTVERSION} diff --git a/math/R-cran-RcppArmadillo/Makefile b/math/R-cran-RcppArmadillo/Makefile index 81f33ef9be41..11c33567beff 100644 --- a/math/R-cran-RcppArmadillo/Makefile +++ b/math/R-cran-RcppArmadillo/Makefile @@ -3,6 +3,7 @@ PORTNAME= RcppArmadillo PORTVERSION= 0.3.820 +PORTREVISION= 1 CATEGORIES= math DISTNAME= ${PORTNAME}_${PORTVERSION} diff --git a/math/R-cran-SuppDists/Makefile b/math/R-cran-SuppDists/Makefile index 434b9d5644a2..2a169124b11b 100644 --- a/math/R-cran-SuppDists/Makefile +++ b/math/R-cran-SuppDists/Makefile @@ -3,6 +3,7 @@ PORTNAME= SuppDists DISTVERSION= 1.1-9 +PORTREVISION= 1 CATEGORIES= math MASTER_SITES= ${MASTER_SITE_CRAN} \ http://r.research.att.com/benchmarks/:benchmark \ diff --git a/math/R-cran-Zelig/Makefile b/math/R-cran-Zelig/Makefile index 10b8ff82c6e8..1b7472c24489 100644 --- a/math/R-cran-Zelig/Makefile +++ b/math/R-cran-Zelig/Makefile @@ -3,6 +3,7 @@ PORTNAME= Zelig DISTVERSION= 4.1-3 +PORTREVISION= 1 CATEGORIES= math DISTNAME= ${PORTNAME}_${DISTVERSION} diff --git a/math/R-cran-bdsmatrix/Makefile b/math/R-cran-bdsmatrix/Makefile index ae51a16d7990..0b4a09dcd898 100644 --- a/math/R-cran-bdsmatrix/Makefile +++ b/math/R-cran-bdsmatrix/Makefile @@ -3,6 +3,7 @@ PORTNAME= bdsmatrix DISTVERSION= 1.3-1 +PORTREVISION= 1 CATEGORIES= math DISTNAME= ${PORTNAME}_${DISTVERSION} diff --git a/math/R-cran-car/Makefile b/math/R-cran-car/Makefile index 817a63ecf658..0adf7d8a9dda 100644 --- a/math/R-cran-car/Makefile +++ b/math/R-cran-car/Makefile @@ -3,6 +3,7 @@ PORTNAME= car DISTVERSION= 2.0-17 +PORTREVISION= 1 CATEGORIES= math DISTNAME= ${PORTNAME}_${DISTVERSION} diff --git a/math/R-cran-coda/Makefile b/math/R-cran-coda/Makefile index a77df8472d4d..6f5fef30f7ba 100644 --- a/math/R-cran-coda/Makefile +++ b/math/R-cran-coda/Makefile @@ -3,7 +3,7 @@ PORTNAME= coda DISTVERSION= 0.16-1 -PORTREVISION= 1 +PORTREVISION= 2 CATEGORIES= math DISTNAME= ${PORTNAME}_${DISTVERSION} diff --git a/math/R-cran-deldir/Makefile b/math/R-cran-deldir/Makefile index abcc7edf5fed..658d98294717 100644 --- a/math/R-cran-deldir/Makefile +++ b/math/R-cran-deldir/Makefile @@ -3,6 +3,7 @@ PORTNAME= deldir DISTVERSION= 0.0-22 +PORTREVISION= 1 CATEGORIES= math DISTNAME= ${PORTNAME}_${DISTVERSION} diff --git a/math/R-cran-dlmodeler/Makefile b/math/R-cran-dlmodeler/Makefile index 990c14f90382..cdaf01635d3e 100644 --- a/math/R-cran-dlmodeler/Makefile +++ b/math/R-cran-dlmodeler/Makefile @@ -3,7 +3,7 @@ PORTNAME= dlmodeler DISTVERSION= 1.2-1 -PORTREVISION= 2 +PORTREVISION= 3 CATEGORIES= math DISTNAME= ${PORTNAME}_${DISTVERSION} diff --git a/math/R-cran-forecast/Makefile b/math/R-cran-forecast/Makefile index bb99398e35d8..81ea6c42fe1c 100644 --- a/math/R-cran-forecast/Makefile +++ b/math/R-cran-forecast/Makefile @@ -3,6 +3,7 @@ PORTNAME= forecast PORTVERSION= 4.04 +PORTREVISION= 1 CATEGORIES= math DISTNAME= ${PORTNAME}_${PORTVERSION} diff --git a/math/R-cran-fracdiff/Makefile b/math/R-cran-fracdiff/Makefile index 9167235a6efe..dac42417ad4d 100644 --- a/math/R-cran-fracdiff/Makefile +++ b/math/R-cran-fracdiff/Makefile @@ -3,6 +3,7 @@ PORTNAME= fracdiff DISTVERSION= 1.4-2 +PORTREVISION= 1 CATEGORIES= math DISTNAME= ${PORTNAME}_${DISTVERSION} diff --git a/math/R-cran-gpclib/Makefile b/math/R-cran-gpclib/Makefile index d4a70610662b..6fffd09d0fbb 100644 --- a/math/R-cran-gpclib/Makefile +++ b/math/R-cran-gpclib/Makefile @@ -3,6 +3,7 @@ PORTNAME= gpclib DISTVERSION= 1.5-5 +PORTREVISION= 1 CATEGORIES= math DISTNAME= ${PORTNAME}_${DISTVERSION} diff --git a/math/R-cran-gss/Makefile b/math/R-cran-gss/Makefile index 32951f21de21..aaf956c33a46 100644 --- a/math/R-cran-gss/Makefile +++ b/math/R-cran-gss/Makefile @@ -3,6 +3,7 @@ PORTNAME= gss DISTVERSION= 2.0-14 +PORTREVISION= 1 CATEGORIES= math DISTNAME= ${PORTNAME}_${DISTVERSION} diff --git a/math/R-cran-gtable/Makefile b/math/R-cran-gtable/Makefile index 74c9dab36d48..39399399d6d6 100644 --- a/math/R-cran-gtable/Makefile +++ b/math/R-cran-gtable/Makefile @@ -2,7 +2,7 @@ PORTNAME= gtable PORTVERSION= 0.1.2 -PORTREVISION= 2 +PORTREVISION= 3 CATEGORIES= math DISTNAME= ${PORTNAME}_${PORTVERSION} diff --git a/math/R-cran-igraph/Makefile b/math/R-cran-igraph/Makefile index 13deb26fdea2..03672f2d9c13 100644 --- a/math/R-cran-igraph/Makefile +++ b/math/R-cran-igraph/Makefile @@ -3,7 +3,7 @@ PORTNAME= igraph DISTVERSION= 0.6.5-1 -PORTREVISION= 1 +PORTREVISION= 2 CATEGORIES= math DISTNAME= ${PORTNAME}_${DISTVERSION} diff --git a/math/R-cran-inline/Makefile b/math/R-cran-inline/Makefile index 0eacbe35e4f3..4a5a13922d9f 100644 --- a/math/R-cran-inline/Makefile +++ b/math/R-cran-inline/Makefile @@ -3,6 +3,7 @@ PORTNAME= inline PORTVERSION= 0.3.11 +PORTREVISION= 1 CATEGORIES= math DISTNAME= ${PORTNAME}_${PORTVERSION} diff --git a/math/R-cran-labeling/Makefile b/math/R-cran-labeling/Makefile index 4c9b72a47dc0..566553f9f59a 100644 --- a/math/R-cran-labeling/Makefile +++ b/math/R-cran-labeling/Makefile @@ -3,7 +3,7 @@ PORTNAME= labeling PORTVERSION= 0.1 -PORTREVISION= 3 +PORTREVISION= 4 CATEGORIES= math DISTNAME= ${PORTNAME}_${PORTVERSION} diff --git a/math/R-cran-labeling/distinfo b/math/R-cran-labeling/distinfo index 232943365ef7..6ac82bba56ff 100644 --- a/math/R-cran-labeling/distinfo +++ b/math/R-cran-labeling/distinfo @@ -1,2 +1,2 @@ -SHA256 (labeling_0.1.tar.gz) = 7a7c0fedd64eeb15ff518bdf93c5d8f4ecf34d3f9293dd8b491e3dff7f419332 -SIZE (labeling_0.1.tar.gz) = 9049 +SHA256 (labeling_0.1.tar.gz) = 381e9ee4c981eec1640926885f410067408e4ac75abe553d7311e566400f8299 +SIZE (labeling_0.1.tar.gz) = 9992 diff --git a/math/R-cran-memisc/Makefile b/math/R-cran-memisc/Makefile index ed2c45ebe936..7240d95bea29 100644 --- a/math/R-cran-memisc/Makefile +++ b/math/R-cran-memisc/Makefile @@ -3,6 +3,7 @@ PORTNAME= memisc DISTVERSION= 0.96-4 +PORTREVISION= 1 CATEGORIES= math DISTNAME= ${PORTNAME}_${DISTVERSION} diff --git a/math/R-cran-mvtnorm/Makefile b/math/R-cran-mvtnorm/Makefile index 2a327bb16412..99f3c3a97f44 100644 --- a/math/R-cran-mvtnorm/Makefile +++ b/math/R-cran-mvtnorm/Makefile @@ -3,7 +3,7 @@ PORTNAME= mvtnorm PORTVERSION= 0.9.96 -PORTREVISION= 10 +PORTREVISION= 11 CATEGORIES= math DISTNAME= ${PORTNAME}_${PORTVERSION:C/\./-/g:C/-/\./1} diff --git a/math/R-cran-nnls/Makefile b/math/R-cran-nnls/Makefile index 508c3b9c5201..e7fc3613f045 100644 --- a/math/R-cran-nnls/Makefile +++ b/math/R-cran-nnls/Makefile @@ -3,7 +3,7 @@ PORTNAME= nnls PORTVERSION= 1.4 -PORTREVISION= 2 +PORTREVISION= 3 CATEGORIES= math DISTNAME= ${PORTNAME}_${PORTVERSION} diff --git a/math/R-cran-outliers/Makefile b/math/R-cran-outliers/Makefile index f3e4f15e9856..5b63d1575d8b 100644 --- a/math/R-cran-outliers/Makefile +++ b/math/R-cran-outliers/Makefile @@ -3,6 +3,7 @@ PORTNAME= outliers PORTVERSION= 0.14 +PORTREVISION= 1 CATEGORIES= math DISTNAME= ${PORTNAME}_${PORTVERSION} diff --git a/math/R-cran-psych/Makefile b/math/R-cran-psych/Makefile index dc5c5aa6c8af..1b66368260b5 100644 --- a/math/R-cran-psych/Makefile +++ b/math/R-cran-psych/Makefile @@ -3,7 +3,7 @@ PORTNAME= psych PORTVERSION= 1.2.1 -PORTREVISION= 3 +PORTREVISION= 4 CATEGORIES= math science DISTNAME= ${PORTNAME}_${PORTVERSION} diff --git a/math/R-cran-quadprog/Makefile b/math/R-cran-quadprog/Makefile index eb0061770c0a..d68f5339a3fb 100644 --- a/math/R-cran-quadprog/Makefile +++ b/math/R-cran-quadprog/Makefile @@ -3,6 +3,7 @@ PORTNAME= quadprog DISTVERSION= 1.5-5 +PORTREVISION= 1 CATEGORIES= math DISTNAME= ${PORTNAME}_${DISTVERSION} diff --git a/math/R-cran-sandwich/Makefile b/math/R-cran-sandwich/Makefile index 2a86ca1012bf..4dc51959c1a2 100644 --- a/math/R-cran-sandwich/Makefile +++ b/math/R-cran-sandwich/Makefile @@ -3,6 +3,7 @@ PORTNAME= sandwich DISTVERSION= 2.2-10 +PORTREVISION= 1 CATEGORIES= math DISTNAME= ${PORTNAME}_${DISTVERSION} diff --git a/math/R-cran-sm/Makefile b/math/R-cran-sm/Makefile index 91630d7ffd84..116b0c505d15 100644 --- a/math/R-cran-sm/Makefile +++ b/math/R-cran-sm/Makefile @@ -3,7 +3,7 @@ PORTNAME= sm DISTVERSION= 2.2-4.1 -PORTREVISION= 10 +PORTREVISION= 11 CATEGORIES= math DISTNAME= ${PORTNAME}_${DISTVERSION} diff --git a/math/R-cran-sp/Makefile b/math/R-cran-sp/Makefile index 180b15513f29..d3541ff93c7b 100644 --- a/math/R-cran-sp/Makefile +++ b/math/R-cran-sp/Makefile @@ -3,6 +3,7 @@ PORTNAME= sp DISTVERSION= 1.0-9 +PORTREVISION= 1 CATEGORIES= math DISTNAME= ${PORTNAME}_${DISTVERSION} diff --git a/math/R-cran-spdep/Makefile b/math/R-cran-spdep/Makefile index 7e3844d65809..fc9e11e83c4b 100644 --- a/math/R-cran-spdep/Makefile +++ b/math/R-cran-spdep/Makefile @@ -3,7 +3,7 @@ PORTNAME= spdep DISTVERSION= 0.5-56 -PORTREVISION= 1 +PORTREVISION= 2 CATEGORIES= math DISTNAME= ${PORTNAME}_${DISTVERSION} diff --git a/math/R-cran-stabledist/Makefile b/math/R-cran-stabledist/Makefile index dd6d30eaf09e..e57944c2370f 100644 --- a/math/R-cran-stabledist/Makefile +++ b/math/R-cran-stabledist/Makefile @@ -3,7 +3,7 @@ PORTNAME= stabledist DISTVERSION= 0.6-5 -PORTREVISION= 2 +PORTREVISION= 3 CATEGORIES= math DISTNAME= ${PORTNAME}_${DISTVERSION} diff --git a/math/R-cran-xts/Makefile b/math/R-cran-xts/Makefile index 0c2e24acb70c..79dcb8afddee 100644 --- a/math/R-cran-xts/Makefile +++ b/math/R-cran-xts/Makefile @@ -3,7 +3,7 @@ PORTNAME= xts DISTVERSION= 0.9-3 -PORTREVISION= 1 +PORTREVISION= 2 CATEGORIES= math DISTNAME= ${PORTNAME}_${DISTVERSION} diff --git a/math/R-cran-zoo/Makefile b/math/R-cran-zoo/Makefile index 23b920b4f66e..e26daa587caf 100644 --- a/math/R-cran-zoo/Makefile +++ b/math/R-cran-zoo/Makefile @@ -3,7 +3,7 @@ PORTNAME= zoo DISTVERSION= 1.7-9 -PORTREVISION= 2 +PORTREVISION= 3 CATEGORIES= math DISTNAME= ${PORTNAME}_${DISTVERSION} diff --git a/math/R/Makefile b/math/R/Makefile index b64dea7c1dbb..82cfb4618c59 100644 --- a/math/R/Makefile +++ b/math/R/Makefile @@ -2,22 +2,23 @@ # $FreeBSD$ PORTNAME?= R -PORTVERSION= 2.15.3 +PORTVERSION= 3.0.1 CATEGORIES= math lang -MASTER_SITES= http://cran.r-project.org/src/base/R-2/ \ - ftp://cran.r-project.org/pub/R/src/base/R-2/ \ - http://cran.at.r-project.org/src/base/R-2/ \ - http://cran.au.r-project.org/src/base/R-2/ \ - http://cran.br.r-project.org/src/base/R-2/ \ - http://cran.ch.r-project.org/src/base/R-2/ \ - http://cran.es.r-project.org/src/base/R-2/ \ - http://cran.dk.r-project.org/src/base/R-2/ \ - http://cran.uk.r-project.org/src/base/R-2/ \ - http://cran.us.r-project.org/src/base/R-2/ \ - ftp://ftp.u-aizu.ac.jp/pub/lang/R/CRAN/src/base/R-2/ \ - http://lib.stat.cmu.edu/R/CRAN/src/base/R-2/ \ - http://cran.stat.ucla.edu/src/base/R-2/ \ - http://probability.ca/cran/src/base/R-2/ +MASTER_SITES= http://cran.r-project.org/%SUBDIR%/ \ + ftp://cran.r-project.org/pub/R/%SUBDIR%/ \ + http://cran.at.r-project.org/%SUBDIR%/ \ + http://cran.au.r-project.org/%SUBDIR%/ \ + http://cran.br.r-project.org/%SUBDIR%/ \ + http://cran.ch.r-project.org/%SUBDIR%/ \ + http://cran.es.r-project.org/%SUBDIR%/ \ + http://cran.dk.r-project.org/%SUBDIR%/ \ + http://cran.uk.r-project.org/%SUBDIR%/ \ + http://cran.us.r-project.org/%SUBDIR%/ \ + ftp://ftp.u-aizu.ac.jp/pub/lang/R/CRAN/%SUBDIR%/ \ + http://lib.stat.cmu.edu/R/CRAN/%SUBDIR%/ \ + http://cran.stat.ucla.edu/%SUBDIR%/ \ + http://probability.ca/cran/%SUBDIR%/ +MASTER_SITE_SUBDIR= src/base/R-${PORTVERSION:C|\..*||} DISTNAME= R-${PORTVERSION} MAINTAINER= bf@FreeBSD.org @@ -27,7 +28,8 @@ LICENSE= GPLv2 BUILD_DEPENDS= ${LOCALBASE}/bin/gsed:${PORTSDIR}/textproc/gsed -CONFIGURE_ENV= SED="${LOCALBASE}/bin/gsed" +CONFIGURE_ENV= SED="${LOCALBASE}/bin/gsed" \ + ac_cv_have_decl_powl=yes ac_cv_have_decl_log1pl=yes OPTIONS_DEFINE= MISSING @@ -59,10 +61,12 @@ ATLAS_DESC= Use ATLAS instead of BLAS/LAPACK ICU_DESC= Use ICU for collation in multibyte locales PCRE_PORT_DESC = Use devel/pcre instead of the bundled PCRE -OPTIONS_DEFAULT= ICU PCRE_PORT THREADS +OPTIONS_DEFAULT+= ICU PCRE_PORT THREADS .if !defined(LIBR_SLAVEPORT) RUN_DEPENDS+= ${LOCALBASE}/bin/gsed:${PORTSDIR}/textproc/gsed USE_LDCONFIG= ${PREFIX}/lib/R/lib +#now only used to build the R.1 manpage: +USE_PERL5_BUILD= yes MAN1= R.1 Rscript.1 @@ -92,12 +96,11 @@ USES+= iconv .endif # LIBRMATH_SLAVEPORT GNU_CONFIGURE= yes MAKE_JOBS_UNSAFE= yes -R_SOVERSION= 0 +R_SOVERSION= 1 RBLAS_SOVERSION= 2 RLAPACK_SOVERSION= 4 RMATH_SOVERSION= 0 USE_FORTRAN= yes -USE_PERL5_BUILD= yes .include <bsd.port.options.mk> @@ -146,7 +149,7 @@ CONFIGURE_ARGS+= --without-ICU .endif .if ${PORT_OPTIONS:MNLS} -USES+= gettext +USES+= gettext PLIST_SUB+= NLS="" .else CONFIGURE_ARGS+= --disable-nls @@ -242,9 +245,9 @@ INFO= R-FAQ R-admin R-data R-exts R-intro R-lang .endif .if ${PORT_OPTIONS:MPDF_MANUALS} && ${PORT_OPTIONS:MDOCS} -BROKEN = The PDF_MANUALS option cannot be used, because\ - print/texinfo is incompatible with print/teTeX-base -USE_TEX= tex:build +BROKEN= The PDF_MANUALS option cannot be used, because it\ + requires broken components of texlive +USE_TEX= texlive pdftex:build BUILD_DEPENDS += texi2dvi:${PORTSDIR}/print/texinfo ALL_TARGET+= pdf CONFIGURE_ENV += INSTALL_INFO="${LOCALBASE}/bin/install-info" \ @@ -259,9 +262,15 @@ PLIST_SUB+= PDF_MANUAL="@comment " post-patch: .if !${PORT_OPTIONS:MMISSING} - @${REINPLACE_CMD} -e 's|logl(|(long double)logq((__float128)|' \ +.if ${OSVERSION} < 1000016 + @${REINPLACE_CMD} -e 's/# define EXP expl/# define EXP(x) (long double)expq((__float128)(x))/' \ + ${WRKSRC}/src/nmath/pnchisq.c +.endif + @${REINPLACE_CMD} -Ee 's/(log)(1p)?l\(/(long double)\1\2q((__float128)/' \ ${WRKSRC}/src/nmath/dnbeta.c \ ${WRKSRC}/src/nmath/pnbeta.c + @${REINPLACE_CMD} -Ee 's/powl\((.*)(long double)/(long double)powq((__float128)\1__float128/' \ + ${WRKSRC}/src/main/format.c .endif @${REINPLACE_CMD} -e \ '\|#include <math.h>|{x;s|^.*$$|#include ${LIBMH}|;H;x;}' \ @@ -277,8 +286,7 @@ post-patch: ${WRKSRC}/src/scripts/javareconf @${REINPLACE_CMD} -e "s|/usr/local|${LOCALBASE}|g" \ ${WRKSRC}/configure \ - ${WRKSRC}/config.site \ - ${WRKSRC}/src/extra/tzone/tzfile.h \ + ${WRKSRC}/src/library/profile/Rprofile.unix \ ${WRKSRC}/src/scripts/javareconf .if !defined(LIBRMATH_SLAVEPORT) .if !${PORT_OPTIONS:MNLS} @@ -287,6 +295,8 @@ post-patch: ${TAR} -czf temptgz --exclude='*/po/*' @$$tarfile ; \ ${MV} temptgz $$tarfile ; \ done) + @${REINPLACE_CMD} -e '/ls -d $$(srcdir)\/inst/d' \ + ${WRKSRC}/src/library/translations/Makefile.in .endif .if !${PORT_OPTIONS:MMISSING} @@ -312,6 +322,9 @@ do-install: .else # LIBR_SLAVEPORT +pre-configure-script: + @${FIND} ${WRKSRC} \( -name '*.orig' -o -name '*.bak' \) -delete + check regression-test test: build @(cd ${WRKSRC}; ${SETENV} ${MAKE_ENV} LANGUAGE=en \ LC_COLLATE=C LC_TIME=C ${MAKE} ${_MAKE_JOBS} ${MAKE_ARGS} \ diff --git a/math/R/distinfo b/math/R/distinfo index 8a5ff735289e..32a127b92334 100644 --- a/math/R/distinfo +++ b/math/R/distinfo @@ -1,2 +1,2 @@ -SHA256 (R-2.15.3.tar.gz) = c583a38f8dad3bc012c08116f4ba1eb2182cadfad4b0f8d7bd3cdba24bc255d6 -SIZE (R-2.15.3.tar.gz) = 25409925 +SHA256 (R-3.0.1.tar.gz) = af90488af3141103b211dc81b6f17d1f0faf4f17684c579a32dfeb25d0d87134 +SIZE (R-3.0.1.tar.gz) = 25508280 diff --git a/math/R/files/patch-20130526 b/math/R/files/patch-20130526 new file mode 100644 index 000000000000..5f3c74252ae9 --- /dev/null +++ b/math/R/files/patch-20130526 @@ -0,0 +1,2831 @@ +diff -ruN R-3.0.1/NEWS R-patched/NEWS +--- NEWS 2013-05-16 03:05:47.000000000 -0400 ++++ NEWS 2013-05-26 18:10:19.000000000 -0400 +@@ -1,5 +1,44 @@ + R News + ++CHANGES IN R 3.0.1 patched: ++ ++ NEW FEATURES: ++ ++ o The macros used for the texinfo manuals have been changed to work ++ better with the incompatible changes made in texinfo 5.x. ++ ++ o The example() and tools::Rd2ex() functions now have parameters to ++ allow them to ignore \dontrun markup in examples. (Suggested by ++ Peter Solymos.) ++ ++ C-LEVEL FACILITIES: ++ ++ o Rdefines.h has been tweaked so it can be included in C++ code ++ with R_exts/Boolean.h (which is included by R.h). Note though ++ that Rdefines.h is not kept up-to-date, and Rinternals.h is ++ preferred for new code. ++ ++ BUG FIXES: ++ ++ o help.request() could not determine the current version of R on ++ CRAN. (PR#15241) ++ ++ o On Windows, file.info() failed on root directories unless the ++ path was terminated with an explicit ".". (PR#15302) ++ ++ o The regmatches<-() replacement function mishandled results coming ++ from regexpr(). (PR#15311) ++ ++ o Documentation for setClass and representation still suggested the ++ deprecated argument representation=. (PR#15312) ++ ++ o R CMD config failed in an installed build of R 3.0.1 (only) when ++ a sub-architecture was used. (Reported by Berwin Turlach.) ++ ++ o On Windows, the installer modified the etc/Rconsole and ++ etc/Rprofile.site files even when default options were chosen. ++ (Reported by Tal Galili.) ++ + CHANGES IN R 3.0.1: + + NEW FEATURES: +Files R-3.0.1/NEWS.pdf and R-patched/NEWS.pdf differ +diff -ruN R-3.0.1/SVN-REVISION R-patched/SVN-REVISION +--- SVN-REVISION 2013-05-16 03:01:22.000000000 -0400 ++++ SVN-REVISION 2013-05-26 18:06:20.000000000 -0400 +@@ -1,2 +1,2 @@ +-Revision: 62743 +-Last Changed Date: 2013-05-16 ++Revision: 62815 ++Last Changed Date: 2013-05-26 +diff -ruN R-3.0.1/VERSION R-patched/VERSION +--- VERSION 2013-05-16 03:00:06.000000000 -0400 ++++ VERSION 2013-05-16 03:11:45.000000000 -0400 +@@ -1 +1 @@ +-3.0.1 ++3.0.1 Patched +diff -ruN R-3.0.1/doc/CRAN_mirrors.csv R-patched/doc/CRAN_mirrors.csv +--- doc/CRAN_mirrors.csv 2013-04-18 18:05:05.000000000 -0400 ++++ doc/CRAN_mirrors.csv 2013-05-24 18:05:06.000000000 -0400 +@@ -32,7 +32,6 @@ + "France (Paris 2)",France,Paris,http://cran.univ-paris1.fr/,"Universite Paris 1 Pantheon-Sorbonne","pierre.latouche # univ-paris1.fr",1,fr + "Germany (Berlin)",Germany,Berlin,http://mirrors.softliste.de/cran/,"Softliste.de, Berlin","docko # docko.sk",1,de + "Germany (Bonn)",Germany,Bonn,http://cran.r-mirror.de/,"Stefan Drees, Bonn","stefan # drees.name",1,de +-"Germany (Falkenstein)",Germany,Falkenstein,http://mirror.layerjet.com/cran,layerjet.com,"Elton Chung <elton # layerjet.com>",1,de + "Germany (Goettingen)",Germany,Goettingen,http://ftp5.gwdg.de/pub/misc/cran/,"GWDG Goettingen","Eberhard Moenkeberg <emoenke # gwdg.de>",1,de + Greece,Greece,Crete,http://cran.cc.uoc.gr/,"University of Crete","mirrors # Cc.uoc.gr",1,gr + Hungary,Hungary,Budapest,http://cran.rapporter.net/,"Rapporter.net, Budapest","Daróczi Gergely <gergely # snowl.net>",1,hu +@@ -48,7 +47,6 @@ + "Japan (Tokyo)",Japan,Tokyo,http://cran.ism.ac.jp/,"Institute of Statistical Mathematics, Tokyo","Junji Nakano <nakanoj # ism.ac.jp>",1,jp + "Korea (Seoul 1)",Korea,Seoul,http://cran.nexr.com/,"NexR Corporation, Seoul","mining # nexr.com",1,kr + "Korea (Seoul 2)",Korea,Seoul,http://biostat.cau.ac.kr/CRAN/,"Chung-Ang University, Seoul","Sunghow # gmail.com",1,kr +-Latvia,Latvia,Riga,http://mirrors.webhostinggeeks.com/cran/,Webhostinggeeks,"whg.igp # gmail.com",1,lv + "Mexico (Mexico City)",Mexico,"Mexico City",http://cran.itam.mx/,"Instituto Tecnologico Autonomo de Mexico","Ernesto Barrios <ebarrios # Itam.mx>",1,mx + "Mexico (Texcoco)",Mexico,Texcoco,http://www.est.colpos.mx/R-mirror/,"Colegio de Postgraduados, Texcoco","perpdgo # gmail.com",1,mx + "Netherlands (Amsterdam)",Netherlands,Amsterdam,http://cran.xl-mirror.nl/,"XL-Data, Amsterdam","werner # xl-mirror.nl",1,nl +@@ -57,6 +55,7 @@ + Norway,Norway,Bergen,http://cran.uib.no/,"University of Bergen","sundrift # It.uib.no",1,no + Philippines,Philippines,"Quezon City",http://cran.stat.upd.edu.ph/,"University of the Philippines and PREGINET","edward.p.santos # Up.edu.ph",1,ph + Poland,Poland,Wroclaw,http://r.meteo.uni.wroc.pl/,"University of Wroclaw","PaweÅ‚ Netzel <netzel # meteo.uni.wroc.pl>",1,pl ++Portugal,Portugal,Porto,http://cran.dcc.fc.up.pt/,"University of Porto","labcc # labcc.dcc.fc.up.pt",1,pt + Russia,Russia,Moscow,http://cran.gis-lab.info/,GIS-Lab.info,"sim # gis-lab.info",1,ru + Singapore,Singapore,Singapore,http://cran.stat.nus.edu.sg/,"National University of Singapore","Zhang Rong <ccezr # nus.edu.sg>",1,sg + Slovakia,Slovakia,Bratislava,http://cran.fyxm.net/,"FYXM.net, Bratislava","docko # docko.sk",1,sk +@@ -74,7 +73,7 @@ + "UK (St Andrews)",UK,"St Andrews",http://star-www.st-andrews.ac.uk/cran/,"St Andrews University","Lee Kelvin <lsk9 # St-andrews.ac.uk>",1,uk + "USA (CA 1)",USA,Berkeley,http://cran.cnr.Berkeley.edu,"University of California, Berkeley, CA","casterln # nature.berkeley.edu",1,us + "USA (CA 2)",USA,"Los Angeles",http://cran.stat.ucla.edu/,"University of California, Los Angeles, CA","Jose Hales-Garcia <jose # stat.ucla.edu>",1,us +-"USA (IA)",USA,Ames,http://streaming.stat.iastate.edu/CRAN/,"Iowa State University, Ames, IA","Ted Peterson <statit # iastate.edu>",1,us ++"USA (IA)",USA,Ames,http://streaming.stat.iastate.edu/CRAN/,"Iowa State University, Ames, IA","statit # iastate.edu",1,us + "USA (IN)",USA,Bloomington,http://ftp.ussg.iu.edu/CRAN/,"Indiana University","rtadmin # indiana.edu",1,us + "USA (KS)",USA,Lawrence,http://rweb.quant.ku.edu/cran/,"University of Kansas, Lawrence, KS","Paul Johnson <pauljohn # ku.edu>",1,us + "USA (MD)",USA,Bethesda,http://watson.nci.nih.gov/cran_mirror/,"National Cancer Institute, Bethesda, MD","Sean Davis <sdavis2 # mail.nih.gov>",1,us +diff -ruN R-3.0.1/doc/NEWS.Rd R-patched/doc/NEWS.Rd +--- doc/NEWS.Rd 2013-05-11 18:05:03.000000000 -0400 ++++ doc/NEWS.Rd 2013-05-25 18:05:04.000000000 -0400 +@@ -7,6 +7,53 @@ + \title{ R News} + \encoding{UTF-8} + ++\section{\Rlogo CHANGES IN R 3.0.1 patched}{ ++ \subsection{NEW FEATURES}{ ++ \itemize{ ++ \item The macros used for the texinfo manuals have been changed to ++ work better with the incompatible changes made in texinfo 5.x. ++ ++ \item The \code{example()} and \code{tools::Rd2ex()} functions now ++ have parameters to allow them to ignore \verb{\dontrun} markup in ++ examples. (Suggested by Peter Solymos.) ++ } ++ } ++ ++ \subsection{C-LEVEL FACILITIES}{ ++ \itemize{ ++ \item \file{Rdefines.h} has been tweaked so it can be included in ++ C++ code with \file{R_exts/Boolean.h} (which is included by ++ \file{R.h}). Note though that \file{Rdefines.h} is not kept ++ up-to-date, and \file{Rinternals.h} is preferred for new code. ++ } ++ } ++ ++ \subsection{BUG FIXES}{ ++ \itemize{ ++ \item \code{help.request()} could not determine the current version ++ of \R on CRAN. (\PR{15241}) ++ ++ \item On Windows, \code{file.info()} failed on root directories unless ++ the path was terminated with an explicit \code{"."}. (\PR{15302}) ++ ++ \item The \code{regmatches<-()} replacement function mishandled ++ results coming from \code{regexpr()}. (\PR{15311}) ++ ++ \item Documentation for \code{setClass} and ++ \code{representation} still suggested the deprecated argument ++ \code{representation=}. (\PR{15312}) ++ ++ \item \command{R CMD config} failed in an installed build of \R ++ 3.0.1 (only) when a sub-architecture was used. (Reported by ++ Berwin Turlach.) ++ ++ \item On Windows, the installer modified the \file{etc/Rconsole} and ++ \file{etc/Rprofile.site} files even when default options were ++ chosen. (Reported by Tal Galili.) ++ } ++ } ++} ++ + \section{\Rlogo CHANGES IN R 3.0.1}{ + \subsection{NEW FEATURES}{ + \itemize{ +@@ -142,28 +189,28 @@ + \item \code{as.dendrogram()}'s \code{hclust} method uses less + memory and hence gets considerably faster for large (n ~ 1000) + clusterings, thanks to Daniel Müllner. (\PR{15174}) +- ++ + \item The return value when all workers failed from + \code{parallel::mclapply(mc.presechedule = TRUE)} was a list of + strings and not of error objects. (Spotted by Karl Forner and +- Bernd Bischl.) +- ++ Bernd Bischl.) ++ + \item In \R 3.0.0, when \code{help()} found multiple pages with + the same alias, the HTML display of all the selections was not +- produced. (\PR{15282}) +- ++ produced. (\PR{15282}) ++ + \item \code{splinefun(method="monoH.FC")} now produces a + function with first argument named \code{x} and allows +- \code{deriv=3}, as documented. (\PR{15273}) +- +- \item \code{summaryRprof()} would only read the first ++ \code{deriv=3}, as documented. (\PR{15273}) ++ ++ \item \code{summaryRprof()} would only read the first + \code{chunksize} lines of an \code{Rprof} file produced with + \code{line.profiling=TRUE}. By default, this is the first 100 + seconds. (\PR{15288}) +- ++ + \item \code{lsfit()} produced an incorrect error message when + argument \code{x} had more columns than rows or \code{x} had a +- different number of rows than \code{y}. (Spotted by Renaud Gaujoux.) ++ different number of rows than \code{y}. (Spotted by Renaud Gaujoux.) + + \item Binary operations on equal length vectors copied the + class name from the second operand when the first had no +diff -ruN R-3.0.1/doc/html/NEWS.html R-patched/doc/html/NEWS.html +--- doc/html/NEWS.html 2013-05-16 03:05:47.000000000 -0400 ++++ doc/html/NEWS.html 2013-05-26 18:10:20.000000000 -0400 +@@ -8,6 +8,76 @@ + + <h2> R News</h2> + ++<h3><img src="../help/figures/../../html/logo.jpg" alt="../../html/logo.jpg" /> CHANGES IN R 3.0.1 patched</h3> ++ ++ ++ ++<h4>NEW FEATURES</h4> ++ ++ ++<ul> ++<li><p> The macros used for the texinfo manuals have been changed to ++work better with the incompatible changes made in texinfo 5.x. ++</p> ++</li> ++<li><p> The <code>example()</code> and <code>tools::Rd2ex()</code> functions now ++have parameters to allow them to ignore </p> ++<PRE>\dontrun</PRE> markup in ++examples. (Suggested by Peter Solymos.) ++</li></ul> ++ ++ ++ ++ ++<h4>C-LEVEL FACILITIES</h4> ++ ++ ++<ul> ++<li> <p>‘<span class="file">Rdefines.h</span>’ has been tweaked so it can be included in ++C++ code with ‘<span class="file">R_exts/Boolean.h</span>’ (which is included by ++‘<span class="file">R.h</span>’). Note though that ‘<span class="file">Rdefines.h</span>’ is not kept ++up-to-date, and ‘<span class="file">Rinternals.h</span>’ is preferred for new code. ++</p> ++</li></ul> ++ ++ ++ ++ ++<h4>BUG FIXES</h4> ++ ++ ++<ul> ++<li> <p><code>help.request()</code> could not determine the current version ++of <font face="Courier New,Courier" color="#666666"><b>R</b></font> on CRAN. (<a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=15241">PR#15241</a>) ++</p> ++</li> ++<li><p> On Windows, <code>file.info()</code> failed on root directories unless ++the path was terminated with an explicit <code>"."</code>. (<a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=15302">PR#15302</a>) ++</p> ++</li> ++<li><p> The <code>regmatches<-()</code> replacement function mishandled ++results coming from <code>regexpr()</code>. (<a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=15311">PR#15311</a>) ++</p> ++</li> ++<li><p> Documentation for <code>setClass</code> and ++<code>representation</code> still suggested the deprecated argument ++<code>representation=</code>. (<a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=15312">PR#15312</a>) ++</p> ++</li> ++<li> <p><CODE>R CMD config</CODE> failed in an installed build of <font face="Courier New,Courier" color="#666666"><b>R</b></font> ++3.0.1 (only) when a sub-architecture was used. (Reported by ++Berwin Turlach.) ++</p> ++</li> ++<li><p> On Windows, the installer modified the ‘<span class="file">etc/Rconsole</span>’ and ++‘<span class="file">etc/Rprofile.site</span>’ files even when default options were ++chosen. (Reported by Tal Galili.) ++</p> ++</li></ul> ++ ++ ++ ++ + <h3><img src="../help/figures/../../html/logo.jpg" alt="../../html/logo.jpg" /> CHANGES IN R 3.0.1</h3> + + +@@ -191,20 +261,20 @@ + <li><p> The return value when all workers failed from + <code>parallel::mclapply(mc.presechedule = TRUE)</code> was a list of + strings and not of error objects. (Spotted by Karl Forner and +-Bernd Bischl.) ++Bernd Bischl.) + </p> + </li> + <li><p> In <font face="Courier New,Courier" color="#666666"><b>R</b></font> 3.0.0, when <code>help()</code> found multiple pages with + the same alias, the HTML display of all the selections was not +-produced. (<a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=15282">PR#15282</a>) ++produced. (<a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=15282">PR#15282</a>) + </p> + </li> + <li> <p><code>splinefun(method="monoH.FC")</code> now produces a + function with first argument named <code>x</code> and allows +-<code>deriv=3</code>, as documented. (<a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=15273">PR#15273</a>) ++<code>deriv=3</code>, as documented. (<a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=15273">PR#15273</a>) + </p> + </li> +-<li> <p><code>summaryRprof()</code> would only read the first ++<li> <p><code>summaryRprof()</code> would only read the first + <code>chunksize</code> lines of an <code>Rprof</code> file produced with + <code>line.profiling=TRUE</code>. By default, this is the first 100 + seconds. (<a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=15288">PR#15288</a>) +@@ -212,7 +282,7 @@ + </li> + <li> <p><code>lsfit()</code> produced an incorrect error message when + argument <code>x</code> had more columns than rows or <code>x</code> had a +-different number of rows than <code>y</code>. (Spotted by Renaud Gaujoux.) ++different number of rows than <code>y</code>. (Spotted by Renaud Gaujoux.) + </p> + </li> + <li><p> Binary operations on equal length vectors copied the +diff -ruN R-3.0.1/doc/html/R-admin.html R-patched/doc/html/R-admin.html +--- doc/html/R-admin.html 2013-05-16 03:11:03.000000000 -0400 ++++ doc/html/R-admin.html 2013-05-26 18:15:13.000000000 -0400 +@@ -245,7 +245,7 @@ + + <p>This is a guide to installation and administration for R. + +- <p>The current version of this document is 3.0.1 (2013-05-16). ++ <p>The current version of this document is 3.0.1 Patched (2013-05-26). + + <p> + +@@ -986,7 +986,7 @@ + perhaps for some network-mounted systems). + + <p>Installation is <em>via</em> the installer +-<samp><span class="file">R-3.0.1-win.exe</span></samp>. Just double-click on the icon and ++<samp><span class="file">R-3.0.1patched-win.exe</span></samp>. Just double-click on the icon and + follow the instructions. When installing on a 64-bit version of Windows + the options will include 32- or 64-bit versions of R (and the default is + to install both). You can uninstall R from the Control Panel. +@@ -1286,7 +1286,7 @@ + installation (in double quotes if it contains spaces or backslashes). + + <p>Both methods create an executable with a standard name such as +-<samp><span class="file">R-3.0.1-win.exe</span></samp>, so please rename it to indicate that ++<samp><span class="file">R-3.0.1patched-win.exe</span></samp>, so please rename it to indicate that + it is customized. If you intend to <em>distribute</em> a customized + installer please do check that license requirements are met – note that + the installer will state that the contents are distributed under GPL-2 +@@ -1338,21 +1338,21 @@ + make msi + </pre> + <p class="noindent">which will result in a file with a name like +-<samp><span class="file">R-3.0.1-win32.msi</span></samp>. This can be double-clicked to be ++<samp><span class="file">R-3.0.1patched-win32.msi</span></samp>. This can be double-clicked to be + installed, but those who need it will know what to do with it (usually + by running <samp><span class="command">msiexec /i</span></samp> with additional options). Properties + that users might want to set from the <samp><span class="command">msiexec</span></samp> command line + include ‘<samp><span class="samp">ALLUSERS</span></samp>’, ‘<samp><span class="samp">INSTALLDIR</span></samp>’ (something like +-<samp><span class="file">c:\Program Files\R\R-3.0.1</span></samp>) and ‘<samp><span class="samp">RMENU</span></samp>’ (the path ++<samp><span class="file">c:\Program Files\R\R-3.0.1patched</span></samp>) and ‘<samp><span class="samp">RMENU</span></samp>’ (the path + to the ‘<samp><span class="samp">R</span></samp>’ folder on the start menu) and ‘<samp><span class="samp">STARTDIR</span></samp>’ (the + starting directory for R shortcuts, defaulting to something like + <samp><span class="file">c:\Users\name\Documents\R</span></samp>). + + <p>The MSI installer can be built both from a 32-bit build of R +-(<samp><span class="file">R-3.0.1-win32.msi</span></samp>) and from a 64-bit build of R +-(<samp><span class="file">R-3.0.1-win64.msi</span></samp>, optionally including 32-bit files ++(<samp><span class="file">R-3.0.1patched-win32.msi</span></samp>) and from a 64-bit build of R ++(<samp><span class="file">R-3.0.1patched-win64.msi</span></samp>, optionally including 32-bit files + by setting the macro <code>HOME32</code>, when the name is +-<samp><span class="file">R-3.0.1-win.msi</span></samp>). Unlike the main installer, a 64-bit ++<samp><span class="file">R-3.0.1patched-win.msi</span></samp>). Unlike the main installer, a 64-bit + MSI installer can only be run on 64-bit Windows. + + <p>Thanks to David del Campo (Dept of Statistics, University of Oxford) +@@ -1421,10 +1421,6 @@ + should run on all Macs from mid-2008 on. For older Intel Macs and some + older versions of the OS you can install R from the sources. + +- <p>Note that unlike <acronym>CRAN</acronym> binary distributions of R 2.x.y, +-there is only a 64-bit version (and hence no separate <code>R64.app</code> +-application, nor <samp><span class="command">R64</span></samp>/<samp><span class="command">R32</span></samp> front-ends). +- + <p>To install, just double-click on the icon of the file you downloaded. + At the `Installation Type' stage, note the option to `Customize'. This + currently shows three components (`Package Name'). Everyone will need +@@ -1789,8 +1785,7 @@ + <acronym>CRAN</acronym> or local files. + + <p>Note that many binary packages including compiled code are tied to a +-particular series (e.g. R 2.15.x or 3.0.x) of R: in any case R 3.0.x +-cannot use any binary packages built for R 2.15.x or earlier. ++particular series (e.g. R 3.0.x or 3.1.x) of R. + + <p>Installing source packages which do not contain compiled code should + work with no additional tools. For others you will need the `Command +@@ -2611,7 +2606,7 @@ + <samp><span class="file">texinfo.tex</span></samp> need to be compatible: we have seen problems with + older TeX distributions (TeXLive 2007 and MiKTeX 2.8) used with + <strong>texinfo</strong> 4.13. It should be possible to use <samp><span class="command">makeinfo</span></samp> +-version 5.0, but e.g.. 4.13 produces better-formatted output. ++version 5.x. + + <p><a name="index-Vignettes-69"></a>The PDF documentation (including <samp><span class="file">doc/NEWS.pdf</span></samp>) and building + vignettes needs <samp><span class="command">pdftex</span></samp> and <samp><span class="command">pdflatex</span></samp>. We require +@@ -4693,7 +4688,7 @@ + + <h3 class="section">D.2 The Inno Setup installer</h3> + +-<p>To make the installer package (<samp><span class="file">R-3.0.1-win.exe</span></samp>) we ++<p>To make the installer package (<samp><span class="file">R-3.0.1patched-win.exe</span></samp>) we + currently require the Unicode version of Inno Setup 5.3.7 or later from + <a href="http://jrsoftware.org/">http://jrsoftware.org/</a>. This is <em>not</em> included in + <samp><span class="file">Rtools*.exe</span></samp>. +diff -ruN R-3.0.1/doc/manual/R-admin.texi R-patched/doc/manual/R-admin.texi +--- doc/manual/R-admin.texi 2013-04-29 07:05:23.000000000 -0400 ++++ doc/manual/R-admin.texi 2013-05-24 18:05:06.000000000 -0400 +@@ -1473,10 +1473,6 @@ + should run on all Macs from mid-2008 on. For older Intel Macs and some + older versions of the OS you can install @R{} from the sources. + +-Note that unlike @acronym{CRAN} binary distributions of @R{} 2.x.y, +-there is only a 64-bit version (and hence no separate @code{R64.app} +-application, nor @command{R64}/@command{R32} front-ends). +- + To install, just double-click on the icon of the file you downloaded. + At the `Installation Type' stage, note the option to `Customize'. This + currently shows three components (`Package Name'). Everyone will need +@@ -1904,8 +1900,7 @@ + @acronym{CRAN} or local files. + + Note that many binary packages including compiled code are tied to a +-particular series (e.g.@: @R{} 2.15.x or 3.0.x) of @R{}: in any case @R{} 3.0.x +-cannot use any binary packages built for @R{} 2.15.x or earlier. ++particular series (e.g.@: @R{} 3.0.x or 3.1.x) of @R{}. + + Installing source packages which do not contain compiled code should + work with no additional tools. For others you will need the `Command +@@ -2863,7 +2858,7 @@ + @file{texinfo.tex} need to be compatible: we have seen problems with + older @TeX{} distributions (TeXLive 2007 and MiKTeX 2.8) used with + @pkg{texinfo} 4.13. It should be possible to use @command{makeinfo} +-version 5.0, but e.g..@: 4.13 produces better-formatted output. ++version 5.x. + + @cindex Vignettes + The PDF documentation (including @file{doc/NEWS.pdf}) and building +diff -ruN R-3.0.1/doc/manual/R-defs.texi R-patched/doc/manual/R-defs.texi +--- doc/manual/R-defs.texi 2013-04-03 18:05:07.000000000 -0400 ++++ doc/manual/R-defs.texi 2013-05-24 18:05:06.000000000 -0400 +@@ -17,16 +17,18 @@ + @acronym{HTML} + @end macro + +-@macro eqn {t, a} + @iftex ++@macro eqn {t, a} + @tex + $\t\$% + @end tex ++@end macro + @end iftex + @ifnottex +-\a\@c +-@end ifnottex ++@macro eqn {t, a} ++\a\ + @end macro ++@end ifnottex + + @macro pkg {p} + @strong{\p\} +diff -ruN R-3.0.1/doc/manual/R-exts.R R-patched/doc/manual/R-exts.R +--- doc/manual/R-exts.R 2011-06-17 06:39:34.000000000 -0400 ++++ doc/manual/R-exts.R 2013-05-26 18:05:04.000000000 -0400 +@@ -33,9 +33,6 @@ + u <- rep(1, 5) + conv(u, u) + +-conv <- function(a, b) .Call("convolve2b", a, b) +-conv(u, u) +- + convE <- function(a, b) .External("convolveE", a, b) + convE(u, u) + +@@ -71,7 +68,7 @@ + + ## ----- numerical derivatives ----- + +-numeric.deriv <- function(expr, theta, rho=sys.frame(sys.parent())) ++numeric.deriv <- function(expr, theta, rho = sys.frame(sys.parent())) + { + eps <- sqrt(.Machine$double.eps) + ans <- eval(substitute(expr), rho) +diff -ruN R-3.0.1/doc/manual/R-exts.c R-patched/doc/manual/R-exts.c +--- doc/manual/R-exts.c 2013-02-04 18:05:11.000000000 -0500 ++++ doc/manual/R-exts.c 2013-05-26 18:05:04.000000000 -0400 +@@ -13,27 +13,22 @@ + /* second version */ + SEXP out(SEXP x, SEXP y) + { +- int i, j, nx = length(x), ny = length(y); +- double tmp, *rx = REAL(x), *ry = REAL(y), *rans; +- SEXP ans, dim, dimnames; +- +- PROTECT(ans = allocMatrix(REALSXP, nx, ny)); +- rans = REAL(ans); +- for(i = 0; i < nx; i++) { +- tmp = rx[i]; +- for(j = 0; j < ny; j++) ++ int nx = length(x), ny = length(y); ++ SEXP ans = PROTECT(allocMatrix(REALSXP, nx, ny)); ++ double *rx = REAL(x), *ry = REAL(y), *rans = REAL(ans); ++ ++ for(int i = 0; i < nx; i++) { ++ double tmp = rx[i]; ++ for(int j = 0; j < ny; j++) + rans[i + nx*j] = tmp * ry[j]; + } +- PROTECT(dim = allocVector(INTSXP, 2)); +- INTEGER(dim)[0] = nx; INTEGER(dim)[1] = ny; +- setAttrib(ans, R_DimSymbol, dim); + +- PROTECT(dimnames = allocVector(VECSXP, 2)); ++ SEXP dimnames = PROTECT(allocVector(VECSXP, 2)); + SET_VECTOR_ELT(dimnames, 0, getAttrib(x, R_NamesSymbol)); + SET_VECTOR_ELT(dimnames, 1, getAttrib(y, R_NamesSymbol)); + setAttrib(ans, R_DimNamesSymbol, dimnames); +- UNPROTECT(3); +- return(ans); ++ UNPROTECT(2); ++ return ans; + } + + /* get the list element named str, or return NULL */ +@@ -60,69 +55,48 @@ + error("rho should be an environment"); + ans = findVar(install(CHAR(STRING_ELT(name, 0))), rho); + Rprintf("first value is %f\n", REAL(ans)[0]); +- return(R_NilValue); ++ return R_NilValue; + } + + /* ----- Convolution via .Call ----- */ + +-#include <Rdefines.h> ++#include <Rinternals.h> + SEXP convolve2(SEXP a, SEXP b) + { +- int i, j, na, nb, nab; ++ int na, nb, nab; + double *xa, *xb, *xab; + SEXP ab; + +- PROTECT(a = AS_NUMERIC(a)); +- PROTECT(b = AS_NUMERIC(b)); +- na = LENGTH(a); nb = LENGTH(b); nab = na + nb - 1; +- PROTECT(ab = NEW_NUMERIC(nab)); +- xa = NUMERIC_POINTER(a); xb = NUMERIC_POINTER(b); +- xab = NUMERIC_POINTER(ab); +- for(i = 0; i < nab; i++) xab[i] = 0.0; +- for(i = 0; i < na; i++) +- for(j = 0; j < nb; j++) xab[i + j] += xa[i] * xb[j]; +- UNPROTECT(3); +- return(ab); +-} +- +-SEXP convolve2b(SEXP a, SEXP b) +-{ +- int i, j, na, nb, nab; +- double *xa, *xb, *xab; +- SEXP ab; +- +- PROTECT(a = coerceVector(a, REALSXP)); +- PROTECT(b = coerceVector(b, REALSXP)); ++ a = PROTECT(coerceVector(a, REALSXP)); ++ b = PROTECT(coerceVector(b, REALSXP)); + na = length(a); nb = length(b); nab = na + nb - 1; +- PROTECT(ab = allocVector(REALSXP, nab)); +- xa = REAL(a); xb = REAL(b); +- xab = REAL(ab); +- for(i = 0; i < nab; i++) xab[i] = 0.0; +- for(i = 0; i < na; i++) +- for(j = 0; j < nb; j++) xab[i + j] += xa[i] * xb[j]; ++ ab = PROTECT(allocVector(REALSXP, nab)); ++ xa = REAL(a); xb = REAL(b); xab = REAL(ab); ++ for(int i = 0; i < nab; i++) xab[i] = 0.0; ++ for(int i = 0; i < na; i++) ++ for(int j = 0; j < nb; j++) xab[i + j] += xa[i] * xb[j]; + UNPROTECT(3); +- return(ab); ++ return ab; + } + + /* ----- Convolution via .External ----- */ + + SEXP convolveE(SEXP args) + { +- int i, j, na, nb, nab; ++ int na, nb, nab; + double *xa, *xb, *xab; + SEXP a, b, ab; + +- PROTECT(a = coerceVector(CADR(args), REALSXP)); +- PROTECT(b = coerceVector(CADDR(args), REALSXP)); ++ a = PROTECT(coerceVector(CADR(args), REALSXP)); ++ b = PROTECT(coerceVector(CADDR(args), REALSXP)); + na = length(a); nb = length(b); nab = na + nb - 1; +- PROTECT(ab = allocVector(REALSXP, nab)); +- xa = REAL(a); xb = REAL(b); +- xab = REAL(ab); +- for(i = 0; i < nab; i++) xab[i] = 0.0; +- for(i = 0; i < na; i++) +- for(j = 0; j < nb; j++) xab[i + j] += xa[i] * xb[j]; ++ ab = PROTECT(allocVector(REALSXP, nab)); ++ xa = REAL(a); xb = REAL(b); xab = REAL(ab); ++ for(int i = 0; i < nab; i++) xab[i] = 0.0; ++ for(int i = 0; i < na; i++) ++ for(int j = 0; j < nb; j++) xab[i + j] += xa[i] * xb[j]; + UNPROTECT(3); +- return(ab); ++ return ab; + } + + /* ----- Show arguments ----- */ +@@ -160,7 +134,7 @@ + Rprintf("[%d] '%s' R type\n", i+1, name); + } + } +- return(R_NilValue); ++ return R_NilValue; + } + + SEXP showArgs1(SEXP largs) +@@ -193,45 +167,45 @@ + Rprintf("[%d] '%s' R type\n", i+1, name); + } + } +- return(R_NilValue); ++ return R_NilValue; + } + + /* ----- Skeleton lapply ----- */ + + SEXP lapply(SEXP list, SEXP expr, SEXP rho) + { +- int i, n = length(list); ++ int n = length(list); + SEXP ans; + + if(!isNewList(list)) error("'list' must be a list"); + if(!isEnvironment(rho)) error("'rho' should be an environment"); +- PROTECT(ans = allocVector(VECSXP, n)); +- for(i = 0; i < n; i++) { ++ ans = PROTECT(allocVector(VECSXP, n)); ++ for(int i = 0; i < n; i++) { + defineVar(install("x"), VECTOR_ELT(list, i), rho); + SET_VECTOR_ELT(ans, i, eval(expr, rho)); + } + setAttrib(ans, R_NamesSymbol, getAttrib(list, R_NamesSymbol)); + UNPROTECT(1); +- return(ans); ++ return ans; + } + + SEXP lapply2(SEXP list, SEXP fn, SEXP rho) + { +- int i, n = length(list); ++ int n = length(list); + SEXP R_fcall, ans; + + if(!isNewList(list)) error("'list' must be a list"); + if(!isFunction(fn)) error("'fn' must be a function"); + if(!isEnvironment(rho)) error("'rho' should be an environment"); +- PROTECT(R_fcall = lang2(fn, R_NilValue)); +- PROTECT(ans = allocVector(VECSXP, n)); +- for(i = 0; i < n; i++) { ++ R_fcall = PROTECT(lang2(fn, R_NilValue)); ++ ans = PROTECT(allocVector(VECSXP, n)); ++ for(int i = 0; i < n; i++) { + SETCADR(R_fcall, VECTOR_ELT(list, i)); + SET_VECTOR_ELT(ans, i, eval(R_fcall, rho)); + } + setAttrib(ans, R_NamesSymbol, getAttrib(list, R_NamesSymbol)); + UNPROTECT(2); +- return(ans); ++ return ans; + } + + /* ----- Zero-finding ----- */ +@@ -239,7 +213,7 @@ + SEXP mkans(double x) + { + SEXP ans; +- PROTECT(ans = allocVector(REALSXP, 1)); ++ ans = PROTECT(allocVector(REALSXP, 1)); + REAL(ans)[0] = x; + UNPROTECT(1); + return ans; +@@ -248,7 +222,7 @@ + double feval(double x, SEXP f, SEXP rho) + { + defineVar(install("x"), mkans(x), rho); +- return(REAL(eval(f, rho))[0]); ++ return REAL(eval(f, rho))[0]; + } + + SEXP zero(SEXP f, SEXP guesses, SEXP stol, SEXP rho) +@@ -285,7 +259,7 @@ + { + SEXP theta, expr, rho, ans, ans1, gradient, par, dimnames; + double tt, xx, delta, eps = sqrt(DOUBLE_EPS), *rgr, *rans; +- int start, i, j; ++ int i, start; + + expr = CADR(args); + if(!isString(theta = CADDR(args))) +@@ -293,8 +267,8 @@ + if(!isEnvironment(rho = CADDDR(args))) + error("rho should be an environment"); + +- PROTECT(ans = coerceVector(eval(expr, rho), REALSXP)); +- PROTECT(gradient = allocMatrix(REALSXP, LENGTH(ans), LENGTH(theta))); ++ ans = PROTECT(coerceVector(eval(expr, rho), REALSXP)); ++ gradient = PROTECT(allocMatrix(REALSXP, LENGTH(ans), LENGTH(theta))); + rgr = REAL(gradient); rans = REAL(ans); + + for(i = 0, start = 0; i < LENGTH(theta); i++, start += LENGTH(ans)) { +@@ -303,14 +277,14 @@ + xx = fabs(tt); + delta = (xx < 1) ? eps : xx*eps; + REAL(par)[0] += delta; +- PROTECT(ans1 = coerceVector(eval(expr, rho), REALSXP)); +- for(j = 0; j < LENGTH(ans); j++) ++ ans1 = PROTECT(coerceVector(eval(expr, rho), REALSXP)); ++ for(int j = 0; j < LENGTH(ans); j++) + rgr[j + start] = (REAL(ans1)[j] - rans[j])/delta; + REAL(par)[0] = tt; + UNPROTECT(2); /* par, ans1 */ + } + +- PROTECT(dimnames = allocVector(VECSXP, 2)); ++ dimnames = PROTECT(allocVector(VECSXP, 2)); + SET_VECTOR_ELT(dimnames, 1, theta); + dimnamesgets(gradient, dimnames); + setAttrib(ans, install("gradient"), gradient); +diff -ruN R-3.0.1/doc/manual/R-exts.texi R-patched/doc/manual/R-exts.texi +--- doc/manual/R-exts.texi 2013-04-22 18:05:03.000000000 -0400 ++++ doc/manual/R-exts.texi 2013-05-26 18:05:04.000000000 -0400 +@@ -219,13 +219,19 @@ + @pxref{Lazy loading, , Lazy loading, R-ints, R Internals}.) + @end ifset + ++@cindex CRAN ++@acronym{CRAN} is a network of WWW sites holding the @R{} distributions ++and contributed code, especially @R{} packages. Users of @R{} are ++encouraged to join in the collaborative project and to submit their own ++packages to @acronym{CRAN}: current instructions are linked from ++@uref{http://CRAN.R-project.org/banner.shtml#submitting}. ++ + + @menu + * Package structure:: + * Configure and cleanup:: + * Checking and building packages:: + * Writing package vignettes:: +-* Submitting a package to CRAN:: + * Package namespaces:: + * Writing portable packages:: + * Diagnostic messages:: +@@ -1236,7 +1242,7 @@ + @end example + + @noindent +-then downoad the sources from ++then download the sources from + @uref{http://sourceforge.net/projects/tcllib/files/BWidget/} and + at the command line run + +@@ -2596,7 +2602,7 @@ + who do not have access to Windows but wish to provide binaries for the + Windows platform. + +-@node Writing package vignettes, Submitting a package to CRAN, Checking and building packages, Creating R packages ++@node Writing package vignettes, Package namespaces, Checking and building packages, Creating R packages + @section Writing package vignettes + @cindex vignettes + @cindex Sweave +@@ -2854,21 +2860,8 @@ + See the @code{?tools::vignetteEngine} help topic for details + on engine registration. + +-@node Submitting a package to CRAN, Package namespaces, Writing package vignettes, Creating R packages +-@section Submitting a package to @acronym{CRAN} +-@cindex CRAN +-@cindex CRAN submission +-@cindex Submitting to CRAN +- +-@acronym{CRAN} is a network of WWW sites holding the @R{} distributions +-and contributed code, especially @R{} packages. Users of @R{} are +-encouraged to join in the collaborative project and to submit their own +-packages to @acronym{CRAN}. + +-Current submission instructions are linked from +-@uref{http://CRAN.R-project.org/banner.shtml#submitting}. +- +-@node Package namespaces, Writing portable packages, Submitting a package to CRAN, Creating R packages ++@node Package namespaces, Writing portable packages, Writing package vignettes, Creating R packages + @section Package namespaces + @cindex namespaces + +@@ -7287,12 +7280,12 @@ + @group + void convolve(double *a, int *na, double *b, int *nb, double *ab) + @{ +- int i, j, nab = *na + *nb - 1; ++ int nab = *na + *nb - 1; + +- for(i = 0; i < nab; i++) ++ for(int i = 0; i < nab; i++) + ab[i] = 0.0; +- for(i = 0; i < *na; i++) +- for(j = 0; j < *nb; j++) ++ for(int i = 0; i < *na; i++) ++ for(int j = 0; j < *nb; j++) + ab[i + j] += a[i] * b[j]; + @} + @end group +@@ -8066,28 +8059,24 @@ + package @pkg{packB} is incorporated when package @pkg{packA} is + installed, we only need to find the static library at install time for + package @pkg{packB}. The only issue is to find package @pkg{packB}, and +-for that we can ask @R{} by something like (lines broken for display here) ++for that we can ask @R{} by something like (long lines broken for display here) + + @example +-PKGB_PATH=`echo 'cat(system.file("libs", .Platform$$r_arch, +- package="packB", mustWork=TRUE))' \ ++PKGB_PATH=`echo 'library(packB); ++ cat(system.file("libs", package="packB", mustWork=TRUE))' \ + | "$@{R_HOME@}/bin/R" --vanilla --slave` +-PKG_LIBS="$(PKGB_PATH)/libpackB.a" ++PKG_LIBS="$(PKGB_PATH)$(R_ARCH)/libpackB.a" + @end example + +-@noindent +-which will give an empty path component if sub-architectures are not in +-use (but that works on current platforms). +- + For a dynamic library @file{packB/libs/libpackB.so} + (@file{packB/libs/libpackB.dylib} on OS X: note that you cannot link to + a shared object, @file{.so} on that platform) we could use + + @example +-PKGB_PATH=`echo 'cat(system.file("libs", .Platform$$r_arch, +- package="packB", mustWork=TRUE))' \ ++PKGB_PATH=`echo 'library(packB); ++ cat(system.file("libs", package="packB", mustWork=TRUE))' \ + | "$@{R_HOME@}/bin/R" --vanilla --slave` +-PKG_LIBS=-L"$(PKGB_PATH)" -lpackB ++PKG_LIBS=-L"$(PKGB_PATH)$(R_ARCH)" -lpackB + @end example + + @noindent +@@ -8105,9 +8094,10 @@ + this can be done by e.g.@: + + @example +-PKGB_PATH=`echo 'library(packB); cat(system.file("libs", package="packB"))' \ ++PKGB_PATH=`echo 'library(packB); ++ cat(system.file("libs", package="packB", mustWork=TRUE)))' \ + | "$@{R_HOME@}/bin/R" --vanilla --slave` +-PKG_LIBS=-L"$(PKGB_PATH)" -rpath "$(PKGB_PATH)" -lpackB ++PKG_LIBS=-L"$(PKGB_PATH)$(R_ARCH)" -rpath "$(PKGB_PATH)$(R_ARCH)" -lpackB + @end example + + @noindent +@@ -8154,9 +8144,10 @@ + where it is by something like + + @example +-PKGB_PATH=`echo 'library(packB); cat(system.file("libs", package="packB"))' \ ++PKGB_PATH=`echo 'library(packB); ++ cat(system.file("libs", package="packB", mustWork=TRUE))' \ + | rterm --vanilla --slave` +-PKG_LIBS= -L"$(PKGB_PATH)"$(R_ARCH) -lexB ++PKG_LIBS= -L"$(PKGB_PATH)$(R_ARCH)" -lexB + @end example + + Another possibility is to use an import library, shipping with package +@@ -8182,7 +8173,7 @@ + @file{packB.dll} or @file{packB.dll} depends on it) and @pkg{packB} has + been loaded before @pkg{packA}, then nothing more needs to be done as + @file{exB.dll} will already be loaded into the @R{} executable. (This +-is the most common scenario). ++is the most common scenario.) + + More generally, we can use the @code{DLLpath} argument to + @code{library.dynam} to ensure that @code{exB.dll} is found, for example +@@ -8209,9 +8200,8 @@ + @code{.Call} and @code{.External} functions. The syntax for the calling + function in @R{} in each case is similar to that of @code{.C}, but the + two functions have different C interfaces. Generally the @code{.Call} +-interface (which is modelled on the interface of the same name in @Sl{} +-version 4) is a little simpler to use, but @code{.External} is a little +-more general. ++interface is simpler to use, but @code{.External} is a little more ++general. + @findex .Call + @findex .External + +@@ -8259,48 +8249,39 @@ + Here @code{args} is a @code{LISTSXP}, a Lisp-style pairlist from which + the arguments can be extracted. + +-In each case the @R{} objects are available for manipulation @emph{via} a set +-of functions and macros defined in the header file @file{Rinternals.h} +-or some S4-compatibility macros defined in @file{Rdefines.h}. See +-@ref{Interface functions .Call and .External} for details on +-@code{.Call} and @code{.External}. ++In each case the @R{} objects are available for manipulation @emph{via} ++a set of functions and macros defined in the header file ++@file{Rinternals.h} or some @Sl{}-compatibility macros@footnote{That is, ++similar to those defined in @Sl{} version 4 from the 1990s: these are ++not kept up to date and are not recommended for new projects.} defined ++in @file{Rdefines.h}. See @ref{Interface functions .Call and .External} ++for details on @code{.Call} and @code{.External}. + + Before you decide to use @code{.Call} or @code{.External}, you should + look at other alternatives. First, consider working in interpreted @R{} + code; if this is fast enough, this is normally the best option. You + should also see if using @code{.C} is enough. If the task to be + performed in C is simple enough involving only atomic vectors and +-requiring no call to @R{}, @code{.C} suffices. The new interfaces are +-relatively recent additions to @Sl{} and @R{}, and a great deal of +-useful code has been written using just @code{.C} before they were +-available. The @code{.Call} and @code{.External} interfaces allow much +-more control, but they also impose much greater responsibilities so need +-to be used with care. Neither @code{.Call} nor @code{.External} copy +-their arguments: you should treat arguments you receive through these ++requiring no call to @R{}, @code{.C} suffices. A great deal of useful ++code was written using just @code{.C} before @code{.Call} and ++@code{.External} were available. These interfaces allow much more ++control, but they also impose much greater responsibilities so need to ++be used with care. Neither @code{.Call} nor @code{.External} copy their ++arguments: you should treat arguments you receive through these + interfaces as read-only. + +-There are two approaches that can be taken to handling @R{} objects from +-within C code. The first (historically) is to use the macros and +-functions that have been used to implement the core parts of @R{} +-through @code{.Internal} calls. A public@footnote{ @pxref{The R API}: +-note that these are not all part of the API.} subset of these is +-defined in the header file @file{Rinternals.h} in the directory +-@file{@var{R_INCLUDE_DIR}} (default @file{@var{R_HOME}/include}) that +-should be available on any @R{} installation. +- +-Another approach is to use @R{} versions of the macros and functions +-defined for the @Sl{} version 4 interface @code{.Call}, which are +-defined in the header file @file{Rdefines.h}. This is a somewhat +-simpler approach, and is to be preferred if the code is intended to be +-shared with @Sl{}. However, it is less well documented and even less +-tested. Note too that some idiomatic S4 constructions with these macros +-(such as assigning elements of character vectors or lists) are invalid +-in @R{}. +- +-A substantial amount of @R{} is implemented using the functions and +-macros described here, so the @R{} source code provides a rich source of +-examples and ``how to do it'': do make use of the source code for +-inspirational examples. ++To handle @R{} objects from within C code we use the macros and functions ++that have been used to implement the core parts of @R{}. A ++public@footnote{ @pxref{The R API}: note that these are not all part of ++the API.} subset of these is defined in the header file ++@file{Rinternals.h} in the directory @file{@var{R_INCLUDE_DIR}} (default ++@file{@var{R_HOME}/include}) that should be available on any @R{} ++installation. ++ ++A substantial amount of @R{}, including the standard packages, is ++implemented using the functions and macros described here, so the @R{} ++source code provides a rich source of examples and ``how to do it'': do ++make use of the source code for inspirational examples. + + It is necessary to know something about how @R{} objects are handled in + C code. All the @R{} objects you will deal with will be handled with +@@ -8374,8 +8355,7 @@ + warn about @code{"stack imbalance in .Call"} (or @code{.External}) if + the housekeeping is wrong. + +-Here is a small example of creating an @R{} numeric vector in C code. +-First we use the macros in @file{Rinternals.h}: ++Here is a small example of creating an @R{} numeric vector in C code: + + @example + @group +@@ -8384,30 +8364,13 @@ + + SEXP ab; + .... +- PROTECT(ab = allocVector(REALSXP, 2)); ++ ab = PROTECT(allocVector(REALSXP, 2)); + REAL(ab)[0] = 123.45; + REAL(ab)[1] = 67.89; + UNPROTECT(1); + @end group + @end example + +-@noindent +-and then those in @file{Rdefines.h}: +- +-@example +-@group +-#include <R.h> +-#include <Rdefines.h> +- +- SEXP ab; +- .... +- PROTECT(ab = NEW_NUMERIC(2)); +- NUMERIC_POINTER(ab)[0] = 123.45; +- NUMERIC_POINTER(ab)[1] = 67.89; +- UNPROTECT(1); +-@end group +-@end example +- + Now, the reader may ask how the @R{} object could possibly get removed + during those manipulations, as it is just our C code that is running. + As it happens, we can do without the protection in this example, but in +@@ -8448,8 +8411,8 @@ + PROTECT_INDEX ipx; + + .... +- PROTECT_WITH_INDEX(s = eval(OS->R_fcall, OS->R_env), &ipx); +- REPROTECT(s = coerceVector(s, REALSXP), ipx); ++ s = PROTECT_WITH_INDEX(eval(OS->R_fcall, OS->R_env), &ipx); ++ s = REPROTECT(coerceVector(s, REALSXP), ipx); + @end example + + Note that it is dangerous to mix @code{UNPROTECT_PTR} with +@@ -8463,10 +8426,7 @@ + + For many purposes it is sufficient to allocate @R{} objects and + manipulate those. There are quite a few @code{alloc@var{Xxx}} functions +-defined in @file{Rinternals.h}---you may want to explore them. These +-allocate @R{} objects of various types, and for the standard vector +-types there are equivalent @code{NEW_@var{XXX}} macros defined in +-@file{Rdefines.h}. ++defined in @file{Rinternals.h}---you may want to explore them. + + If storage is required for C objects during the calculations this is + best allocating by calling @code{R_alloc}; @pxref{Memory allocation}. +@@ -8479,12 +8439,10 @@ + @cindex Details of R types + + Users of the @file{Rinternals.h} macros will need to know how the @R{} +-types are known internally: if the @file{Rdefines.h} macros are used +-then S4-compatible names are used. +- +-The different @R{} data types are represented in C by @dfn{SEXPTYPE}. +-Some of these are familiar from @R{} and some are internal data types. +-The usual @R{} object modes are given in the table. ++types are known internally. The different @R{} data types are ++represented in C by @dfn{SEXPTYPE}. Some of these are familiar from ++@R{} and some are internal data types. The usual @R{} object modes are ++given in the table. + + @quotation + @multitable {SEXPTYPE} {numeric with storage mode integer integer} +@@ -8519,25 +8477,17 @@ + and @code{isString} to do type checking. See the header file + @file{Rinternals.h} for definitions of other such functions. All of + these take a @code{SEXP} as argument and return 1 or 0 to indicate +-@var{TRUE} or @var{FALSE}. Once again there are two ways to do this, +-and @file{Rdefines.h} has macros such as @code{IS_NUMERIC}. ++@var{TRUE} or @var{FALSE}. + + What happens if the @code{SEXP} is not of the correct type? Sometimes + you have no other option except to generate an error. You can use the + function @code{error} for this. It is usually better to coerce the + object to the correct type. For example, if you find that an + @code{SEXP} is of the type @code{INTEGER}, but you need a @code{REAL} +-object, you can change the type by using, equivalently, +- +-@example +-PROTECT(@var{newSexp} = coerceVector(@var{oldSexp}, REALSXP)); +-@end example +- +-@noindent +-or ++object, you can change the type by using + + @example +-PROTECT(@var{newSexp} = AS_NUMERIC(@var{oldSexp})); ++@var{newSexp} = PROTECT(coerceVector(@var{oldSexp}, REALSXP)); + @end example + + @noindent +@@ -8594,19 +8544,16 @@ + + SEXP out(SEXP x, SEXP y) + @{ +- int i, j, nx = length(x), ny = length(y); +- double tmp, *rx = REAL(x), *ry = REAL(y), *rans; +- SEXP ans; +- +- PROTECT(ans = allocMatrix(REALSXP, nx, ny)); +- rans = REAL(ans); +- for(i = 0; i < nx; i++) @{ +- tmp = rx[i]; +- for(j = 0; j < ny; j++) ++ int nx = length(x), ny = length(y); ++ SEXP ans = PROTECT(allocMatrix(REALSXP, nx, ny)); ++ double *rx = REAL(x), *ry = REAL(y), *rans = REAL(ans); ++ for(int i = 0; i < nx; i++) @{ ++ double tmp = rx[i]; ++ for(int j = 0; j < ny; j++) + rans[i + nx*j] = tmp * ry[j]; + @} + UNPROTECT(1); +- return(ans); ++ return ans; + @} + @end group + @end example +@@ -8626,29 +8573,17 @@ + @group + SEXP out(SEXP x, SEXP y) + @{ +- int i, j, nx = length(x), ny = length(y); +- double tmp, *rx = REAL(x), *ry = REAL(y), *rans; +- SEXP ans, dim, dimnames; +-@end group +- +-@group +- PROTECT(ans = allocVector(REALSXP, nx*ny)); +- rans = REAL(ans); +- for(i = 0; i < nx; i++) @{ +- tmp = rx[i]; +- for(j = 0; j < ny; j++) +- rans[i + nx*j] = tmp * ry[j]; ++ int nx = length(x), ny = length(y); ++ SEXP ans = PROTECT(allocMatrix(REALSXP, nx, ny)); ++ double *rx = REAL(x), *ry = REAL(y), *rans = REAL(ans); ++ ++ for(int i = 0; i < nx; i++) @{ ++ double tmp = rx[i]; ++ for(int j = 0; j < ny; j++) ++ rans[i + nx*j] = tmp * ry[j]; + @} +-@end group + +-@group +- PROTECT(dim = allocVector(INTSXP, 2)); +- INTEGER(dim)[0] = nx; INTEGER(dim)[1] = ny; +- setAttrib(ans, R_DimSymbol, dim); +-@end group +- +-@group +- PROTECT(dimnames = allocVector(VECSXP, 2)); ++ SEXP dimnames = PROTECT(allocVector(VECSXP, 2)); + SET_VECTOR_ELT(dimnames, 0, getAttrib(x, R_NamesSymbol)); + SET_VECTOR_ELT(dimnames, 1, getAttrib(y, R_NamesSymbol)); + setAttrib(ans, R_DimNamesSymbol, dimnames); +@@ -8656,7 +8591,7 @@ + + @group + UNPROTECT(3); +- return(ans); ++ return ans; + @} + @end group + @end example +@@ -8685,7 +8620,7 @@ + @example + @group + SEXP version; +- PROTECT(version = allocVector(REALSXP, 1)); ++ version = PROTECT(allocVector(REALSXP, 1)); + REAL(version)[0] = 3.0; + setAttrib(ans, install("version"), version); + UNPROTECT(1); +@@ -8704,7 +8639,18 @@ + @end example + + @noindent +-if it is to be done frequently. ++if it is to be done frequently. ++ ++This example can be simplified by another convenience function: ++ ++@example ++@group ++ SEXP version = PROTECT(ScalarReal(3.0)); ++ setAttrib(ans, install("version"), version); ++ UNPROTECT(1); ++@end group ++@end example ++ + + @node Classes, Handling lists, Attributes, Handling R objects in C + @subsection Classes +@@ -8718,15 +8664,15 @@ + @example + @group + #include <R.h> +-#include <Rdefines.h> ++#include <Rinternals.h> + .... + SEXP ans, dim, dimnames, class; + .... +- PROTECT(class = allocVector(STRSXP, 1)); ++ class = PROTECT(allocVector(STRSXP, 1)); + SET_STRING_ELT(class, 0, mkChar("mat")); + classgets(ans, class); + UNPROTECT(4); +- return(ans); ++ return ans; + @} + @end group + @end example +@@ -8852,7 +8798,7 @@ + error("rho should be an environment"); + ans = findVar(install(CHAR(STRING_ELT(name, 0))), rho); + Rprintf("first value is %f\n", REAL(ans)[0]); +- return(R_NilValue); ++ return R_NilValue; + @} + @end group + @end example +@@ -9073,44 +9019,16 @@ + + @findex .Call + +-Let us convert our finite convolution example to use @code{.Call}, first +-using the @file{Rdefines.h} macros. The calling function in @R{} is ++Let us convert our finite convolution example to use @code{.Call}. The ++calling function in @R{} is + + @example + conv <- function(a, b) .Call("convolve2", a, b) + @end example + + @noindent +-which could hardly be simpler, but as we shall see all the type checking +-must be transferred to the C code, which is +- +-@example +-@group +-#include <R.h> +-#include <Rdefines.h> +- +-SEXP convolve2(SEXP a, SEXP b) +-@{ +- int i, j, na, nb, nab; +- double *xa, *xb, *xab; +- SEXP ab; +- +- PROTECT(a = AS_NUMERIC(a)); +- PROTECT(b = AS_NUMERIC(b)); +- na = LENGTH(a); nb = LENGTH(b); nab = na + nb - 1; +- PROTECT(ab = NEW_NUMERIC(nab)); +- xa = NUMERIC_POINTER(a); xb = NUMERIC_POINTER(b); +- xab = NUMERIC_POINTER(ab); +- for(i = 0; i < nab; i++) xab[i] = 0.0; +- for(i = 0; i < na; i++) +- for(j = 0; j < nb; j++) xab[i + j] += xa[i] * xb[j]; +- UNPROTECT(3); +- return(ab); +-@} +-@end group +-@end example +- +-Now for the version in @file{Rinternals.h} style. Only the C code changes. ++which could hardly be simpler, but as we shall see all the type ++coercion is transferred to the C code, which is + + @example + @group +@@ -9119,28 +9037,24 @@ + + SEXP convolve2(SEXP a, SEXP b) + @{ +- int i, j, na, nb, nab; ++ int na, nb, nab; + double *xa, *xb, *xab; + SEXP ab; + +- PROTECT(a = coerceVector(a, REALSXP)); +- PROTECT(b = coerceVector(b, REALSXP)); ++ a = PROTECT(coerceVector(a, REALSXP)); ++ b = PROTECT(coerceVector(b, REALSXP)); + na = length(a); nb = length(b); nab = na + nb - 1; +- PROTECT(ab = allocVector(REALSXP, nab)); +- xa = REAL(a); xb = REAL(b); +- xab = REAL(ab); +- for(i = 0; i < nab; i++) xab[i] = 0.0; +- for(i = 0; i < na; i++) +- for(j = 0; j < nb; j++) xab[i + j] += xa[i] * xb[j]; ++ ab = PROTECT(allocVector(REALSXP, nab)); ++ xa = REAL(a); xb = REAL(b); xab = REAL(ab); ++ for(int i = 0; i < nab; i++) xab[i] = 0.0; ++ for(int i = 0; i < na; i++) ++ for(int j = 0; j < nb; j++) xab[i + j] += xa[i] * xb[j]; + UNPROTECT(3); +- return(ab); ++ return ab; + @} + @end group + @end example + +-@noindent +-This is called in exactly the same way. +- + @node Calling .External, Missing and special values, Calling .Call, Interface functions .Call and .External + @subsection Calling @code{.External} + +@@ -9169,8 +9083,8 @@ + double *xa, *xb, *xab; + SEXP a, b, ab; + +- PROTECT(a = coerceVector(CADR(args), REALSXP)); +- PROTECT(b = coerceVector(CADDR(args), REALSXP)); ++ a = PROTECT(coerceVector(CADR(args), REALSXP)); ++ b = PROTECT(coerceVector(CADDR(args), REALSXP)); + ... + @} + @end group +@@ -9260,7 +9174,7 @@ + Rprintf("[%d] '%s' R type\n", i+1, name); + @} + @} +- return(R_NilValue); ++ return R_NilValue; + @} + @end group + @end example +@@ -9304,8 +9218,8 @@ + @example + @group + ... +- for(i = 0; i < na; i++) +- for(j = 0; j < nb; j++) ++ for(int i = 0; i < na; i++) ++ for(int j = 0; j < nb; j++) + if(ISNA(xa[i]) || ISNA(xb[j]) || ISNA(xab[i + j])) + xab[i + j] = NA_REAL; + else +@@ -9360,19 +9274,19 @@ + @group + SEXP lapply(SEXP list, SEXP expr, SEXP rho) + @{ +- int i, n = length(list); ++ int n = length(list); + SEXP ans; + + if(!isNewList(list)) error("'list' must be a list"); + if(!isEnvironment(rho)) error("'rho' should be an environment"); +- PROTECT(ans = allocVector(VECSXP, n)); +- for(i = 0; i < n; i++) @{ ++ ans = PROTECT(allocVector(VECSXP, n)); ++ for(int i = 0; i < n; i++) @{ + defineVar(install("x"), VECTOR_ELT(list, i), rho); + SET_VECTOR_ELT(ans, i, eval(expr, rho)); + @} + setAttrib(ans, R_NamesSymbol, getAttrib(list, R_NamesSymbol)); + UNPROTECT(1); +- return(ans); ++ return ans; + @} + @end group + @end example +@@ -9387,21 +9301,21 @@ + @group + SEXP lapply2(SEXP list, SEXP fn, SEXP rho) + @{ +- int i, n = length(list); ++ int n = length(list); + SEXP R_fcall, ans; + + if(!isNewList(list)) error("'list' must be a list"); + if(!isFunction(fn)) error("'fn' must be a function"); + if(!isEnvironment(rho)) error("'rho' should be an environment"); +- PROTECT(R_fcall = lang2(fn, R_NilValue)); +- PROTECT(ans = allocVector(VECSXP, n)); +- for(i = 0; i < n; i++) @{ ++ R_fcall = PROTECT(lang2(fn, R_NilValue)); ++ ans = PROTECT(allocVector(VECSXP, n)); ++ for(int i = 0; i < n; i++) @{ + SETCADR(R_fcall, VECTOR_ELT(list, i)); + SET_VECTOR_ELT(ans, i, eval(R_fcall, rho)); + @} + setAttrib(ans, R_NamesSymbol, getAttrib(list, R_NamesSymbol)); + UNPROTECT(2); +- return(ans); ++ return ans; + @} + @end group + @end example +@@ -9429,7 +9343,7 @@ + See do_docall for the template for this sort of thing. + */ + SEXP s, t; +- PROTECT(t = s = allocList(3)); ++ t = s = PROTECT(allocList(3)); + SET_TYPEOF(s, LANGSXP); + SETCAR(t, install("print")); t = CDR(t); + SETCAR(t, CAR(a)); t = CDR(t); +@@ -9490,7 +9404,7 @@ + SEXP mkans(double x) + @{ + SEXP ans; +- PROTECT(ans = allocVector(REALSXP, 1)); ++ ans = PROTECT(allocVector(REALSXP, 1)); + REAL(ans)[0] = x; + UNPROTECT(1); + return ans; +@@ -9501,7 +9415,7 @@ + double feval(double x, SEXP f, SEXP rho) + @{ + defineVar(install("x"), mkans(x), rho); +- return(REAL(eval(f, rho))[0]); ++ return REAL(eval(f, rho))[0]; + @} + @end group + +@@ -9605,7 +9519,7 @@ + @{ + SEXP theta, expr, rho, ans, ans1, gradient, par, dimnames; + double tt, xx, delta, eps = sqrt(DOUBLE_EPS), *rgr, *rans; +- int start, i, j; ++ int i, start; + @end group + + @group +@@ -9617,20 +9531,20 @@ + @end group + + @group +- PROTECT(ans = coerceVector(eval(expr, rho), REALSXP)); +- PROTECT(gradient = allocMatrix(REALSXP, LENGTH(ans), LENGTH(theta))); ++ ans = PROTECT(coerceVector(eval(expr, rho), REALSXP)); ++ gradient = PROTECT(allocMatrix(REALSXP, LENGTH(ans), LENGTH(theta))); + rgr = REAL(gradient); rans = REAL(ans); + @end group + + @group + for(i = 0, start = 0; i < LENGTH(theta); i++, start += LENGTH(ans)) @{ +- PROTECT(par = findVar(install(CHAR(STRING_ELT(theta, i))), rho)); ++ par = PROTECT(findVar(install(CHAR(STRING_ELT(theta, i))), rho)); + tt = REAL(par)[0]; + xx = fabs(tt); + delta = (xx < 1) ? eps : xx*eps; + REAL(par)[0] += delta; +- PROTECT(ans1 = coerceVector(eval(expr, rho), REALSXP)); +- for(j = 0; j < LENGTH(ans); j++) ++ ans1 = PROTECT(coerceVector(eval(expr, rho), REALSXP)); ++ for(int j = 0; j < LENGTH(ans); j++) + rgr[j + start] = (REAL(ans1)[j] - rans[j])/delta; + REAL(par)[0] = tt; + UNPROTECT(2); /* par, ans1 */ +@@ -9638,7 +9552,7 @@ + @end group + + @group +- PROTECT(dimnames = allocVector(VECSXP, 2)); ++ dimnames = PROTECT(allocVector(VECSXP, 2)); + SET_VECTOR_ELT(dimnames, 1, theta); + dimnamesgets(gradient, dimnames); + setAttrib(ans, install("gradient"), gradient); +@@ -9671,14 +9585,14 @@ + environment @code{rho}, by + + @example +- PROTECT(ans = coerceVector(eval(expr, rho), REALSXP)); ++ ans = PROTECT(coerceVector(eval(expr, rho), REALSXP)); + @end example + + @noindent + We then allocate space for the calculated derivative by + + @example +- PROTECT(gradient = allocMatrix(REALSXP, LENGTH(ans), LENGTH(theta))); ++ gradient = PROTECT(allocMatrix(REALSXP, LENGTH(ans), LENGTH(theta))); + @end example + + @noindent +@@ -9689,7 +9603,7 @@ + @example + @group + for(i = 0, start = 0; i < LENGTH(theta); i++, start += LENGTH(ans)) @{ +- PROTECT(par = findVar(install(CHAR(STRING_ELT(theta, i))), rho)); ++ par = PROTECT(findVar(install(CHAR(STRING_ELT(theta, i))), rho)); + @end group + @end example + +@@ -9710,7 +9624,7 @@ + xx = fabs(tt); + delta = (xx < 1) ? eps : xx*eps; + REAL(par)[0] += delta; +- PROTECT(ans1 = coerceVector(eval(expr, rho), REALSXP)); ++ ans1 = PROTECT(coerceVector(eval(expr, rho), REALSXP)); + @end group + @end example + +@@ -9725,7 +9639,7 @@ + + @example + @group +- for(j = 0; j < LENGTH(ans); j++) ++ for(int j = 0; j < LENGTH(ans); j++) + rgr[j + start] = (REAL(ans1)[j] - rans[j])/delta; + REAL(par)[0] = tt; + UNPROTECT(2); +@@ -9739,7 +9653,7 @@ + + @example + @group +- PROTECT(dimnames = allocVector(VECSXP, 2)); ++ dimnames = PROTECT(allocVector(VECSXP, 2)); + SET_VECTOR_ELT(dimnames, 1, theta); + dimnamesgets(gradient, dimnames); + setAttrib(ans, install("gradient"), gradient); +@@ -9785,7 +9699,7 @@ + ParseStatus status; + ... + if(done == 1) @{ +- PROTECT(cmdSexp = allocVector(STRSXP, 1)); ++ cmdSexp = PROTECT(allocVector(STRSXP, 1)); + SET_STRING_ELT(cmdSexp, 0, mkChar(cmd)); + cmdexpr = PROTECT(R_ParseVector(cmdSexp, -1, &status, R_NilValue)); + if (status != PARSE_OK) @{ +@@ -9989,7 +9903,7 @@ + + @example + SEXP ans, ptr; +- PROTECT(ans = allocVector(INTSXP, 1)); ++ ans = PROTECT(allocVector(INTSXP, 1)); + ptr = R_MakeExternalPtr(thisHandle, install("RODBC_channel"), R_NilValue); + PROTECT(ptr); + R_RegisterCFinalizerEx(ptr, chanFinalizer, TRUE); +@@ -10615,6 +10529,12 @@ + The standard packages, for example @pkg{stats}, are a rich source of + further examples. + ++Passing character strings from C to FORTRAN 77 or @emph{vice versa} is ++not portable (and to Fortran 90 or later is even less so). We have ++found that it helps to ensure that a C string to be passed is followed ++by several @code{nul}s (and not just the one needed as a C terminator). ++But for maximal portability character strings in FORTRAN should be ++avoided. + + + @node Numerical analysis subroutines, Optimization, Calling C from FORTRAN and vice versa, The R API +diff -ruN R-3.0.1/doc/manual/R-intro.texi R-patched/doc/manual/R-intro.texi +--- doc/manual/R-intro.texi 2013-04-03 18:05:07.000000000 -0400 ++++ doc/manual/R-intro.texi 2013-05-24 18:05:06.000000000 -0400 +@@ -84,7 +84,9 @@ + @top An Introduction to R + + This is an introduction to R (``GNU S''), a language and environment for +-statistical computing and graphics. R is similar to the award-winning S ++statistical computing and graphics. R is similar to the ++award-winning@footnote{ACM Software Systems award, 1998: ++@uref{http://awards.acm.org/award_winners/chambers_6640862.cfm}.} S + system, which was developed at Bell Laboratories by John Chambers et al. + It provides a wide variety of statistical and graphical techniques + (linear and nonlinear modelling, statistical tests, time series +@@ -149,8 +151,8 @@ + and more importantly some instant feedback on what actually happens. + + Many users will come to @R{} mainly for its graphical facilities. +-@ref{Graphics} on the graphics facilities can be read at almost any time +-and need not wait until all the preceding sections have been digested. ++@xref{Graphics}, which can be read at almost any time and need not wait ++until all the preceding sections have been digested. + + @menu + * Introduction and preliminaries:: +@@ -1981,12 +1983,27 @@ + @node Matrix facilities, Forming partitioned matrices, Generalized transpose of an array, Arrays and matrices + @section Matrix facilities + ++@iftex + @macro xTx{} +- @eqn{@strong{x}^T @strong{x}, x'x} ++@tex ++$@strong{x}^T @strong{x}$% ++@end tex + @end macro + @macro xxT{} +- @eqn{@strong{x}@strong{x}^T, x x'} ++@tex ++$@strong{x}@strong{x}^T$% ++@end tex + @end macro ++@end iftex ++ ++@ifnottex ++@macro xTx{} ++x'x ++@end macro ++@macro xxT{} ++x x' ++@end macro ++@end ifnottex + + As noted above, a matrix is just an array with two subscripts. However + it is such an important special case it needs a separate discussion. +@@ -2047,8 +2064,7 @@ + result. The matrix @xxT{} may be calculated either by @code{cbind(x) + %*% x} or @code{x %*% rbind(x)} since the result of @code{rbind()} or + @code{cbind()} is always a matrix. However, the best way to compute +-@xTx{} or @xxT{} is @code{crossprod(x)} or @code{x %o% x} +-respectively.} ++@xTx{} or @xxT{} is @code{crossprod(x)} or @code{x %o% x} respectively.} + + @findex crossprod + The function @code{crossprod()} forms ``crossproducts'', meaning that +@@ -2103,13 +2119,13 @@ + potentially unstable to compute @code{x <- solve(A) %*% b} instead of + @code{solve(A,b)}. + +-The quadratic form @eqn{@strong{x^T A^{-1} x},@ @code{x %*% A^@{-1@} %*% ++The quadratic form @eqn{@strong{x^T A^{-1} x},@ @code{x %*% A^@{-1@} %*% + x} @ } which is used in multivariate computations, should be computed by + something like@footnote{Even better would be to form a matrix square +-root @eqn{B, B} with @eqn{A = BB^T, A = BB'} and find the squared length of the +-solution of @eqn{By = x, By = x}, perhaps using the Cholesky or +-eigendecomposition of @eqn{A, A}.} @code{x %*% solve(A,x)}, rather than +-computing the inverse of @code{A}. ++root @eqn{B, B} with @eqn{A = BB^T, A = BB'} and find the squared length ++of the solution of @eqn{By = x, By = x} , perhaps using the Cholesky or ++eigen decomposition of @eqn{A, A}. } @code{x %*% solve(A,x)}, rather ++than computing the inverse of @code{A}. + + @node Eigenvalues and eigenvectors, Singular value decomposition and determinants, Linear equations and inversion, Matrix facilities + @subsection Eigenvalues and eigenvectors +@@ -2728,9 +2744,9 @@ + facilities are simple and their requirements are fairly strict and even + rather inflexible. There is a clear presumption by the designers of + @R{} that you will be able to modify your input files using other tools, +-such as file editors or Perl@footnote{Under UNIX, the utilities Sed or +-Awk can be used.} to fit in with the requirements of @R{}. Generally +-this is very simple. ++such as file editors or Perl@footnote{Under UNIX, the utilities ++@command{sed} or@command{awk} can be used.} to fit in with the ++requirements of @R{}. Generally this is very simple. + + If variables are to be held mainly in data frames, as we strongly + suggest they should be, an entire data frame can be read directly with +@@ -5340,13 +5356,15 @@ + display a wide variety of statistical graphs and also to build entirely + new types of graph. + +-The graphics facilities can be used in both interactive and batch modes, but in +-most cases, interactive use is more productive. Interactive use is also +-easy because at startup time @R{} initiates a graphics @emph{device +-driver} which opens a special @emph{graphics window} for the display of +-interactive graphics. Although this is done automatically, it is useful +-to know that the command used is @code{X11()} under UNIX, +-@code{windows()} under Windows and @code{quartz()} under OS X. ++The graphics facilities can be used in both interactive and batch modes, ++but in most cases, interactive use is more productive. Interactive use ++is also easy because at startup time @R{} initiates a graphics ++@emph{device driver} which opens a special @emph{graphics window} for ++the display of interactive graphics. Although this is done ++automatically, it may useful to know that the command used is ++@code{X11()} under UNIX, @code{windows()} under Windows and ++@code{quartz()} under OS X. A new device can always be opened by ++@code{dev.new()}. + + Once the device driver is running, @R{} plotting commands can be used to + produce a variety of graphical displays and to create entirely new kinds +diff -ruN R-3.0.1/share/licenses/license.db R-patched/share/licenses/license.db +--- share/licenses/license.db 2013-03-22 19:05:06.000000000 -0400 ++++ share/licenses/license.db 2013-05-24 18:05:06.000000000 -0400 +@@ -128,7 +128,7 @@ + Abbrev: BSD_2_clause + OSI: open (http://opensource.org/licenses/BSD-2-Clause) + FSF: free_and_GPLv3_compatible (http://www.gnu.org/licenses/license-list.html#FreeBSD) +-File: src/licenses/BSD_2_clause ++File: share/licenses/BSD_2_clause + URL: http://opensource.org/licenses/BSD-2-Clause + FOSS: yes + Extensible: yes +@@ -138,7 +138,7 @@ + Abbrev: BSD_3_clause + OSI: open (http://opensource.org/licenses/BSD-2-Clause) + FSF: free_and_GPLv3_compatible (http://www.gnu.org/licenses/license-list.html#ModifiedBSD) +-File: src/licenses/BSD_3_clause ++File: share/licenses/BSD_3_clause + URL: http://opensource.org/licenses/BSD-3-Clause + FOSS: yes + Extensible: yes +diff -ruN R-3.0.1/src/include/Rdefines.h R-patched/src/include/Rdefines.h +--- src/include/Rdefines.h 2012-04-15 18:05:02.000000000 -0400 ++++ src/include/Rdefines.h 2013-05-26 18:05:04.000000000 -0400 +@@ -1,6 +1,6 @@ + /* + * R : A Computer Language for Statistical Data Analysis +- * Copyright (C) 1999-2007 The R Core Team. ++ * Copyright (C) 1999-2013 The R Core Team. + * + * This program is free software; you can redistribute it and/or modify + * it under the terms of the GNU Lesser General Public License as published by +@@ -133,6 +133,7 @@ + #define SET_DIMNAMES(x, n) setAttrib(x, R_DimNamesSymbol, n) + #define SET_LEVELS(x, l) setAttrib(x, R_LevelsSymbol, l) + #define SET_NAMES(x, n) setAttrib(x, R_NamesSymbol, n) ++/* These do not support long vectors */ + #define GET_LENGTH(x) length(x) + #define SET_LENGTH(x, n) (x = lengthgets(x, n)) + +@@ -146,11 +147,25 @@ + + #define s_object SEXPREC + #define S_EVALUATOR /**/ +-#ifndef TRUE +-#define TRUE 1 +-#endif +-#ifndef FALSE +-#define FALSE 0 ++ ++/* These conflict with definitions in R_ext/Boolean.h, ++ but spatstat relies on them in a C file */ ++#ifdef __cplusplus ++# ifndef R_EXT_BOOLEAN_H_ ++# ifndef TRUE ++# define TRUE 1 ++# endif ++# ifndef FALSE ++# define FALSE 0 ++# endif ++# endif ++#else ++# ifndef TRUE ++# define TRUE 1 ++# endif ++# ifndef FALSE ++# define FALSE 0 ++# endif + #endif + + #define COPY_TO_USER_STRING(x) mkChar(x) +Files R-3.0.1/src/library/Recommended/foreign.tgz and R-patched/src/library/Recommended/foreign.tgz differ +Files R-3.0.1/src/library/Recommended/foreign_0.8-53.tar.gz and R-patched/src/library/Recommended/foreign_0.8-53.tar.gz differ +Files R-3.0.1/src/library/Recommended/foreign_0.8-54.tar.gz and R-patched/src/library/Recommended/foreign_0.8-54.tar.gz differ +Files R-3.0.1/src/library/Recommended/mgcv.tgz and R-patched/src/library/Recommended/mgcv.tgz differ +Files R-3.0.1/src/library/Recommended/mgcv_1.7-22.tar.gz and R-patched/src/library/Recommended/mgcv_1.7-22.tar.gz differ +Files R-3.0.1/src/library/Recommended/mgcv_1.7-23.tar.gz and R-patched/src/library/Recommended/mgcv_1.7-23.tar.gz differ +diff -ruN R-3.0.1/src/library/base/R/grep.R R-patched/src/library/base/R/grep.R +--- src/library/base/R/grep.R 2013-03-05 18:02:33.000000000 -0500 ++++ src/library/base/R/grep.R 2013-05-16 18:05:04.000000000 -0400 +@@ -302,6 +302,7 @@ + stop("must have replacement values for matches") + value <- rep_len(value, np) + } ++ y <- y[pos] + x[pos] <- paste0(sapply(y, `[`, 1L), value, sapply(y, `[`, 2L)) + return(x) + } +diff -ruN R-3.0.1/src/library/base/man/sort.Rd R-patched/src/library/base/man/sort.Rd +--- src/library/base/man/sort.Rd 2013-03-05 18:02:35.000000000 -0500 ++++ src/library/base/man/sort.Rd 2013-05-24 18:05:05.000000000 -0400 +@@ -72,7 +72,7 @@ + are more than 10.) Names are discarded for partial sorting. + + Method \code{"shell"} uses Shellsort (an \eqn{O(n^{4/3})} variant from +- Sedgewick (1996)). If \code{x} has names a stable modification is ++ Sedgewick (1986)). If \code{x} has names a stable modification is + used, so ties are not reordered. (This only matters if names are + present.) + +diff -ruN R-3.0.1/src/library/grDevices/man/Japanese.Rd R-patched/src/library/grDevices/man/Japanese.Rd +--- src/library/grDevices/man/Japanese.Rd 2012-12-05 09:37:58.000000000 -0500 ++++ src/library/grDevices/man/Japanese.Rd 2013-05-16 18:05:04.000000000 -0400 +@@ -37,8 +37,8 @@ + par(cex = 3) + Vf <- c("serif", "plain") + % doubled "\" -> can't execute here! +-text(4, 2, "\\\\#J2438\\\\#J2421\\\\#J2451\\\\#J2473", vfont = Vf) +-text(4, 4, "\\\\#J2538\\\\#J2521\\\\#J2551\\\\#J2573", vfont = Vf) ++text(4, 2, "\\\\#J244b\\\\#J245b\\\\#J2473", vfont = Vf) ++text(4, 4, "\\\\#J2538\\\\#J2563\\\\#J2551\\\\#J2573", vfont = Vf) + text(4, 6, "\\\\#J467c\\\\#J4b5c", vfont = Vf) + text(4, 8, "Japan", vfont = Vf) + par(cex = 1) +diff -ruN R-3.0.1/src/library/graphics/man/par.Rd R-patched/src/library/graphics/man/par.Rd +--- src/library/graphics/man/par.Rd 2013-03-05 18:02:29.000000000 -0500 ++++ src/library/graphics/man/par.Rd 2013-05-24 18:05:04.000000000 -0400 +@@ -729,10 +729,12 @@ + plot(0:1, 0:1, type = "n", axes = FALSE, ann = FALSE) + y <- (n:1)/(n+1) + clty <- as.character(ltys) +- mytext <- function(x,y, txt) text(x, y, txt, adj = c(0, -.3), cex = 0.8, ...) ++ mytext <- function(x, y, txt) ++ text(x, y, txt, adj = c(0, -.3), cex = 0.8, ...) + abline(h = y, lty = ltys, ...); mytext(xoff, y, clty) + y <- y - 1/(3*(n+1)) +- abline(h = y, lty = ltys, lwd = 2, ...); mytext(1/8+xoff, y, paste(clty," lwd = 2")) ++ abline(h = y, lty = ltys, lwd = 2, ...) ++ mytext(1/8+xoff, y, paste(clty," lwd = 2")) + } + showLty(c("solid", "dashed", "dotted", "dotdash", "longdash", "twodash")) + par(new = TRUE) # the same: +Files R-3.0.1/src/library/grid/inst/doc/displaylist.pdf and R-patched/src/library/grid/inst/doc/displaylist.pdf differ +Files R-3.0.1/src/library/grid/inst/doc/frame.pdf and R-patched/src/library/grid/inst/doc/frame.pdf differ +Files R-3.0.1/src/library/grid/inst/doc/grid.pdf and R-patched/src/library/grid/inst/doc/grid.pdf differ +Files R-3.0.1/src/library/grid/inst/doc/grobs.pdf and R-patched/src/library/grid/inst/doc/grobs.pdf differ +Files R-3.0.1/src/library/grid/inst/doc/interactive.pdf and R-patched/src/library/grid/inst/doc/interactive.pdf differ +Files R-3.0.1/src/library/grid/inst/doc/locndimn.pdf and R-patched/src/library/grid/inst/doc/locndimn.pdf differ +Files R-3.0.1/src/library/grid/inst/doc/moveline.pdf and R-patched/src/library/grid/inst/doc/moveline.pdf differ +Files R-3.0.1/src/library/grid/inst/doc/nonfinite.pdf and R-patched/src/library/grid/inst/doc/nonfinite.pdf differ +Files R-3.0.1/src/library/grid/inst/doc/plotexample.pdf and R-patched/src/library/grid/inst/doc/plotexample.pdf differ +Files R-3.0.1/src/library/grid/inst/doc/rotated.pdf and R-patched/src/library/grid/inst/doc/rotated.pdf differ +Files R-3.0.1/src/library/grid/inst/doc/saveload.pdf and R-patched/src/library/grid/inst/doc/saveload.pdf differ +Files R-3.0.1/src/library/grid/inst/doc/sharing.pdf and R-patched/src/library/grid/inst/doc/sharing.pdf differ +Files R-3.0.1/src/library/grid/inst/doc/viewports.pdf and R-patched/src/library/grid/inst/doc/viewports.pdf differ +diff -ruN R-3.0.1/src/library/methods/man/representation.Rd R-patched/src/library/methods/man/representation.Rd +--- src/library/methods/man/representation.Rd 2013-03-05 18:02:31.000000000 -0500 ++++ src/library/methods/man/representation.Rd 2013-05-16 18:05:04.000000000 -0400 +@@ -8,13 +8,15 @@ + \alias{prototype} + \title{ Construct a Representation or a Prototype for a Class Definition} + \description{ +- In calls to +- \code{\link{setClass}}, these two functions construct, +- respectively, the \code{representation} and \code{prototype} +- arguments. They do various checks and handle special cases. You're +- encouraged to use them when defining classes that, for +- example, extend other classes as a data part or have multiple +- superclasses, or that combine extending a class and slots. ++ These are old utility functions to construct, respectively ++ a list designed to represent the slots and superclasses and ++ a list of prototype specifications. The \code{representation()} ++ function is no longer useful, since the arguments \code{slots} and ++ \code{contains} to \code{\link{setClass}} are now recommended. ++ ++ The \code{prototype()} function may still be used for the ++ corresponding argument, but a ++ simple list of the same arguments works as well. + } + \usage{ + representation(...) +diff -ruN R-3.0.1/src/library/methods/man/setClass.Rd R-patched/src/library/methods/man/setClass.Rd +--- src/library/methods/man/setClass.Rd 2013-03-05 18:02:31.000000000 -0500 ++++ src/library/methods/man/setClass.Rd 2013-05-16 18:05:04.000000000 -0400 +@@ -15,7 +15,7 @@ + is returned as the value of \code{setClass()}, suitable for creating + objects from the class if the class is not virtual. Of the many + arguments to the function only \code{Class}, +- \code{representation} and \code{contains} are usually needed. ++ \code{slots=} and \code{contains=} are usually needed. + } + \usage{ + setClass(Class, representation, prototype, contains=character(), +diff -ruN R-3.0.1/src/library/methods/src/slot.c R-patched/src/library/methods/src/slot.c +--- src/library/methods/src/slot.c 2012-04-15 18:05:17.000000000 -0400 ++++ src/library/methods/src/slot.c 2013-05-25 18:05:04.000000000 -0400 +@@ -1,6 +1,6 @@ + /* + * R : A Computer Language for Statistical Data Analysis +- * Copyright (C) 2001-2005 The R Core Team. ++ * Copyright (C) 2001-2013 The R Core Team. + * + * This program is free software; you can redistribute it and/or modify + * it under the terms of the GNU General Public License as published by +@@ -18,7 +18,6 @@ + */ + + #include <R.h> +-#include <Rdefines.h> + #include <Rinternals.h> + #include "methods.h" + +Files R-3.0.1/src/library/parallel/inst/doc/parallel.pdf and R-patched/src/library/parallel/inst/doc/parallel.pdf differ +diff -ruN R-3.0.1/src/library/stats/R/median.R R-patched/src/library/stats/R/median.R +--- src/library/stats/R/median.R 2012-08-05 18:05:06.000000000 -0400 ++++ src/library/stats/R/median.R 2013-05-24 18:05:04.000000000 -0400 +@@ -21,8 +21,9 @@ + median.default <- function(x, na.rm = FALSE) + { + if(is.factor(x) || is.data.frame(x)) stop("need numeric data") +- ## all other objects only need sort() & mean() to be working ++ ## all other objects only need is.na(), sort() & mean() to be working + if(length(names(x))) names(x) <- NULL # for e.g., c(x = NA_real_) ++## if(na.rm) x <- x[!is.na(x)] else if(anyNA(x)) return(x[FALSE][NA]) + if(na.rm) x <- x[!is.na(x)] else if(any(is.na(x))) return(x[FALSE][NA]) + n <- length(x) + if (n == 0L) return(x[FALSE][NA]) +diff -ruN R-3.0.1/src/library/stats/man/median.Rd R-patched/src/library/stats/man/median.Rd +--- src/library/stats/man/median.Rd 2013-03-05 18:02:25.000000000 -0500 ++++ src/library/stats/man/median.Rd 2013-05-24 18:05:04.000000000 -0400 +@@ -21,10 +21,11 @@ + } + \details{ + This is a generic function for which methods can be written. However, +- the default method makes use of \code{sort} and \code{mean} from +- package \pkg{base} both of which are generic, and so the default +- method will work for most classes (e.g. \code{"\link{Date}"}) for +- which a median is a reasonable concept. ++ the default method makes use of \code{is.na}, \code{sort} and ++ \code{mean} from package \pkg{base} all of which are generic, and so ++ the default method will work for most classes ++ (e.g. \code{"\link{Date}"}) for which a median is a reasonable ++ concept. + } + \value{ + The default method returns a length-one object of the same type as +diff -ruN R-3.0.1/src/library/stats/src/distance.c R-patched/src/library/stats/src/distance.c +--- src/library/stats/src/distance.c 2013-03-05 18:02:24.000000000 -0500 ++++ src/library/stats/src/distance.c 2013-05-24 18:05:04.000000000 -0400 +@@ -29,7 +29,7 @@ + #include <Rmath.h> + #include <float.h> + #include "stats.h" +-#ifdef HAVE_OPENMP ++#ifdef _OPENMP + # include <R_ext/MathThreads.h> + #endif + +@@ -201,7 +201,7 @@ + int dc, i, j; + size_t ij; /* can exceed 2^31 - 1 */ + double (*distfun)(double*, int, int, int, int) = NULL; +-#ifdef HAVE_OPENMP ++#ifdef _OPENMP + int nthreads; + #endif + +@@ -229,7 +229,7 @@ + error(_("distance(): invalid distance")); + } + dc = (*diag) ? 0 : 1; /* diag=1: we do the diagonal */ +-#ifdef HAVE_OPENMP ++#ifdef _OPENMP + if (R_num_math_threads > 0) + nthreads = R_num_math_threads; + else +diff -ruN R-3.0.1/src/library/tools/R/Rd2ex.R R-patched/src/library/tools/R/Rd2ex.R +--- src/library/tools/R/Rd2ex.R 2012-08-05 18:05:08.000000000 -0400 ++++ src/library/tools/R/Rd2ex.R 2013-05-25 18:05:03.000000000 -0400 +@@ -20,7 +20,7 @@ + + Rd2ex <- + function(Rd, out="", defines=.Platform$OS.type, stages="render", +- outputEncoding="UTF-8", ...) ++ outputEncoding="UTF-8", commentDontrun = TRUE, ...) + { + encode_warn <- FALSE + WriteLines <- function(x, con, outputEncoding, ...) { +@@ -73,21 +73,22 @@ + writeLines("", con) + of1("## End Don't show") + } else if (tag == "\\dontrun") { +- ## Special case for one line. +- if (length(x) == 1L) { ++ if (commentDontrun) + of1("## Not run: ") ++ ## Special case for one line. ++ if (length(x) == 1L && commentDontrun) { + render(x[[1L]], prefix) + } else { +- of1("## Not run: ") + if (!grepl("^\n", x[[1L]][1L], perl = TRUE) && RdTags(x)[1L] != "COMMENT") { + writeLines("", con) +- render(x[[1L]], paste("##D", prefix)) ++ render(x[[1L]], paste0(if (commentDontrun) "##D ", prefix)) + } else render(x[[1L]], prefix) +- for(i in 2:length(x)) render(x[[i]], paste("##D", prefix)) ++ for(i in 2:length(x)) render(x[[i]], paste0(if (commentDontrun) "##D ", prefix)) + last <- x[[length(x)]] + if (!grepl("\n$", last[length(last)], perl = TRUE)) + writeLines("", con) +- of1("## End(Not run)") ++ if (commentDontrun) ++ of1("## End(Not run)") + } + } else if (tag == "\\donttest") { + of1("## No test: ") +diff -ruN R-3.0.1/src/library/tools/R/check.R R-patched/src/library/tools/R/check.R +--- src/library/tools/R/check.R 2013-04-22 18:05:03.000000000 -0400 ++++ src/library/tools/R/check.R 2013-05-20 18:05:04.000000000 -0400 +@@ -3313,9 +3313,10 @@ + " -v, --version print version info and exit", + " -l, --library=LIB library directory used for test installation", + " of packages (default is outdir)", +- " -o, --outdir=DIR directory used for logfiles, R output, etc.", +- " (default is 'pkg.Rcheck' in current directory,", +- " where 'pkg' is the name of the package checked)", ++ " -o, --output=DIR directory for output, default is current directory.", ++ " Logfiles, R output, etc. will be placed in 'pkg.Rcheck'", ++ " in this directory, where 'pkg' is the name of the", ++ " checked package", + " --no-clean do not clean 'outdir' before using it", + " --no-codoc do not check for code/documentation mismatches", + " --no-examples do not run the examples in the Rd files", +diff -ruN R-3.0.1/src/library/tools/man/Rd2HTML.Rd R-patched/src/library/tools/man/Rd2HTML.Rd +--- src/library/tools/man/Rd2HTML.Rd 2013-03-05 18:02:28.000000000 -0500 ++++ src/library/tools/man/Rd2HTML.Rd 2013-05-25 18:05:03.000000000 -0400 +@@ -30,7 +30,8 @@ + fragment = FALSE, ..., writeEncoding = TRUE) + + Rd2ex(Rd, out = "", defines = .Platform$OS.type, +- stages = "render", outputEncoding = "UTF-8", ...) ++ stages = "render", outputEncoding = "UTF-8", ++ commentDontrun = TRUE, ...) + } + \arguments{ + \item{Rd}{ a filename or \code{Rd} object to use as input. } +@@ -57,6 +58,8 @@ + \code{Rd} is a filename. } + \item{writeEncoding}{should \verb{\inputencoding} lines be written in + the file for non-ASCII encodings?} ++ \item{commentDontrun}{should \verb{\dontrun} sections be commented ++ out?} + } + \details{ + These functions convert help documents: \code{Rd2HTML} produces HTML, +diff -ruN R-3.0.1/src/library/tools/src/Makefile.in R-patched/src/library/tools/src/Makefile.in +--- src/library/tools/src/Makefile.in 2013-03-05 18:02:28.000000000 -0500 ++++ src/library/tools/src/Makefile.in 2013-05-16 07:42:08.000000000 -0400 +@@ -64,6 +64,6 @@ + $(srcdir)/gramLatex.c: @MAINTAINER_MODE_TRUE@ $(srcdir)/gramLatex.y + @$(ECHO) "re-making gramLatex.c" + $(YACC) $(YFLAGS) $(srcdir)/gramLatex.y +- $(SHELL) $(top_srcdir)/tools/move-if-change y.tab.c $(srcdir)/gramLatex. ++ $(SHELL) $(top_srcdir)/tools/move-if-change y.tab.c $(srcdir)/gramLatex.c + + ## Automagically generated dependencies: +diff -ruN R-3.0.1/src/library/utils/R/example.R R-patched/src/library/utils/R/example.R +--- src/library/utils/R/example.R 2012-08-05 18:05:07.000000000 -0400 ++++ src/library/utils/R/example.R 2013-05-25 18:05:03.000000000 -0400 +@@ -22,7 +22,8 @@ + character.only = FALSE, give.lines = FALSE, local = FALSE, + echo = TRUE, verbose = getOption("verbose"), setRNG = FALSE, + ask = getOption("example.ask"), +- prompt.prefix = abbreviate(topic, 6)) ++ prompt.prefix = abbreviate(topic, 6), ++ run.dontrun = FALSE) + { + if (!character.only) { + topic <- substitute(topic) +@@ -39,7 +40,7 @@ + pkgname <- basename(packagePath) + lib <- dirname(packagePath) + tf <- tempfile("Rex") +- tools::Rd2ex(.getHelpFile(file), tf) ++ tools::Rd2ex(.getHelpFile(file), tf, commentDontrun = !run.dontrun) + if (!file.exists(tf)) { + if(give.lines) return(character()) + warning(gettextf("%s has a help file but no examples", sQuote(topic)), +diff -ruN R-3.0.1/src/library/utils/R/help.request.R R-patched/src/library/utils/R/help.request.R +--- src/library/utils/R/help.request.R 2013-03-05 18:02:26.000000000 -0500 ++++ src/library/utils/R/help.request.R 2013-05-16 18:05:04.000000000 -0400 +@@ -1,7 +1,7 @@ + # File src/library/utils/R/unix/help.request.R + # Part of the R package, http://www.R-project.org + # +-# Copyright (C) 1995-2012 The R Core Team ++# Copyright (C) 1995-2013 The R Core Team + # + # This program is free software; you can redistribute it and/or modify + # it under the terms of the GNU General Public License as published by +@@ -95,10 +95,9 @@ + if(no(other)) return("Please do this first.") + } + +- man <- url("http://cran.r-project.org/manuals.html") +- ver <- scan(man, what = character(0L), sep = "\n", skip = 13L, nlines = 1L, +- quiet = TRUE) +- ver <- strsplit(ver, " ")[[1L]][3L] ++ page <- url("http://cran.r-project.org/bin/windows/base") ++ title <- grep("<title>", readLines(page, 10L), fixed = TRUE, value = TRUE) ++ ver <- sub("^.*R-([^ ]*) for Windows.*$", "\\1", title) + if (getRversion() < numeric_version(ver)) { + update <- readMyLine("Your R version is out-of-date,", + "would you like to update now?") +Files R-3.0.1/src/library/utils/inst/doc/Sweave.pdf and R-patched/src/library/utils/inst/doc/Sweave.pdf differ +diff -ruN R-3.0.1/src/library/utils/man/example.Rd R-patched/src/library/utils/man/example.Rd +--- src/library/utils/man/example.Rd 2012-12-05 09:37:55.000000000 -0500 ++++ src/library/utils/man/example.Rd 2013-05-25 18:05:03.000000000 -0400 +@@ -16,7 +16,8 @@ + character.only = FALSE, give.lines = FALSE, local = FALSE, + echo = TRUE, verbose = getOption("verbose"), + setRNG = FALSE, ask = getOption("example.ask"), +- prompt.prefix = abbreviate(topic, 6)) ++ prompt.prefix = abbreviate(topic, 6), ++ run.dontrun = FALSE) + } + \arguments{ + \item{topic}{name or literal character string: the online +@@ -53,6 +54,8 @@ + device and to any devices opened by the example code.} + \item{prompt.prefix}{character; prefixes the prompt to be used if + \code{echo = TRUE}.} ++ \item{run.dontrun}{logical indicating that \verb{\dontrun} ++ should be ignored.} + } + \value{ + The value of the last evaluated expression, unless \code{give.lines} +diff -ruN R-3.0.1/src/main/RNG.c R-patched/src/main/RNG.c +--- src/main/RNG.c 2013-03-18 19:05:08.000000000 -0400 ++++ src/main/RNG.c 2013-05-24 18:05:05.000000000 -0400 +@@ -441,7 +441,7 @@ + /* Choose a new kind of RNG. + * Initialize its seed by calling the old RNG's unif_rand() + */ +- if (newkind == -1) newkind = RNG_DEFAULT; ++ if (newkind == (RNGtype)-1) newkind = RNG_DEFAULT; + switch(newkind) { + case WICHMANN_HILL: + case MARSAGLIA_MULTICARRY: +@@ -465,7 +465,7 @@ + { + /* N01type is an enumeration type, so this will probably get + mapped to an unsigned integer type. */ +- if (kind == -1) kind = N01_DEFAULT; ++ if (kind == (N01type)-1) kind = N01_DEFAULT; + if (kind > KINDERMAN_RAMAGE) + error(_("invalid Normal type in 'RNGkind'")); + if (kind == USER_NORM) { +diff -ruN R-3.0.1/src/main/array.c R-patched/src/main/array.c +--- src/main/array.c 2013-04-19 18:05:04.000000000 -0400 ++++ src/main/array.c 2013-05-24 18:05:05.000000000 -0400 +@@ -1267,7 +1267,7 @@ + + if (OP == 0 || OP == 1) { /* columns */ + PROTECT(ans = allocVector(REALSXP, p)); +-#ifdef HAVE_OPENMP ++#ifdef _OPENMP + int nthreads; + /* This gives a spurious -Wunused-but-set-variable error */ + if (R_num_math_threads > 0) +diff -ruN R-3.0.1/src/main/platform.c R-patched/src/main/platform.c +--- src/main/platform.c 2013-04-15 18:05:05.000000000 -0400 ++++ src/main/platform.c 2013-05-16 18:05:04.000000000 -0400 +@@ -830,10 +830,16 @@ + for (i = 0; i < n; i++) { + #ifdef Win32 + wchar_t *wfn = filenameToWchar(STRING_ELT(fn, i), TRUE); +- /* 'Sharpie' and fellow ignorami use trailing / on Windows, +- where it is not valid */ +- wchar_t *p = wfn + (wcslen(wfn) - 1); +- if (*p == L'/' || *p == L'\\') *p = 0; ++ /* trailing \ is not valid on Windows except for the ++ root directory on a drive, specified as "\", or "D:\", ++ or "\\?\D:\", etc. We remove it in other cases, ++ to help those who think they're on Unix. */ ++ size_t len = wcslen(wfn); ++ if (len) { ++ wchar_t *p = wfn + (len - 1); ++ if (len > 1 && (*p == L'/' || *p == L'\\') && ++ *(p-1) != L':') *p = 0; ++ } + #else + const char *efn = R_ExpandFileName(translateChar(STRING_ELT(fn, i))); + #endif +diff -ruN R-3.0.1/src/scripts/config R-patched/src/scripts/config +--- src/scripts/config 2013-04-18 18:05:05.000000000 -0400 ++++ src/scripts/config 2013-05-18 18:05:03.000000000 -0400 +@@ -20,7 +20,7 @@ + ## A copy of the GNU General Public License is available at + ## http://www.r-project.org/Licenses/ + +-revision='$Revision: 62610 $' ++revision='$Revision: 62759 $' + version=`set - ${revision}; echo ${2}` + version="R configuration information retrieval script: ${R_VERSION} (r${version}) + +@@ -219,7 +219,7 @@ + makefiles="${makefiles} -f ${HOME}/.R/Makevars" + fi + else +- . ${R_HOME}/etc/Renviron ++ . ${R_HOME}/etc${R_ARCH}/Renviron + if test -n "${R_MAKEVARS_USER}"; then + makefiles="${makefiles} -f ${R_MAKEVARS_USER}" + elif test -f "${HOME}/.R/Makevars-${R_PLATFORM}"; then +diff -ruN R-3.0.1/tests/Examples/datasets-Ex.Rout.save R-patched/tests/Examples/datasets-Ex.Rout.save +--- tests/Examples/datasets-Ex.Rout.save 2013-03-30 19:05:05.000000000 -0400 ++++ tests/Examples/datasets-Ex.Rout.save 2013-05-24 18:05:05.000000000 -0400 +@@ -1,5 +1,5 @@ + +-R version 3.0.0 RC (2013-03-29 r62438) -- "Masked Marvel" ++R version 3.0.1 Patched (2013-05-24 r62792) -- "Good Sport" + Copyright (C) 2013 The R Foundation for Statistical Computing + Platform: x86_64-unknown-linux-gnu (64-bit) + +@@ -3434,8 +3434,9 @@ + > + > ### * <FOOTER> + > ### ++> options(digits = 7L) + > base::cat("Time elapsed: ", proc.time() - base::get("ptime", pos = 'CheckExEnv'),"\n") +-Time elapsed: 1.83 0.038 1.874 0 0 ++Time elapsed: 1.864 0.034 1.905 0 0 + > grDevices::dev.off() + null device + 1 +diff -ruN R-3.0.1/tests/Examples/grDevices-Ex.Rout.save R-patched/tests/Examples/grDevices-Ex.Rout.save +--- tests/Examples/grDevices-Ex.Rout.save 2013-03-30 19:05:05.000000000 -0400 ++++ tests/Examples/grDevices-Ex.Rout.save 2013-05-24 18:05:05.000000000 -0400 +@@ -1,5 +1,5 @@ + +-R version 3.0.0 RC (2013-03-29 r62438) -- "Masked Marvel" ++R version 3.0.1 Patched (2013-05-24 r62792) -- "Good Sport" + Copyright (C) 2013 The R Foundation for Statistical Computing + Platform: x86_64-unknown-linux-gnu (64-bit) + +@@ -115,8 +115,8 @@ + + main = "example(Japanese)", xlab = "using Hershey fonts") + > par(cex = 3) + > Vf <- c("serif", "plain") +-> text(4, 2, "\\#J2438\\#J2421\\#J2451\\#J2473", vfont = Vf) +-> text(4, 4, "\\#J2538\\#J2521\\#J2551\\#J2573", vfont = Vf) ++> text(4, 2, "\\#J244b\\#J245b\\#J2473", vfont = Vf) ++> text(4, 4, "\\#J2538\\#J2563\\#J2551\\#J2573", vfont = Vf) + > text(4, 6, "\\#J467c\\#J4b5c", vfont = Vf) + > text(4, 8, "Japan", vfont = Vf) + > par(cex = 1) +@@ -3705,8 +3705,9 @@ + > + > ### * <FOOTER> + > ### ++> options(digits = 7L) + > base::cat("Time elapsed: ", proc.time() - base::get("ptime", pos = 'CheckExEnv'),"\n") +-Time elapsed: 8.757 0.186 8.972 0 0 ++Time elapsed: 8.732 0.198 8.968 0 0 + > grDevices::dev.off() + null device + 1 +diff -ruN R-3.0.1/tests/Examples/graphics-Ex.Rout.save R-patched/tests/Examples/graphics-Ex.Rout.save +--- tests/Examples/graphics-Ex.Rout.save 2013-05-02 18:05:04.000000000 -0400 ++++ tests/Examples/graphics-Ex.Rout.save 2013-05-24 18:05:05.000000000 -0400 +@@ -1,5 +1,5 @@ + +-R version 3.0.0 Patched (2013-05-01 r62701) -- "Masked Marvel" ++R version 3.0.1 Patched (2013-05-24 r62792) -- "Good Sport" + Copyright (C) 2013 The R Foundation for Statistical Computing + Platform: x86_64-unknown-linux-gnu (64-bit) + +@@ -1622,10 +1622,12 @@ + + plot(0:1, 0:1, type = "n", axes = FALSE, ann = FALSE) + + y <- (n:1)/(n+1) + + clty <- as.character(ltys) +-+ mytext <- function(x,y, txt) text(x, y, txt, adj = c(0, -.3), cex = 0.8, ...) +++ mytext <- function(x, y, txt) +++ text(x, y, txt, adj = c(0, -.3), cex = 0.8, ...) + + abline(h = y, lty = ltys, ...); mytext(xoff, y, clty) + + y <- y - 1/(3*(n+1)) +-+ abline(h = y, lty = ltys, lwd = 2, ...); mytext(1/8+xoff, y, paste(clty," lwd = 2")) +++ abline(h = y, lty = ltys, lwd = 2, ...) +++ mytext(1/8+xoff, y, paste(clty," lwd = 2")) + + } + > showLty(c("solid", "dashed", "dotted", "dotdash", "longdash", "twodash")) + > par(new = TRUE) # the same: +@@ -2025,7 +2027,7 @@ + > points.default # to see how it calls "plot.xy(xy.coords(x, y), ...)" + function (x, y = NULL, type = "p", ...) + plot.xy(xy.coords(x, y), type = type, ...) +-<bytecode: 0x3f8a6b8> ++<bytecode: 0x3b03758> + <environment: namespace:graphics> + > + > +@@ -2925,7 +2927,7 @@ + u <- par("usr") + xy * c(u[2L] - u[1L], u[4L] - u[3L])/par("pin") + } +-<bytecode: 0x4773828> ++<bytecode: 0x4755578> + <environment: namespace:graphics> + > + > ## plot labels offset 0.12 inches to the right +@@ -3005,7 +3007,7 @@ + > ### + > options(digits = 7L) + > base::cat("Time elapsed: ", proc.time() - base::get("ptime", pos = 'CheckExEnv'),"\n") +-Time elapsed: 7.676 0.165 7.975 0 0 ++Time elapsed: 3.625 0.055 3.69 0 0 + > grDevices::dev.off() + null device + 1 +diff -ruN R-3.0.1/tests/Examples/grid-Ex.Rout.save R-patched/tests/Examples/grid-Ex.Rout.save +--- tests/Examples/grid-Ex.Rout.save 2013-03-30 19:05:05.000000000 -0400 ++++ tests/Examples/grid-Ex.Rout.save 2013-05-24 18:05:05.000000000 -0400 +@@ -1,5 +1,5 @@ + +-R version 3.0.0 RC (2013-03-29 r62438) -- "Masked Marvel" ++R version 3.0.1 Patched (2013-05-24 r62792) -- "Good Sport" + Copyright (C) 2013 The R Foundation for Statistical Computing + Platform: x86_64-unknown-linux-gnu (64-bit) + +@@ -1960,8 +1960,9 @@ + > + > ### * <FOOTER> + > ### ++> options(digits = 7L) + > base::cat("Time elapsed: ", proc.time() - base::get("ptime", pos = 'CheckExEnv'),"\n") +-Time elapsed: 1.44 0.026 1.472 0 0 ++Time elapsed: 1.393 0.019 1.417 0 0 + > grDevices::dev.off() + null device + 1 +diff -ruN R-3.0.1/tests/Examples/splines-Ex.Rout.save R-patched/tests/Examples/splines-Ex.Rout.save +--- tests/Examples/splines-Ex.Rout.save 2013-03-30 19:05:05.000000000 -0400 ++++ tests/Examples/splines-Ex.Rout.save 2013-05-24 18:05:05.000000000 -0400 +@@ -1,5 +1,5 @@ + +-R version 3.0.0 RC (2013-03-29 r62438) -- "Masked Marvel" ++R version 3.0.1 Patched (2013-05-24 r62792) -- "Good Sport" + Copyright (C) 2013 The R Foundation for Statistical Computing + Platform: x86_64-unknown-linux-gnu (64-bit) + +@@ -612,8 +612,9 @@ + > + > ### * <FOOTER> + > ### ++> options(digits = 7L) + > base::cat("Time elapsed: ", proc.time() - base::get("ptime", pos = 'CheckExEnv'),"\n") +-Time elapsed: 1.443 0.013 1.462 0 0 ++Time elapsed: 1.422 0.023 1.451 0 0 + > grDevices::dev.off() + null device + 1 +diff -ruN R-3.0.1/tests/Examples/stats-Ex.Rout.save R-patched/tests/Examples/stats-Ex.Rout.save +--- tests/Examples/stats-Ex.Rout.save 2013-04-04 18:05:03.000000000 -0400 ++++ tests/Examples/stats-Ex.Rout.save 2013-05-24 18:05:05.000000000 -0400 +@@ -1,5 +1,5 @@ + +-R version 3.0.0 Patched (2013-04-04 r62492) -- "Masked Marvel" ++R version 3.0.1 Patched (2013-05-24 r62792) -- "Good Sport" + Copyright (C) 2013 The R Foundation for Statistical Computing + Platform: x86_64-unknown-linux-gnu (64-bit) + +@@ -3713,7 +3713,7 @@ + > + > asOneSidedFormula("age") + ~age +-<environment: 0x45ca580> ++<environment: 0x3b883b8> + > asOneSidedFormula(~ age) + ~age + > +@@ -4714,7 +4714,7 @@ + r[cbind(1L:p, 1L:p)] <- 1 + r + } +-<bytecode: 0x7542ac8> ++<bytecode: 0x7166e98> + <environment: namespace:stats> + > stopifnot(all.equal(Cl, cov2cor(cov(longley))), + + all.equal(cor(longley, method = "kendall"), +@@ -6731,8 +6731,8 @@ + > gf$linkinv + function (eta) + 1/eta +-<bytecode: 0x49b50a8> +-<environment: 0x9e6a100> ++<bytecode: 0x3b63990> ++<environment: 0x89f5328> + > gf$variance(-3:4) #- == (.)^2 + [1] 9 4 1 0 1 4 9 16 + > +@@ -7133,7 +7133,7 @@ + > environment(as.formula("y ~ x")) + <environment: R_GlobalEnv> + > environment(as.formula("y ~ x", env = new.env())) +-<environment: 0xa03f7b0> ++<environment: 0x8ad7090> + > + > + > ## Create a formula for a model with a large number of variables: +@@ -11709,26 +11709,26 @@ + $linkfun + function (mu) + mu +-<bytecode: 0x49b2298> +-<environment: 0x97631a8> ++<bytecode: 0x3b61340> ++<environment: 0xa483b80> + + $linkinv + function (eta) + eta +-<bytecode: 0x49b2228> +-<environment: 0x97631a8> ++<bytecode: 0x3b612d0> ++<environment: 0xa483b80> + + $mu.eta + function (eta) + rep.int(1, length(eta)) +-<bytecode: 0x49b21b8> +-<environment: 0x97631a8> ++<bytecode: 0x3b61260> ++<environment: 0xa483b80> + + $valideta + function (eta) + TRUE +-<bytecode: 0x49b1ff8> +-<environment: 0x97631a8> ++<bytecode: 0x3b610a0> ++<environment: 0xa483b80> + + $name + [1] "identity" +@@ -11739,14 +11739,14 @@ + $linkfun + function (mu) + mu^lambda +-<bytecode: 0x9b36060> +-<environment: 0x9cff078> ++<bytecode: 0xa485138> ++<environment: 0xa431038> + + $linkinv + function (eta) + pmax(eta^(1/lambda), .Machine$double.eps) +-<bytecode: 0x9ae7638> +-<environment: 0x9cff078> ++<bytecode: 0xa485288> ++<environment: 0xa431038> + + > + > +@@ -15540,8 +15540,8 @@ + > unclass(sfun0) + function (v) + .approxfun(x, y, v, method, yleft, yright, f) +-<bytecode: 0x4486820> +-<environment: 0x9b6c3f0> ++<bytecode: 0x3d223d0> ++<environment: 0x9ecb258> + attr(,"call") + stepfun(1:3, y0, f = 0) + > ls(envir = environment(sfun0)) +@@ -17793,7 +17793,7 @@ + > ### + > options(digits = 7L) + > base::cat("Time elapsed: ", proc.time() - base::get("ptime", pos = 'CheckExEnv'),"\n") +-Time elapsed: 14.992 0.275 15.886 0 0 ++Time elapsed: 7.265 0.173 7.469 0 0 + > grDevices::dev.off() + null device + 1 +diff -ruN R-3.0.1/tests/Examples/stats4-Ex.Rout.save R-patched/tests/Examples/stats4-Ex.Rout.save +--- tests/Examples/stats4-Ex.Rout.save 2013-03-30 19:05:05.000000000 -0400 ++++ tests/Examples/stats4-Ex.Rout.save 2013-05-24 18:05:05.000000000 -0400 +@@ -1,5 +1,5 @@ + +-R version 3.0.0 RC (2013-03-29 r62438) -- "Masked Marvel" ++R version 3.0.1 Patched (2013-05-24 r62792) -- "Good Sport" + Copyright (C) 2013 The R Foundation for Statistical Computing + Platform: x86_64-unknown-linux-gnu (64-bit) + +@@ -182,8 +182,9 @@ + > + > ### * <FOOTER> + > ### ++> options(digits = 7L) + > base::cat("Time elapsed: ", proc.time() - base::get("ptime", pos = 'CheckExEnv'),"\n") +-Time elapsed: 0.465 0.004 0.471 0 0 ++Time elapsed: 0.424 0.005 0.431 0 0 + > grDevices::dev.off() + null device + 1 +diff -ruN R-3.0.1/tests/Examples/tools-Ex.Rout.save R-patched/tests/Examples/tools-Ex.Rout.save +--- tests/Examples/tools-Ex.Rout.save 2013-03-30 19:05:05.000000000 -0400 ++++ tests/Examples/tools-Ex.Rout.save 2013-05-24 18:05:05.000000000 -0400 +@@ -1,5 +1,5 @@ + +-R version 3.0.0 RC (2013-03-29 r62438) -- "Masked Marvel" ++R version 3.0.1 Patched (2013-05-24 r62792) -- "Good Sport" + Copyright (C) 2013 The R Foundation for Statistical Computing + Platform: x86_64-unknown-linux-gnu (64-bit) + +@@ -100,7 +100,7 @@ + $enumFormat + function (n) + sprintf("%d. ", n) +-<environment: 0x382b150> ++<environment: 0x2d47fe0> + + $showURLs + [1] FALSE +@@ -134,7 +134,7 @@ + $enumFormat + function (n) + sprintf("%d. ", n) +-<environment: 0x382b150> ++<environment: 0x2d47fe0> + + $showURLs + [1] FALSE +@@ -168,7 +168,7 @@ + $enumFormat + function (n) + sprintf("%d. ", n) +-<environment: 0x382b150> ++<environment: 0x2d47fe0> + + $showURLs + [1] FALSE +@@ -232,7 +232,7 @@ + > bibstyle("unsorted", sortKeys = function(refs) seq_along(refs), + + fmtPrefix = function(paper) paste0("[", paper$.index, "]"), + + .init = TRUE) +-<environment: 0x3750a78> ++<environment: 0x2d29810> + > print(refs, .bibstyle = "unsorted") + [1] R Core Team (2013). _R: A Language and Environment for Statistical + Computing_. R Foundation for Statistical Computing, Vienna, Austria. +@@ -906,7 +906,7 @@ + > flush(stderr()); flush(stdout()) + > + > ### Name: vignetteEngine +-> ### Title: Set or get a vignette processing engine. ++> ### Title: Set or Get a Vignette Processing Engine + > ### Aliases: vignetteEngine + > ### Keywords: utilities documentation + > +@@ -962,8 +962,9 @@ + > + > ### * <FOOTER> + > ### ++> options(digits = 7L) + > base::cat("Time elapsed: ", proc.time() - base::get("ptime", pos = 'CheckExEnv'),"\n") +-Time elapsed: 0.311 0.014 0.326 0 0 ++Time elapsed: 0.342 0.007 0.35 0 0 + > grDevices::dev.off() + null device + 1 +diff -ruN R-3.0.1/tests/any-all.Rout.save R-patched/tests/any-all.Rout.save +--- tests/any-all.Rout.save 2013-03-30 19:05:05.000000000 -0400 ++++ tests/any-all.Rout.save 2013-05-24 18:05:05.000000000 -0400 +@@ -1,5 +1,5 @@ + +-R version 3.0.0 RC (2013-03-29 r62438) -- "Masked Marvel" ++R version 3.0.1 Patched (2013-05-24 r62792) -- "Good Sport" + Copyright (C) 2013 The R Foundation for Statistical Computing + Platform: x86_64-unknown-linux-gnu (64-bit) + +diff -ruN R-3.0.1/tests/arith-true.Rout.save R-patched/tests/arith-true.Rout.save +--- tests/arith-true.Rout.save 2013-03-30 19:05:05.000000000 -0400 ++++ tests/arith-true.Rout.save 2013-05-24 18:05:05.000000000 -0400 +@@ -1,5 +1,5 @@ + +-R version 3.0.0 RC (2013-03-29 r62438) -- "Masked Marvel" ++R version 3.0.1 Patched (2013-05-24 r62792) -- "Good Sport" + Copyright (C) 2013 The R Foundation for Statistical Computing + Platform: x86_64-unknown-linux-gnu (64-bit) + +@@ -323,5 +323,5 @@ + > + > ## Last Line: + > cat('Time elapsed: ', proc.time() - .proctime00,'\n') +-Time elapsed: 0.241 0.002 0.243 0 0 ++Time elapsed: 0.24 0.004 0.245 0 0 + > +diff -ruN R-3.0.1/tests/arith.Rout.save R-patched/tests/arith.Rout.save +--- tests/arith.Rout.save 2013-03-30 19:05:05.000000000 -0400 ++++ tests/arith.Rout.save 2013-05-24 18:05:05.000000000 -0400 +@@ -1,5 +1,5 @@ + +-R version 3.0.0 RC (2013-03-29 r62438) -- "Masked Marvel" ++R version 3.0.1 Patched (2013-05-24 r62792) -- "Good Sport" + Copyright (C) 2013 The R Foundation for Statistical Computing + Platform: x86_64-unknown-linux-gnu (64-bit) + +diff -ruN R-3.0.1/tests/array-subset.Rout.save R-patched/tests/array-subset.Rout.save +--- tests/array-subset.Rout.save 2013-03-30 19:05:05.000000000 -0400 ++++ tests/array-subset.Rout.save 2013-05-24 18:05:05.000000000 -0400 +@@ -1,5 +1,5 @@ + +-R version 3.0.0 RC (2013-03-29 r62438) -- "Masked Marvel" ++R version 3.0.1 Patched (2013-05-24 r62792) -- "Good Sport" + Copyright (C) 2013 The R Foundation for Statistical Computing + Platform: x86_64-unknown-linux-gnu (64-bit) + +diff -ruN R-3.0.1/tests/complex.Rout.save R-patched/tests/complex.Rout.save +--- tests/complex.Rout.save 2013-03-30 19:05:05.000000000 -0400 ++++ tests/complex.Rout.save 2013-05-24 18:05:05.000000000 -0400 +@@ -1,5 +1,5 @@ + +-R version 3.0.0 RC (2013-03-29 r62438) -- "Masked Marvel" ++R version 3.0.1 Patched (2013-05-24 r62792) -- "Good Sport" + Copyright (C) 2013 The R Foundation for Statistical Computing + Platform: x86_64-unknown-linux-gnu (64-bit) + +diff -ruN R-3.0.1/tests/d-p-q-r-tests.Rout.save R-patched/tests/d-p-q-r-tests.Rout.save +--- tests/d-p-q-r-tests.Rout.save 2013-03-30 19:05:05.000000000 -0400 ++++ tests/d-p-q-r-tests.Rout.save 2013-05-24 18:05:05.000000000 -0400 +@@ -1,5 +1,5 @@ + +-R version 3.0.0 RC (2013-03-29 r62438) -- "Masked Marvel" ++R version 3.0.1 Patched (2013-05-24 r62792) -- "Good Sport" + Copyright (C) 2013 The R Foundation for Statistical Computing + Platform: x86_64-unknown-linux-gnu (64-bit) + +@@ -1315,5 +1315,5 @@ + > + > + > cat("Time elapsed: ", proc.time() - .ptime,"\n") +-Time elapsed: 0.83 0.002 0.835 0 0 ++Time elapsed: 0.847 0.008 0.857 0 0 + > +diff -ruN R-3.0.1/tests/datasets.Rout.save R-patched/tests/datasets.Rout.save +--- tests/datasets.Rout.save 2013-03-30 19:05:05.000000000 -0400 ++++ tests/datasets.Rout.save 2013-05-24 18:05:05.000000000 -0400 +@@ -1,5 +1,5 @@ + +-R version 3.0.0 RC (2013-03-29 r62438) -- "Masked Marvel" ++R version 3.0.1 Patched (2013-05-24 r62792) -- "Good Sport" + Copyright (C) 2013 The R Foundation for Statistical Computing + Platform: x86_64-unknown-linux-gnu (64-bit) + +diff -ruN R-3.0.1/tests/demos.Rout.save R-patched/tests/demos.Rout.save +--- tests/demos.Rout.save 2013-04-26 18:05:04.000000000 -0400 ++++ tests/demos.Rout.save 2013-05-24 18:05:05.000000000 -0400 +@@ -115,8 +115,8 @@ + + "\n\t starting with 'is.' :\t ", + + sum(grepl("^is\\.", ls.base[base.is.f])), "\n", sep = "") + +-Number of base objects: 1265 +-Number of functions in base: 1223 ++Number of base objects: 1264 ++Number of functions in base: 1222 + starting with 'is.' : 49 + + > ## 0.14 : 31 +diff -ruN R-3.0.1/tests/eval-etc.Rout.save R-patched/tests/eval-etc.Rout.save +--- tests/eval-etc.Rout.save 2013-03-30 19:05:05.000000000 -0400 ++++ tests/eval-etc.Rout.save 2013-05-24 18:05:05.000000000 -0400 +@@ -1,5 +1,5 @@ + +-R version 3.0.0 RC (2013-03-29 r62438) -- "Masked Marvel" ++R version 3.0.1 Patched (2013-05-24 r62792) -- "Good Sport" + Copyright (C) 2013 The R Foundation for Statistical Computing + Platform: x86_64-unknown-linux-gnu (64-bit) + +diff -ruN R-3.0.1/tests/iec60559.Rout.save R-patched/tests/iec60559.Rout.save +--- tests/iec60559.Rout.save 2013-03-30 19:05:05.000000000 -0400 ++++ tests/iec60559.Rout.save 2013-05-24 18:05:05.000000000 -0400 +@@ -1,5 +1,5 @@ + +-R version 3.0.0 RC (2013-03-29 r62438) -- "Masked Marvel" ++R version 3.0.1 Patched (2013-05-24 r62792) -- "Good Sport" + Copyright (C) 2013 The R Foundation for Statistical Computing + Platform: x86_64-unknown-linux-gnu (64-bit) + +diff -ruN R-3.0.1/tests/internet.Rout.save R-patched/tests/internet.Rout.save +--- tests/internet.Rout.save 2013-04-03 03:00:03.000000000 -0400 ++++ tests/internet.Rout.save 2013-05-24 18:05:05.000000000 -0400 +@@ -1,5 +1,5 @@ + +-R version 3.0.0 RC (2013-04-02 r62479) -- "Masked Marvel" ++R version 3.0.1 Patched (2013-05-24 r62792) -- "Good Sport" + Copyright (C) 2013 The R Foundation for Statistical Computing + Platform: x86_64-unknown-linux-gnu (64-bit) + +@@ -29,7 +29,7 @@ + > + > # test do_download. + > nrow(available.packages(contrib.url("http://cran.r-project.org"))) +-[1] 4407 ++[1] 4538 + > + > # test url connections on http + > zz <- url("http://cran.r-project.org/") +diff -ruN R-3.0.1/tests/lapack.Rout.save R-patched/tests/lapack.Rout.save +--- tests/lapack.Rout.save 2013-03-30 19:05:05.000000000 -0400 ++++ tests/lapack.Rout.save 2013-05-24 18:05:05.000000000 -0400 +@@ -1,5 +1,5 @@ + +-R version 3.0.0 RC (2013-03-29 r62438) -- "Masked Marvel" ++R version 3.0.1 Patched (2013-05-24 r62792) -- "Good Sport" + Copyright (C) 2013 The R Foundation for Statistical Computing + Platform: x86_64-unknown-linux-gnu (64-bit) + +diff -ruN R-3.0.1/tests/lm-tests.Rout.save R-patched/tests/lm-tests.Rout.save +--- tests/lm-tests.Rout.save 2013-03-30 19:05:05.000000000 -0400 ++++ tests/lm-tests.Rout.save 2013-05-24 18:05:05.000000000 -0400 +@@ -1,5 +1,5 @@ + +-R version 3.0.0 RC (2013-03-29 r62438) -- "Masked Marvel" ++R version 3.0.1 Patched (2013-05-24 r62792) -- "Good Sport" + Copyright (C) 2013 The R Foundation for Statistical Computing + Platform: x86_64-unknown-linux-gnu (64-bit) + +diff -ruN R-3.0.1/tests/method-dispatch.Rout.save R-patched/tests/method-dispatch.Rout.save +--- tests/method-dispatch.Rout.save 2013-03-30 19:05:05.000000000 -0400 ++++ tests/method-dispatch.Rout.save 2013-05-24 18:05:05.000000000 -0400 +@@ -1,5 +1,5 @@ + +-R version 3.0.0 RC (2013-03-29 r62438) -- "Masked Marvel" ++R version 3.0.1 Patched (2013-05-24 r62792) -- "Good Sport" + Copyright (C) 2013 The R Foundation for Statistical Computing + Platform: x86_64-unknown-linux-gnu (64-bit) + +diff -ruN R-3.0.1/tests/ok-errors.Rout.save R-patched/tests/ok-errors.Rout.save +--- tests/ok-errors.Rout.save 2013-03-30 19:05:05.000000000 -0400 ++++ tests/ok-errors.Rout.save 2013-05-24 18:05:05.000000000 -0400 +@@ -1,5 +1,5 @@ + +-R version 3.0.0 RC (2013-03-29 r62438) -- "Masked Marvel" ++R version 3.0.1 Patched (2013-05-24 r62792) -- "Good Sport" + Copyright (C) 2013 The R Foundation for Statistical Computing + Platform: x86_64-unknown-linux-gnu (64-bit) + +diff -ruN R-3.0.1/tests/print-tests.Rout.save R-patched/tests/print-tests.Rout.save +--- tests/print-tests.Rout.save 2013-03-30 19:05:05.000000000 -0400 ++++ tests/print-tests.Rout.save 2013-05-24 18:05:05.000000000 -0400 +@@ -1,5 +1,5 @@ + +-R version 3.0.0 RC (2013-03-29 r62438) -- "Masked Marvel" ++R version 3.0.1 Patched (2013-05-24 r62792) -- "Good Sport" + Copyright (C) 2013 The R Foundation for Statistical Computing + Platform: x86_64-unknown-linux-gnu (64-bit) + +diff -ruN R-3.0.1/tests/reg-IO.Rout.save R-patched/tests/reg-IO.Rout.save +--- tests/reg-IO.Rout.save 2013-03-30 19:05:05.000000000 -0400 ++++ tests/reg-IO.Rout.save 2013-05-24 18:05:05.000000000 -0400 +@@ -1,5 +1,5 @@ + +-R version 3.0.0 RC (2013-03-29 r62438) -- "Masked Marvel" ++R version 3.0.1 Patched (2013-05-24 r62792) -- "Good Sport" + Copyright (C) 2013 The R Foundation for Statistical Computing + Platform: x86_64-unknown-linux-gnu (64-bit) + +diff -ruN R-3.0.1/tests/reg-IO2.Rout.save R-patched/tests/reg-IO2.Rout.save +--- tests/reg-IO2.Rout.save 2013-03-30 19:05:05.000000000 -0400 ++++ tests/reg-IO2.Rout.save 2013-05-24 18:05:05.000000000 -0400 +@@ -1,5 +1,5 @@ + +-R version 3.0.0 RC (2013-03-29 r62438) -- "Masked Marvel" ++R version 3.0.1 Patched (2013-05-24 r62792) -- "Good Sport" + Copyright (C) 2013 The R Foundation for Statistical Computing + Platform: x86_64-unknown-linux-gnu (64-bit) + +diff -ruN R-3.0.1/tests/reg-S4.Rout.save R-patched/tests/reg-S4.Rout.save +--- tests/reg-S4.Rout.save 2013-03-30 19:05:05.000000000 -0400 ++++ tests/reg-S4.Rout.save 2013-05-24 18:05:05.000000000 -0400 +@@ -1,5 +1,5 @@ + +-R version 3.0.0 RC (2013-03-29 r62438) -- "Masked Marvel" ++R version 3.0.1 Patched (2013-05-24 r62792) -- "Good Sport" + Copyright (C) 2013 The R Foundation for Statistical Computing + Platform: x86_64-unknown-linux-gnu (64-bit) + +diff -ruN R-3.0.1/tests/reg-plot.Rout.save R-patched/tests/reg-plot.Rout.save +--- tests/reg-plot.Rout.save 2013-03-30 19:05:05.000000000 -0400 ++++ tests/reg-plot.Rout.save 2013-05-24 18:05:05.000000000 -0400 +@@ -1,5 +1,5 @@ + +-R version 3.0.0 RC (2013-03-29 r62438) -- "Masked Marvel" ++R version 3.0.1 Patched (2013-05-24 r62792) -- "Good Sport" + Copyright (C) 2013 The R Foundation for Statistical Computing + Platform: x86_64-unknown-linux-gnu (64-bit) + +diff -ruN R-3.0.1/tests/reg-tests-2.R R-patched/tests/reg-tests-2.R +--- tests/reg-tests-2.R 2013-04-30 18:05:03.000000000 -0400 ++++ tests/reg-tests-2.R 2013-05-16 18:05:05.000000000 -0400 +@@ -2695,4 +2695,11 @@ + + ## PR#15299 : adding a simple vector to a classed object produced a bad result: + 1:2 + table(1:2) +-## Printed the class attribute in R <= 3.0.0 +\ No newline at end of file ++## Printed the class attribute in R <= 3.0.0 ++ ++## PR#15311 : regmatches<- mishandled regexpr results. ++ x <- c('1', 'B', '3') ++ m <- regexpr('\\d', x) ++ regmatches(x, m) <- c('A', 'C') ++ print(x) ++## Gave a warning and a wrong result up to 3.0.1 +\ No newline at end of file +diff -ruN R-3.0.1/tests/reg-tests-2.Rout.save R-patched/tests/reg-tests-2.Rout.save +--- tests/reg-tests-2.Rout.save 2013-04-30 18:05:03.000000000 -0400 ++++ tests/reg-tests-2.Rout.save 2013-05-24 18:05:05.000000000 -0400 +@@ -1,5 +1,5 @@ + +-R version 3.0.0 Patched (2013-04-04 r62492) -- "Masked Marvel" ++R version 3.0.1 Patched (2013-05-24 r62792) -- "Good Sport" + Copyright (C) 2013 The R Foundation for Statistical Computing + Platform: x86_64-unknown-linux-gnu (64-bit) + +@@ -6397,15 +6397,15 @@ + > print.function + function (x, ...) + - attr(*, "srcref")=Class 'srcref' atomic [1:8] 1 19 1 63 19 63 1 1 +- .. ..- attr(*, "srcfile")=Classes 'srcfilecopy', 'srcfile' <environment: 0x3c66fe8> ++ .. ..- attr(*, "srcfile")=Classes 'srcfilecopy', 'srcfile' <environment: 0x4c9d128> + > f + function () + - attr(*, "srcref")=Class 'srcref' atomic [1:8] 1 17 1 28 17 28 1 1 +- .. ..- attr(*, "srcfile")=Classes 'srcfilecopy', 'srcfile' <environment: 0x3c46db0> ++ .. ..- attr(*, "srcfile")=Classes 'srcfilecopy', 'srcfile' <environment: 0x4c72208> + - attr(*, "note")= chr "just a note" + - attr(*, "yada")=function () + ..- attr(*, "srcref")=Class 'srcref' atomic [1:8] 2 24 2 48 24 48 2 2 +- .. .. ..- attr(*, "srcfile")=Classes 'srcfilecopy', 'srcfile' <environment: 0x3c46db0> ++ .. .. ..- attr(*, "srcfile")=Classes 'srcfilecopy', 'srcfile' <environment: 0x4c72208> + > rm(print.function) + > ## auto-printing and printing differed up to R 2.9.x + > +@@ -7067,3 +7067,11 @@ + 2 3 + > ## Printed the class attribute in R <= 3.0.0 + > ++> ## PR#15311 : regmatches<- mishandled regexpr results. ++> x <- c('1', 'B', '3') ++> m <- regexpr('\\d', x) ++> regmatches(x, m) <- c('A', 'C') ++> print(x) ++[1] "A" "B" "C" ++> ## Gave a warning and a wrong result up to 3.0.1 ++> +diff -ruN R-3.0.1/tests/reg-tests-3.Rout.save R-patched/tests/reg-tests-3.Rout.save +--- tests/reg-tests-3.Rout.save 2013-03-30 19:05:05.000000000 -0400 ++++ tests/reg-tests-3.Rout.save 2013-05-24 18:05:05.000000000 -0400 +@@ -1,5 +1,5 @@ + +-R version 3.0.0 RC (2013-03-29 r62438) -- "Masked Marvel" ++R version 3.0.1 Patched (2013-05-24 r62792) -- "Good Sport" + Copyright (C) 2013 The R Foundation for Statistical Computing + Platform: x86_64-unknown-linux-gnu (64-bit) + +diff -ruN R-3.0.1/tests/simple-true.Rout.save R-patched/tests/simple-true.Rout.save +--- tests/simple-true.Rout.save 2013-03-30 19:05:05.000000000 -0400 ++++ tests/simple-true.Rout.save 2013-05-24 18:05:05.000000000 -0400 +@@ -1,5 +1,5 @@ + +-R version 3.0.0 RC (2013-03-29 r62438) -- "Masked Marvel" ++R version 3.0.1 Patched (2013-05-24 r62792) -- "Good Sport" + Copyright (C) 2013 The R Foundation for Statistical Computing + Platform: x86_64-unknown-linux-gnu (64-bit) + diff --git a/math/R/files/patch-doc__manual__refman.top b/math/R/files/patch-doc__manual__refman.top deleted file mode 100644 index 9d239cbd25f1..000000000000 --- a/math/R/files/patch-doc__manual__refman.top +++ /dev/null @@ -1,33 +0,0 @@ ---- doc/manual/refman.top.orig 2011-11-23 12:21:46.000000000 -0500 -+++ doc/manual/refman.top 2011-11-23 12:22:31.000000000 -0500 -@@ -4,18 +4,18 @@ - - %% Set PDF 1.5 and compression, including object compression - %% Needed for MiKTeX -- most other distributions default to this --\ifx\pdfoutput\undefined --\else -- \ifx\pdfoutput\relax -- \else -- \ifnum\pdfoutput>0 -- % PDF output -- \pdfminorversion=5 -- \pdfcompresslevel=9 -- \pdfobjcompresslevel=2 -- \fi -- \fi --\fi -+%%\ifx\pdfoutput\undefined -+%%\else -+%% \ifx\pdfoutput\relax -+%% \else -+%% \ifnum\pdfoutput>0 -+%% % PDF output -+%% \pdfminorversion=5 -+%% \pdfcompresslevel=9 -+%% \pdfobjcompresslevel=2 -+%% \fi -+%% \fi -+%%\fi - - \makeatletter - \renewcommand\@pnumwidth{2.05em} % over 1000 pages diff --git a/math/R/pkg-plist b/math/R/pkg-plist index dd58f67ee34a..b64d35b49c92 100644 --- a/math/R/pkg-plist +++ b/math/R/pkg-plist @@ -56,6 +56,7 @@ lib/R/bin/pager lib/R/bin/rtags lib/R/etc/Makeconf lib/R/etc/Renviron +lib/R/etc/javaconf lib/R/etc/ldpaths lib/R/etc/repositories lib/R/include/Rconfig.h @@ -67,6 +68,7 @@ lib/R/include/R_ext/BLAS.h lib/R/include/R_ext/Boolean.h lib/R/include/R_ext/Callbacks.h lib/R/include/R_ext/Complex.h +lib/R/include/R_ext/Connections.h lib/R/include/R_ext/Constants.h lib/R/include/R_ext/Error.h lib/R/include/R_ext/GetX11Image.h @@ -80,7 +82,6 @@ lib/R/include/R_ext/Parse.h lib/R/include/R_ext/Print.h lib/R/include/R_ext/PrtUtil.h lib/R/include/R_ext/QuartzDevice.h -lib/R/include/R_ext/RConverters.h lib/R/include/R_ext/RS.h lib/R/include/R_ext/RStartup.h lib/R/include/R_ext/Random.h @@ -91,7 +92,6 @@ lib/R/include/R_ext/Utils.h lib/R/include/R_ext/Visibility.h lib/R/include/R_ext/eventloop.h lib/R/include/R_ext/libextern.h -lib/R/include/R_ext/rlocale.h lib/R/include/R_ext/stats_package.h lib/R/include/R_ext/stats_stubs.h lib/R/include/R.h @@ -108,7 +108,6 @@ lib/R/include/S.h %%LIBR%%lib/R/lib/libR.so.%%R_SOVERSION%% lib/R/library/KernSmooth/DESCRIPTION lib/R/library/KernSmooth/INDEX -lib/R/library/KernSmooth/LICENCE lib/R/library/KernSmooth/Meta/Rd.rds lib/R/library/KernSmooth/Meta/hsearch.rds lib/R/library/KernSmooth/Meta/links.rds @@ -128,6 +127,7 @@ lib/R/library/KernSmooth/html/R.css lib/R/library/KernSmooth/libs/KernSmooth.so %%NLS%%lib/R/library/KernSmooth/po/de/LC_MESSAGES/R-KernSmooth.mo %%NLS%%lib/R/library/KernSmooth/po/en@quot/LC_MESSAGES/R-KernSmooth.mo +%%NLS%%lib/R/library/KernSmooth/po/ko/LC_MESSAGES/R-KernSmooth.mo %%NLS%%lib/R/library/KernSmooth/po/pl/LC_MESSAGES/R-KernSmooth.mo lib/R/library/MASS/CITATION lib/R/library/MASS/DESCRIPTION @@ -158,6 +158,7 @@ lib/R/library/MASS/libs/MASS.so %%NLS%%lib/R/library/MASS/po/de/LC_MESSAGES/R-MASS.mo %%NLS%%lib/R/library/MASS/po/en@quot/LC_MESSAGES/R-MASS.mo %%NLS%%lib/R/library/MASS/po/fr/LC_MESSAGES/R-MASS.mo +%%NLS%%lib/R/library/MASS/po/ko/LC_MESSAGES/R-MASS.mo %%NLS%%lib/R/library/MASS/po/pl/LC_MESSAGES/R-MASS.mo lib/R/library/MASS/scripts/ch01.R lib/R/library/MASS/scripts/ch02.R @@ -268,19 +269,6 @@ lib/R/library/base/help/base.rdx lib/R/library/base/help/paths.rds lib/R/library/base/html/00Index.html lib/R/library/base/html/R.css -%%NLS%%lib/R/library/base/po/da/LC_MESSAGES/R-base.mo -%%NLS%%lib/R/library/base/po/de/LC_MESSAGES/R-base.mo -%%NLS%%lib/R/library/base/po/en@quot/LC_MESSAGES/R-base.mo -%%NLS%%lib/R/library/base/po/fr/LC_MESSAGES/R-base.mo -%%NLS%%lib/R/library/base/po/it/LC_MESSAGES/R-base.mo -%%NLS%%lib/R/library/base/po/ja/LC_MESSAGES/R-base.mo -%%NLS%%lib/R/library/base/po/ko/LC_MESSAGES/R-base.mo -%%NLS%%lib/R/library/base/po/nn/LC_MESSAGES/R-base.mo -%%NLS%%lib/R/library/base/po/pl/LC_MESSAGES/R-base.mo 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+%%NLS%%lib/R/library/class/po/ko/LC_MESSAGES/R-class.mo %%NLS%%lib/R/library/class/po/pl/LC_MESSAGES/R-class.mo lib/R/library/cluster/CITATION lib/R/library/cluster/DESCRIPTION @@ -398,16 +388,6 @@ lib/R/library/compiler/help/compiler.rdx lib/R/library/compiler/help/paths.rds lib/R/library/compiler/html/00Index.html lib/R/library/compiler/html/R.css -%%NLS%%lib/R/library/compiler/po/da/LC_MESSAGES/R-compiler.mo -%%NLS%%lib/R/library/compiler/po/de/LC_MESSAGES/R-compiler.mo -%%NLS%%lib/R/library/compiler/po/en@quot/LC_MESSAGES/R-compiler.mo -%%NLS%%lib/R/library/compiler/po/fr/LC_MESSAGES/R-compiler.mo -%%NLS%%lib/R/library/compiler/po/ja/LC_MESSAGES/R-compiler.mo -%%NLS%%lib/R/library/compiler/po/ko/LC_MESSAGES/R-compiler.mo -%%NLS%%lib/R/library/compiler/po/pl/LC_MESSAGES/R-compiler.mo -%%NLS%%lib/R/library/compiler/po/pt_BR/LC_MESSAGES/R-compiler.mo -%%NLS%%lib/R/library/compiler/po/ru/LC_MESSAGES/R-compiler.mo -%%NLS%%lib/R/library/compiler/po/zh_CN/LC_MESSAGES/R-compiler.mo lib/R/library/datasets/DESCRIPTION lib/R/library/datasets/INDEX lib/R/library/datasets/Meta/Rd.rds @@ -431,7 +411,6 @@ lib/R/library/datasets/html/R.css lib/R/library/foreign/COPYRIGHTS lib/R/library/foreign/DESCRIPTION lib/R/library/foreign/INDEX -lib/R/library/foreign/LICENCE lib/R/library/foreign/Meta/Rd.rds lib/R/library/foreign/Meta/hsearch.rds lib/R/library/foreign/Meta/links.rds @@ -463,6 +442,7 @@ lib/R/library/foreign/libs/foreign.so lib/R/library/grDevices/DESCRIPTION lib/R/library/grDevices/INDEX lib/R/library/grDevices/Meta/Rd.rds +lib/R/library/grDevices/Meta/demo.rds lib/R/library/grDevices/Meta/hsearch.rds lib/R/library/grDevices/Meta/links.rds lib/R/library/grDevices/Meta/nsInfo.rds @@ -560,6 +540,8 @@ lib/R/library/grDevices/afm/tib_____.afm.gz lib/R/library/grDevices/afm/tibi____.afm.gz lib/R/library/grDevices/afm/tii_____.afm.gz lib/R/library/grDevices/afm/tir_____.afm.gz +lib/R/library/grDevices/demo/colors.R +lib/R/library/grDevices/demo/hclColors.R lib/R/library/grDevices/enc/AdobeStd.enc lib/R/library/grDevices/enc/AdobeSym.enc lib/R/library/grDevices/enc/CP1250.enc @@ -589,30 +571,6 @@ lib/R/library/grDevices/icc/srgb lib/R/library/grDevices/icc/srgb.flate %%PANGOCAIRO%%lib/R/library/grDevices/libs/cairo.so lib/R/library/grDevices/libs/grDevices.so -%%NLS%%lib/R/library/grDevices/po/da/LC_MESSAGES/R-grDevices.mo -%%NLS%%lib/R/library/grDevices/po/da/LC_MESSAGES/grDevices.mo -%%NLS%%lib/R/library/grDevices/po/de/LC_MESSAGES/R-grDevices.mo -%%NLS%%lib/R/library/grDevices/po/de/LC_MESSAGES/grDevices.mo -%%NLS%%lib/R/library/grDevices/po/en_GB/LC_MESSAGES/R-grDevices.mo -%%NLS%%lib/R/library/grDevices/po/en_GB/LC_MESSAGES/grDevices.mo -%%NLS%%lib/R/library/grDevices/po/en@quot/LC_MESSAGES/R-grDevices.mo -%%NLS%%lib/R/library/grDevices/po/en@quot/LC_MESSAGES/grDevices.mo -%%NLS%%lib/R/library/grDevices/po/fr/LC_MESSAGES/R-grDevices.mo -%%NLS%%lib/R/library/grDevices/po/fr/LC_MESSAGES/grDevices.mo -%%NLS%%lib/R/library/grDevices/po/it/LC_MESSAGES/R-grDevices.mo -%%NLS%%lib/R/library/grDevices/po/it/LC_MESSAGES/grDevices.mo -%%NLS%%lib/R/library/grDevices/po/ja/LC_MESSAGES/R-grDevices.mo -%%NLS%%lib/R/library/grDevices/po/ja/LC_MESSAGES/grDevices.mo -%%NLS%%lib/R/library/grDevices/po/ko/LC_MESSAGES/R-grDevices.mo -%%NLS%%lib/R/library/grDevices/po/ko/LC_MESSAGES/grDevices.mo -%%NLS%%lib/R/library/grDevices/po/pl/LC_MESSAGES/R-grDevices.mo -%%NLS%%lib/R/library/grDevices/po/pl/LC_MESSAGES/grDevices.mo -%%NLS%%lib/R/library/grDevices/po/pt_BR/LC_MESSAGES/R-grDevices.mo -%%NLS%%lib/R/library/grDevices/po/pt_BR/LC_MESSAGES/grDevices.mo -%%NLS%%lib/R/library/grDevices/po/ru/LC_MESSAGES/R-grDevices.mo -%%NLS%%lib/R/library/grDevices/po/ru/LC_MESSAGES/grDevices.mo -%%NLS%%lib/R/library/grDevices/po/zh_CN/LC_MESSAGES/R-grDevices.mo -%%NLS%%lib/R/library/grDevices/po/zh_CN/LC_MESSAGES/grDevices.mo lib/R/library/graphics/DESCRIPTION lib/R/library/graphics/INDEX lib/R/library/graphics/Meta/Rd.rds @@ -645,17 +603,7 @@ lib/R/library/graphics/help/graphics.rdx lib/R/library/graphics/help/paths.rds lib/R/library/graphics/html/00Index.html lib/R/library/graphics/html/R.css -%%NLS%%lib/R/library/graphics/po/da/LC_MESSAGES/R-graphics.mo -%%NLS%%lib/R/library/graphics/po/de/LC_MESSAGES/R-graphics.mo -%%NLS%%lib/R/library/graphics/po/en@quot/LC_MESSAGES/R-graphics.mo -%%NLS%%lib/R/library/graphics/po/fr/LC_MESSAGES/R-graphics.mo -%%NLS%%lib/R/library/graphics/po/it/LC_MESSAGES/R-graphics.mo -%%NLS%%lib/R/library/graphics/po/ja/LC_MESSAGES/R-graphics.mo -%%NLS%%lib/R/library/graphics/po/ko/LC_MESSAGES/R-graphics.mo -%%NLS%%lib/R/library/graphics/po/pl/LC_MESSAGES/R-graphics.mo -%%NLS%%lib/R/library/graphics/po/pt_BR/LC_MESSAGES/R-graphics.mo -%%NLS%%lib/R/library/graphics/po/ru/LC_MESSAGES/R-graphics.mo -%%NLS%%lib/R/library/graphics/po/zh_CN/LC_MESSAGES/R-graphics.mo +lib/R/library/graphics/libs/graphics.so lib/R/library/grid/DESCRIPTION lib/R/library/grid/INDEX lib/R/library/grid/Meta/Rd.rds @@ -689,31 +637,9 @@ lib/R/library/grid/help/paths.rds lib/R/library/grid/html/00Index.html lib/R/library/grid/html/R.css lib/R/library/grid/libs/grid.so -%%NLS%%lib/R/library/grid/po/da/LC_MESSAGES/R-grid.mo -%%NLS%%lib/R/library/grid/po/da/LC_MESSAGES/grid.mo -%%NLS%%lib/R/library/grid/po/de/LC_MESSAGES/R-grid.mo -%%NLS%%lib/R/library/grid/po/de/LC_MESSAGES/grid.mo -%%NLS%%lib/R/library/grid/po/en@quot/LC_MESSAGES/R-grid.mo -%%NLS%%lib/R/library/grid/po/en@quot/LC_MESSAGES/grid.mo -%%NLS%%lib/R/library/grid/po/fr/LC_MESSAGES/R-grid.mo -%%NLS%%lib/R/library/grid/po/fr/LC_MESSAGES/grid.mo -%%NLS%%lib/R/library/grid/po/it/LC_MESSAGES/grid.mo -%%NLS%%lib/R/library/grid/po/ja/LC_MESSAGES/R-grid.mo -%%NLS%%lib/R/library/grid/po/ja/LC_MESSAGES/grid.mo -%%NLS%%lib/R/library/grid/po/ko/LC_MESSAGES/R-grid.mo -%%NLS%%lib/R/library/grid/po/ko/LC_MESSAGES/grid.mo -%%NLS%%lib/R/library/grid/po/pl/LC_MESSAGES/R-grid.mo 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-%%NLS%%lib/R/library/methods/po/zh_CN/LC_MESSAGES/methods.mo lib/R/library/mgcv/CITATION lib/R/library/mgcv/DESCRIPTION lib/R/library/mgcv/INDEX @@ -875,6 +781,7 @@ lib/R/library/nnet/libs/nnet.so %%NLS%%lib/R/library/nnet/po/de/LC_MESSAGES/R-nnet.mo %%NLS%%lib/R/library/nnet/po/en@quot/LC_MESSAGES/R-nnet.mo %%NLS%%lib/R/library/nnet/po/fr/LC_MESSAGES/R-nnet.mo +%%NLS%%lib/R/library/nnet/po/ko/LC_MESSAGES/R-nnet.mo %%NLS%%lib/R/library/nnet/po/pl/LC_MESSAGES/R-nnet.mo lib/R/library/parallel/DESCRIPTION lib/R/library/parallel/INDEX @@ -896,22 +803,6 @@ lib/R/library/parallel/help/paths.rds lib/R/library/parallel/html/00Index.html lib/R/library/parallel/html/R.css lib/R/library/parallel/libs/parallel.so -%%NLS%%lib/R/library/parallel/po/da/LC_MESSAGES/R-parallel.mo -%%NLS%%lib/R/library/parallel/po/da/LC_MESSAGES/parallel.mo -%%NLS%%lib/R/library/parallel/po/de/LC_MESSAGES/R-parallel.mo -%%NLS%%lib/R/library/parallel/po/de/LC_MESSAGES/parallel.mo 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%%NLS%%lib/R/library/rpart/po/fr/LC_MESSAGES/R-rpart.mo %%NLS%%lib/R/library/rpart/po/fr/LC_MESSAGES/rpart.mo +%%NLS%%lib/R/library/rpart/po/ko/LC_MESSAGES/R-rpart.mo +%%NLS%%lib/R/library/rpart/po/ko/LC_MESSAGES/rpart.mo %%NLS%%lib/R/library/rpart/po/pl/LC_MESSAGES/R-rpart.mo %%NLS%%lib/R/library/rpart/po/pl/LC_MESSAGES/rpart.mo %%NLS%%lib/R/library/rpart/po/ru/LC_MESSAGES/R-rpart.mo @@ -1024,26 +917,6 @@ lib/R/library/splines/help/splines.rdx lib/R/library/splines/html/00Index.html lib/R/library/splines/html/R.css lib/R/library/splines/libs/splines.so -%%NLS%%lib/R/library/splines/po/da/LC_MESSAGES/R-splines.mo -%%NLS%%lib/R/library/splines/po/da/LC_MESSAGES/splines.mo -%%NLS%%lib/R/library/splines/po/de/LC_MESSAGES/R-splines.mo -%%NLS%%lib/R/library/splines/po/de/LC_MESSAGES/splines.mo -%%NLS%%lib/R/library/splines/po/en@quot/LC_MESSAGES/R-splines.mo -%%NLS%%lib/R/library/splines/po/en@quot/LC_MESSAGES/splines.mo -%%NLS%%lib/R/library/splines/po/fr/LC_MESSAGES/R-splines.mo 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lib/R/library/stats4/html/00Index.html lib/R/library/stats4/html/R.css -%%NLS%%lib/R/library/stats4/po/da/LC_MESSAGES/R-stats4.mo -%%NLS%%lib/R/library/stats4/po/de/LC_MESSAGES/R-stats4.mo -%%NLS%%lib/R/library/stats4/po/en@quot/LC_MESSAGES/R-stats4.mo -%%NLS%%lib/R/library/stats4/po/fr/LC_MESSAGES/R-stats4.mo -%%NLS%%lib/R/library/stats4/po/it/LC_MESSAGES/R-stats4.mo -%%NLS%%lib/R/library/stats4/po/ja/LC_MESSAGES/R-stats4.mo -%%NLS%%lib/R/library/stats4/po/ko/LC_MESSAGES/R-stats4.mo -%%NLS%%lib/R/library/stats4/po/pl/LC_MESSAGES/R-stats4.mo -%%NLS%%lib/R/library/stats4/po/pt_BR/LC_MESSAGES/R-stats4.mo -%%NLS%%lib/R/library/stats4/po/ru/LC_MESSAGES/R-stats4.mo -%%NLS%%lib/R/library/stats4/po/tr/LC_MESSAGES/R-stats4.mo -%%NLS%%lib/R/library/stats4/po/zh_CN/LC_MESSAGES/R-stats4.mo lib/R/library/stats/COPYRIGHTS.modreg lib/R/library/stats/DESCRIPTION lib/R/library/stats/INDEX @@ -1100,29 +961,6 @@ lib/R/library/stats/help/stats.rdx lib/R/library/stats/html/00Index.html 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+%%NLS%%lib/R/library/translations/zh_CN/LC_MESSAGES/R-compiler.mo +%%NLS%%lib/R/library/translations/zh_CN/LC_MESSAGES/R-grDevices.mo +%%NLS%%lib/R/library/translations/zh_CN/LC_MESSAGES/R-graphics.mo +%%NLS%%lib/R/library/translations/zh_CN/LC_MESSAGES/R-grid.mo +%%NLS%%lib/R/library/translations/zh_CN/LC_MESSAGES/R-methods.mo +%%NLS%%lib/R/library/translations/zh_CN/LC_MESSAGES/R-parallel.mo +%%NLS%%lib/R/library/translations/zh_CN/LC_MESSAGES/R-splines.mo +%%NLS%%lib/R/library/translations/zh_CN/LC_MESSAGES/R-stats.mo +%%NLS%%lib/R/library/translations/zh_CN/LC_MESSAGES/R-stats4.mo +%%NLS%%lib/R/library/translations/zh_CN/LC_MESSAGES/R-tcltk.mo +%%NLS%%lib/R/library/translations/zh_CN/LC_MESSAGES/R-tools.mo +%%NLS%%lib/R/library/translations/zh_CN/LC_MESSAGES/R-utils.mo +%%NLS%%lib/R/library/translations/zh_CN/LC_MESSAGES/R.mo +%%NLS%%lib/R/library/translations/zh_CN/LC_MESSAGES/RGui.mo +%%NLS%%lib/R/library/translations/zh_CN/LC_MESSAGES/grDevices.mo +%%NLS%%lib/R/library/translations/zh_CN/LC_MESSAGES/graphics.mo +%%NLS%%lib/R/library/translations/zh_CN/LC_MESSAGES/grid.mo +%%NLS%%lib/R/library/translations/zh_CN/LC_MESSAGES/methods.mo +%%NLS%%lib/R/library/translations/zh_CN/LC_MESSAGES/parallel.mo +%%NLS%%lib/R/library/translations/zh_CN/LC_MESSAGES/splines.mo +%%NLS%%lib/R/library/translations/zh_CN/LC_MESSAGES/stats.mo +%%NLS%%lib/R/library/translations/zh_CN/LC_MESSAGES/tcltk.mo +%%NLS%%lib/R/library/translations/zh_CN/LC_MESSAGES/tools.mo +%%NLS%%lib/R/library/translations/zh_TW/LC_MESSAGES/R.mo +%%NLS%%lib/R/library/translations/zh_TW/LC_MESSAGES/RGui.mo +%%NLS%%lib/R/library/translations/zh_TW/LC_MESSAGES/graphics.mo lib/R/library/utils/DESCRIPTION lib/R/library/utils/INDEX lib/R/library/utils/Meta/Rd.rds @@ -1276,20 +1348,11 @@ lib/R/library/utils/help/utils.rdx lib/R/library/utils/html/00Index.html lib/R/library/utils/html/R.css lib/R/library/utils/iconvlist +lib/R/library/utils/libs/utils.so lib/R/library/utils/misc/exDIF.csv lib/R/library/utils/misc/exDIF.dif -%%NLS%%lib/R/library/utils/po/da/LC_MESSAGES/R-utils.mo -%%NLS%%lib/R/library/utils/po/de/LC_MESSAGES/R-utils.mo -%%NLS%%lib/R/library/utils/po/en@quot/LC_MESSAGES/R-utils.mo -%%NLS%%lib/R/library/utils/po/fr/LC_MESSAGES/R-utils.mo -%%NLS%%lib/R/library/utils/po/ja/LC_MESSAGES/R-utils.mo -%%NLS%%lib/R/library/utils/po/ko/LC_MESSAGES/R-utils.mo -%%NLS%%lib/R/library/utils/po/pl/LC_MESSAGES/R-utils.mo -%%NLS%%lib/R/library/utils/po/pt_BR/LC_MESSAGES/R-utils.mo -%%NLS%%lib/R/library/utils/po/ru/LC_MESSAGES/R-utils.mo -%%NLS%%lib/R/library/utils/po/tr/LC_MESSAGES/R-utils.mo -%%NLS%%lib/R/library/utils/po/zh_CN/LC_MESSAGES/R-utils.mo %%X11%%lib/R/modules/R_X11.so +%%X11%%lib/R/modules/R_de.so lib/R/modules/internet.so lib/R/modules/lapack.so lib/R/modules/vfonts.so @@ -1298,36 +1361,22 @@ lib/R/share/R/examples-footer.R lib/R/share/R/examples-header.R lib/R/share/R/nspackloader.R lib/R/share/R/tests-startup.R +lib/R/share/dictionaries/en_stats.rds lib/R/share/encodings/Adobe-glyphlist lib/R/share/encodings/character-sets lib/R/share/java/README lib/R/share/java/getsp.class lib/R/share/licenses/AGPL-3 -lib/R/share/licenses/Artistic-1.0 lib/R/share/licenses/Artistic-2.0 +lib/R/share/licenses/BSD_2_clause +lib/R/share/licenses/BSD_3_clause lib/R/share/licenses/GPL-2 lib/R/share/licenses/GPL-3 lib/R/share/licenses/LGPL-2 lib/R/share/licenses/LGPL-2.1 lib/R/share/licenses/LGPL-3 +lib/R/share/licenses/MIT lib/R/share/licenses/license.db -%%NLS%%lib/R/share/locale/da/LC_MESSAGES/R.mo -%%NLS%%lib/R/share/locale/de/LC_MESSAGES/R.mo -%%NLS%%lib/R/share/locale/en_GB/LC_MESSAGES/R.mo -%%NLS%%lib/R/share/locale/en/LC_MESSAGES/R.mo -%%NLS%%lib/R/share/locale/en@quot/LC_MESSAGES/R.mo -%%NLS%%lib/R/share/locale/es/LC_MESSAGES/R.mo -%%NLS%%lib/R/share/locale/fr/LC_MESSAGES/R.mo -%%NLS%%lib/R/share/locale/it/LC_MESSAGES/R.mo -%%NLS%%lib/R/share/locale/ja/LC_MESSAGES/R.mo -%%NLS%%lib/R/share/locale/ko/LC_MESSAGES/R.mo -%%NLS%%lib/R/share/locale/nn/LC_MESSAGES/R.mo -%%NLS%%lib/R/share/locale/pl/LC_MESSAGES/R.mo -%%NLS%%lib/R/share/locale/pt_BR/LC_MESSAGES/R.mo -%%NLS%%lib/R/share/locale/ru/LC_MESSAGES/R.mo -%%NLS%%lib/R/share/locale/tr/LC_MESSAGES/R.mo -%%NLS%%lib/R/share/locale/zh_CN/LC_MESSAGES/R.mo -%%NLS%%lib/R/share/locale/zh_TW/LC_MESSAGES/R.mo lib/R/share/make/basepkg.mk lib/R/share/make/check.mk lib/R/share/make/clean.mk @@ -1373,71 +1422,15 @@ lib/R/share/texmf/tex/latex/upquote.sty @dirrm lib/R/share/texmf @dirrm lib/R/share/sh @dirrm lib/R/share/make -%%NLS%%@dirrm lib/R/share/locale/zh_TW/LC_MESSAGES -%%NLS%%@dirrm lib/R/share/locale/zh_TW -%%NLS%%@dirrm lib/R/share/locale/zh_CN/LC_MESSAGES -%%NLS%%@dirrm lib/R/share/locale/zh_CN -%%NLS%%@dirrm lib/R/share/locale/tr/LC_MESSAGES -%%NLS%%@dirrm lib/R/share/locale/tr -%%NLS%%@dirrm lib/R/share/locale/ru/LC_MESSAGES -%%NLS%%@dirrm lib/R/share/locale/ru -%%NLS%%@dirrm lib/R/share/locale/pt_BR/LC_MESSAGES -%%NLS%%@dirrm lib/R/share/locale/pt_BR -%%NLS%%@dirrm lib/R/share/locale/pl/LC_MESSAGES -%%NLS%%@dirrm lib/R/share/locale/pl -%%NLS%%@dirrm lib/R/share/locale/nn/LC_MESSAGES -%%NLS%%@dirrm lib/R/share/locale/nn -%%NLS%%@dirrm lib/R/share/locale/ko/LC_MESSAGES -%%NLS%%@dirrm lib/R/share/locale/ko -%%NLS%%@dirrm lib/R/share/locale/ja/LC_MESSAGES -%%NLS%%@dirrm lib/R/share/locale/ja -%%NLS%%@dirrm lib/R/share/locale/it/LC_MESSAGES -%%NLS%%@dirrm lib/R/share/locale/it -%%NLS%%@dirrm lib/R/share/locale/fr/LC_MESSAGES -%%NLS%%@dirrm lib/R/share/locale/fr -%%NLS%%@dirrm lib/R/share/locale/es/LC_MESSAGES -%%NLS%%@dirrm lib/R/share/locale/es -%%NLS%%@dirrm lib/R/share/locale/en@quot/LC_MESSAGES -%%NLS%%@dirrm lib/R/share/locale/en@quot -%%NLS%%@dirrm lib/R/share/locale/en/LC_MESSAGES -%%NLS%%@dirrm lib/R/share/locale/en_GB/LC_MESSAGES -%%NLS%%@dirrm lib/R/share/locale/en_GB -%%NLS%%@dirrm lib/R/share/locale/en -%%NLS%%@dirrm lib/R/share/locale/de/LC_MESSAGES -%%NLS%%@dirrm lib/R/share/locale/de -%%NLS%%@dirrm lib/R/share/locale/da/LC_MESSAGES -%%NLS%%@dirrm lib/R/share/locale/da -%%NLS%%@dirrm lib/R/share/locale @dirrm lib/R/share/licenses @dirrm lib/R/share/java @dirrm lib/R/share/encodings +@dirrm lib/R/share/dictionaries @dirrm lib/R/share/R @dirrm lib/R/share @dirrm lib/R/modules -%%NLS%%@dirrm lib/R/library/utils/po/zh_CN/LC_MESSAGES -%%NLS%%@dirrm lib/R/library/utils/po/zh_CN -%%NLS%%@dirrm lib/R/library/utils/po/tr/LC_MESSAGES -%%NLS%%@dirrm lib/R/library/utils/po/tr -%%NLS%%@dirrm lib/R/library/utils/po/ru/LC_MESSAGES -%%NLS%%@dirrm lib/R/library/utils/po/ru -%%NLS%%@dirrm lib/R/library/utils/po/pt_BR/LC_MESSAGES -%%NLS%%@dirrm lib/R/library/utils/po/pt_BR -%%NLS%%@dirrm lib/R/library/utils/po/pl/LC_MESSAGES -%%NLS%%@dirrm lib/R/library/utils/po/pl -%%NLS%%@dirrm lib/R/library/utils/po/ko/LC_MESSAGES -%%NLS%%@dirrm lib/R/library/utils/po/ko -%%NLS%%@dirrm lib/R/library/utils/po/ja/LC_MESSAGES -%%NLS%%@dirrm lib/R/library/utils/po/ja -%%NLS%%@dirrm lib/R/library/utils/po/fr/LC_MESSAGES -%%NLS%%@dirrm lib/R/library/utils/po/fr -%%NLS%%@dirrm lib/R/library/utils/po/en@quot/LC_MESSAGES -%%NLS%%@dirrm lib/R/library/utils/po/en@quot -%%NLS%%@dirrm lib/R/library/utils/po/de/LC_MESSAGES -%%NLS%%@dirrm lib/R/library/utils/po/de -%%NLS%%@dirrm lib/R/library/utils/po/da/LC_MESSAGES -%%NLS%%@dirrm lib/R/library/utils/po/da -%%NLS%%@dirrm lib/R/library/utils/po @dirrm lib/R/library/utils/misc +@dirrm lib/R/library/utils/libs @dirrm lib/R/library/utils/html @dirrm lib/R/library/utils/help @dirrm lib/R/library/utils/doc @@ -1445,60 +1438,49 @@ lib/R/share/texmf/tex/latex/upquote.sty @dirrm lib/R/library/utils/R @dirrm lib/R/library/utils/Meta @dirrm lib/R/library/utils -%%NLS%%@dirrm lib/R/library/tools/po/zh_CN/LC_MESSAGES -%%NLS%%@dirrm lib/R/library/tools/po/zh_CN -%%NLS%%@dirrm lib/R/library/tools/po/tr/LC_MESSAGES -%%NLS%%@dirrm lib/R/library/tools/po/tr -%%NLS%%@dirrm lib/R/library/tools/po/ru/LC_MESSAGES -%%NLS%%@dirrm lib/R/library/tools/po/ru -%%NLS%%@dirrm lib/R/library/tools/po/pt_BR/LC_MESSAGES -%%NLS%%@dirrm lib/R/library/tools/po/pt_BR -%%NLS%%@dirrm lib/R/library/tools/po/pl/LC_MESSAGES -%%NLS%%@dirrm lib/R/library/tools/po/pl -%%NLS%%@dirrm lib/R/library/tools/po/ko/LC_MESSAGES -%%NLS%%@dirrm lib/R/library/tools/po/ko -%%NLS%%@dirrm lib/R/library/tools/po/ja/LC_MESSAGES -%%NLS%%@dirrm lib/R/library/tools/po/ja -%%NLS%%@dirrm lib/R/library/tools/po/it/LC_MESSAGES -%%NLS%%@dirrm lib/R/library/tools/po/it -%%NLS%%@dirrm lib/R/library/tools/po/fr/LC_MESSAGES -%%NLS%%@dirrm lib/R/library/tools/po/fr -%%NLS%%@dirrm lib/R/library/tools/po/en@quot/LC_MESSAGES -%%NLS%%@dirrm lib/R/library/tools/po/en@quot -%%NLS%%@dirrm lib/R/library/tools/po/de/LC_MESSAGES -%%NLS%%@dirrm lib/R/library/tools/po/de -%%NLS%%@dirrm lib/R/library/tools/po/da/LC_MESSAGES -%%NLS%%@dirrm lib/R/library/tools/po/da -%%NLS%%@dirrm lib/R/library/tools/po +%%NLS%%@dirrm lib/R/library/translations/zh_TW/LC_MESSAGES +%%NLS%%@dirrm lib/R/library/translations/zh_TW +%%NLS%%@dirrm lib/R/library/translations/zh_CN/LC_MESSAGES +%%NLS%%@dirrm lib/R/library/translations/zh_CN +%%NLS%%@dirrm lib/R/library/translations/tr/LC_MESSAGES +%%NLS%%@dirrm lib/R/library/translations/tr +%%NLS%%@dirrm lib/R/library/translations/ru/LC_MESSAGES +%%NLS%%@dirrm lib/R/library/translations/ru +%%NLS%%@dirrm lib/R/library/translations/pt_BR/LC_MESSAGES +%%NLS%%@dirrm lib/R/library/translations/pt_BR +%%NLS%%@dirrm lib/R/library/translations/pl/LC_MESSAGES +%%NLS%%@dirrm lib/R/library/translations/pl +%%NLS%%@dirrm lib/R/library/translations/nn/LC_MESSAGES +%%NLS%%@dirrm lib/R/library/translations/nn +%%NLS%%@dirrm lib/R/library/translations/ko/LC_MESSAGES +%%NLS%%@dirrm lib/R/library/translations/ko +%%NLS%%@dirrm lib/R/library/translations/ja/LC_MESSAGES +%%NLS%%@dirrm lib/R/library/translations/ja +%%NLS%%@dirrm lib/R/library/translations/it/LC_MESSAGES +%%NLS%%@dirrm lib/R/library/translations/it +%%NLS%%@dirrm lib/R/library/translations/fr/LC_MESSAGES +%%NLS%%@dirrm lib/R/library/translations/fr +%%NLS%%@dirrm lib/R/library/translations/fa/LC_MESSAGES +%%NLS%%@dirrm lib/R/library/translations/fa +%%NLS%%@dirrm lib/R/library/translations/es/LC_MESSAGES +%%NLS%%@dirrm lib/R/library/translations/es +%%NLS%%@dirrm lib/R/library/translations/en_GB/LC_MESSAGES +%%NLS%%@dirrm lib/R/library/translations/en_GB +%%NLS%%@dirrm lib/R/library/translations/en@quot/LC_MESSAGES +%%NLS%%@dirrm lib/R/library/translations/en@quot +%%NLS%%@dirrm lib/R/library/translations/en/LC_MESSAGES +%%NLS%%@dirrm lib/R/library/translations/en +%%NLS%%@dirrm lib/R/library/translations/de/LC_MESSAGES +%%NLS%%@dirrm lib/R/library/translations/de +%%NLS%%@dirrm lib/R/library/translations/da/LC_MESSAGES +%%NLS%%@dirrm lib/R/library/translations/da +@dirrm lib/R/library/translations @dirrm lib/R/library/tools/libs @dirrm lib/R/library/tools/html @dirrm lib/R/library/tools/help @dirrm lib/R/library/tools/R @dirrm lib/R/library/tools/Meta @dirrm lib/R/library/tools -%%NLS%%@dirrm lib/R/library/tcltk/po/zh_CN/LC_MESSAGES -%%NLS%%@dirrm lib/R/library/tcltk/po/zh_CN -%%NLS%%@dirrm lib/R/library/tcltk/po/ru/LC_MESSAGES -%%NLS%%@dirrm lib/R/library/tcltk/po/ru -%%NLS%%@dirrm lib/R/library/tcltk/po/pt_BR/LC_MESSAGES -%%NLS%%@dirrm lib/R/library/tcltk/po/pt_BR -%%NLS%%@dirrm lib/R/library/tcltk/po/pl/LC_MESSAGES -%%NLS%%@dirrm lib/R/library/tcltk/po/pl -%%NLS%%@dirrm lib/R/library/tcltk/po/ko/LC_MESSAGES -%%NLS%%@dirrm lib/R/library/tcltk/po/ko -%%NLS%%@dirrm lib/R/library/tcltk/po/ja/LC_MESSAGES -%%NLS%%@dirrm lib/R/library/tcltk/po/ja -%%NLS%%@dirrm lib/R/library/tcltk/po/it/LC_MESSAGES -%%NLS%%@dirrm lib/R/library/tcltk/po/it -%%NLS%%@dirrm lib/R/library/tcltk/po/fr/LC_MESSAGES -%%NLS%%@dirrm lib/R/library/tcltk/po/fr -%%NLS%%@dirrm lib/R/library/tcltk/po/en@quot/LC_MESSAGES -%%NLS%%@dirrm lib/R/library/tcltk/po/en@quot -%%NLS%%@dirrm lib/R/library/tcltk/po/de/LC_MESSAGES -%%NLS%%@dirrm lib/R/library/tcltk/po/de -%%NLS%%@dirrm lib/R/library/tcltk/po/da/LC_MESSAGES -%%NLS%%@dirrm lib/R/library/tcltk/po/da -%%NLS%%@dirrm lib/R/library/tcltk/po %%TCLTK%%@dirrm lib/R/library/tcltk/libs @dirrm lib/R/library/tcltk/html @dirrm lib/R/library/tcltk/help @@ -1515,89 +1497,18 @@ lib/R/share/texmf/tex/latex/upquote.sty @dirrm lib/R/library/survival/R @dirrm lib/R/library/survival/Meta @dirrm lib/R/library/survival -%%NLS%%@dirrm lib/R/library/stats/po/zh_CN/LC_MESSAGES -%%NLS%%@dirrm lib/R/library/stats/po/zh_CN -%%NLS%%@dirrm lib/R/library/stats/po/tr/LC_MESSAGES -%%NLS%%@dirrm lib/R/library/stats/po/tr -%%NLS%%@dirrm lib/R/library/stats/po/ru/LC_MESSAGES -%%NLS%%@dirrm lib/R/library/stats/po/ru -%%NLS%%@dirrm lib/R/library/stats/po/pt_BR/LC_MESSAGES -%%NLS%%@dirrm lib/R/library/stats/po/pt_BR -%%NLS%%@dirrm lib/R/library/stats/po/pl/LC_MESSAGES -%%NLS%%@dirrm lib/R/library/stats/po/pl -%%NLS%%@dirrm lib/R/library/stats/po/ko/LC_MESSAGES -%%NLS%%@dirrm lib/R/library/stats/po/ko -%%NLS%%@dirrm lib/R/library/stats/po/ja/LC_MESSAGES -%%NLS%%@dirrm lib/R/library/stats/po/ja -%%NLS%%@dirrm lib/R/library/stats/po/it/LC_MESSAGES -%%NLS%%@dirrm lib/R/library/stats/po/it -%%NLS%%@dirrm lib/R/library/stats/po/fr/LC_MESSAGES -%%NLS%%@dirrm lib/R/library/stats/po/fr -%%NLS%%@dirrm lib/R/library/stats/po/en@quot/LC_MESSAGES -%%NLS%%@dirrm lib/R/library/stats/po/en@quot -%%NLS%%@dirrm lib/R/library/stats/po/de/LC_MESSAGES -%%NLS%%@dirrm lib/R/library/stats/po/de -%%NLS%%@dirrm lib/R/library/stats/po/da/LC_MESSAGES -%%NLS%%@dirrm lib/R/library/stats/po/da -%%NLS%%@dirrm lib/R/library/stats/po @dirrm lib/R/library/stats/libs @dirrm lib/R/library/stats/html @dirrm lib/R/library/stats/help @dirrm lib/R/library/stats/demo @dirrm lib/R/library/stats/R @dirrm lib/R/library/stats/Meta -%%NLS%%@dirrm lib/R/library/stats4/po/zh_CN/LC_MESSAGES -%%NLS%%@dirrm lib/R/library/stats4/po/zh_CN -%%NLS%%@dirrm lib/R/library/stats4/po/tr/LC_MESSAGES -%%NLS%%@dirrm lib/R/library/stats4/po/tr -%%NLS%%@dirrm lib/R/library/stats4/po/ru/LC_MESSAGES -%%NLS%%@dirrm lib/R/library/stats4/po/ru -%%NLS%%@dirrm lib/R/library/stats4/po/pt_BR/LC_MESSAGES -%%NLS%%@dirrm lib/R/library/stats4/po/pt_BR -%%NLS%%@dirrm lib/R/library/stats4/po/pl/LC_MESSAGES -%%NLS%%@dirrm lib/R/library/stats4/po/pl -%%NLS%%@dirrm lib/R/library/stats4/po/ko/LC_MESSAGES -%%NLS%%@dirrm lib/R/library/stats4/po/ko -%%NLS%%@dirrm lib/R/library/stats4/po/ja/LC_MESSAGES -%%NLS%%@dirrm lib/R/library/stats4/po/ja -%%NLS%%@dirrm lib/R/library/stats4/po/it/LC_MESSAGES -%%NLS%%@dirrm lib/R/library/stats4/po/it -%%NLS%%@dirrm lib/R/library/stats4/po/fr/LC_MESSAGES -%%NLS%%@dirrm lib/R/library/stats4/po/fr -%%NLS%%@dirrm lib/R/library/stats4/po/en@quot/LC_MESSAGES -%%NLS%%@dirrm lib/R/library/stats4/po/en@quot -%%NLS%%@dirrm lib/R/library/stats4/po/de/LC_MESSAGES -%%NLS%%@dirrm lib/R/library/stats4/po/de -%%NLS%%@dirrm lib/R/library/stats4/po/da/LC_MESSAGES -%%NLS%%@dirrm lib/R/library/stats4/po/da -%%NLS%%@dirrm lib/R/library/stats4/po @dirrm lib/R/library/stats4/html @dirrm lib/R/library/stats4/help @dirrm lib/R/library/stats4/R @dirrm lib/R/library/stats4/Meta @dirrm lib/R/library/stats4 @dirrm lib/R/library/stats -%%NLS%%@dirrm lib/R/library/splines/po/zh_CN/LC_MESSAGES -%%NLS%%@dirrm lib/R/library/splines/po/zh_CN -%%NLS%%@dirrm lib/R/library/splines/po/ru/LC_MESSAGES -%%NLS%%@dirrm lib/R/library/splines/po/ru -%%NLS%%@dirrm lib/R/library/splines/po/pt_BR/LC_MESSAGES -%%NLS%%@dirrm lib/R/library/splines/po/pt_BR -%%NLS%%@dirrm lib/R/library/splines/po/pl/LC_MESSAGES -%%NLS%%@dirrm lib/R/library/splines/po/pl -%%NLS%%@dirrm lib/R/library/splines/po/ko/LC_MESSAGES -%%NLS%%@dirrm lib/R/library/splines/po/ko -%%NLS%%@dirrm lib/R/library/splines/po/ja/LC_MESSAGES -%%NLS%%@dirrm lib/R/library/splines/po/ja -%%NLS%%@dirrm lib/R/library/splines/po/fr/LC_MESSAGES -%%NLS%%@dirrm lib/R/library/splines/po/fr -%%NLS%%@dirrm lib/R/library/splines/po/en@quot/LC_MESSAGES -%%NLS%%@dirrm lib/R/library/splines/po/en@quot -%%NLS%%@dirrm lib/R/library/splines/po/de/LC_MESSAGES -%%NLS%%@dirrm lib/R/library/splines/po/de -%%NLS%%@dirrm lib/R/library/splines/po/da/LC_MESSAGES -%%NLS%%@dirrm lib/R/library/splines/po/da -%%NLS%%@dirrm lib/R/library/splines/po @dirrm lib/R/library/splines/libs @dirrm lib/R/library/splines/html @dirrm lib/R/library/splines/help @@ -1624,6 +1535,8 @@ lib/R/share/texmf/tex/latex/upquote.sty %%NLS%%@dirrm lib/R/library/rpart/po/ru %%NLS%%@dirrm lib/R/library/rpart/po/pl/LC_MESSAGES %%NLS%%@dirrm lib/R/library/rpart/po/pl +%%NLS%%@dirrm lib/R/library/rpart/po/ko/LC_MESSAGES +%%NLS%%@dirrm lib/R/library/rpart/po/ko %%NLS%%@dirrm lib/R/library/rpart/po/fr/LC_MESSAGES %%NLS%%@dirrm lib/R/library/rpart/po/fr %%NLS%%@dirrm lib/R/library/rpart/po/en@quot/LC_MESSAGES @@ -1639,23 +1552,6 @@ lib/R/share/texmf/tex/latex/upquote.sty @dirrm lib/R/library/rpart/R @dirrm lib/R/library/rpart/Meta @dirrm lib/R/library/rpart -%%NLS%%@dirrm lib/R/library/parallel/po/zh_CN/LC_MESSAGES -%%NLS%%@dirrm lib/R/library/parallel/po/zh_CN -%%NLS%%@dirrm lib/R/library/parallel/po/ru/LC_MESSAGES -%%NLS%%@dirrm lib/R/library/parallel/po/ru -%%NLS%%@dirrm lib/R/library/parallel/po/pl/LC_MESSAGES -%%NLS%%@dirrm lib/R/library/parallel/po/pl -%%NLS%%@dirrm lib/R/library/parallel/po/ko/LC_MESSAGES -%%NLS%%@dirrm lib/R/library/parallel/po/ko -%%NLS%%@dirrm lib/R/library/parallel/po/fr/LC_MESSAGES -%%NLS%%@dirrm lib/R/library/parallel/po/fr -%%NLS%%@dirrm lib/R/library/parallel/po/en@quot/LC_MESSAGES -%%NLS%%@dirrm lib/R/library/parallel/po/en@quot -%%NLS%%@dirrm lib/R/library/parallel/po/de/LC_MESSAGES -%%NLS%%@dirrm lib/R/library/parallel/po/de -%%NLS%%@dirrm lib/R/library/parallel/po/da/LC_MESSAGES -%%NLS%%@dirrm lib/R/library/parallel/po/da -%%NLS%%@dirrm lib/R/library/parallel/po @dirrm lib/R/library/parallel/libs @dirrm lib/R/library/parallel/html @dirrm lib/R/library/parallel/help @@ -1665,6 +1561,8 @@ lib/R/share/texmf/tex/latex/upquote.sty @dirrm lib/R/library/parallel %%NLS%%@dirrm lib/R/library/nnet/po/pl/LC_MESSAGES %%NLS%%@dirrm lib/R/library/nnet/po/pl +%%NLS%%@dirrm lib/R/library/nnet/po/ko/LC_MESSAGES +%%NLS%%@dirrm lib/R/library/nnet/po/ko %%NLS%%@dirrm lib/R/library/nnet/po/fr/LC_MESSAGES %%NLS%%@dirrm lib/R/library/nnet/po/fr %%NLS%%@dirrm lib/R/library/nnet/po/en@quot/LC_MESSAGES @@ -1703,27 +1601,6 @@ lib/R/share/texmf/tex/latex/upquote.sty @dirrm lib/R/library/mgcv/R @dirrm lib/R/library/mgcv/Meta @dirrm lib/R/library/mgcv -%%NLS%%@dirrm lib/R/library/methods/po/zh_CN/LC_MESSAGES -%%NLS%%@dirrm lib/R/library/methods/po/zh_CN -%%NLS%%@dirrm lib/R/library/methods/po/ru/LC_MESSAGES -%%NLS%%@dirrm lib/R/library/methods/po/ru -%%NLS%%@dirrm lib/R/library/methods/po/pt_BR/LC_MESSAGES -%%NLS%%@dirrm lib/R/library/methods/po/pt_BR -%%NLS%%@dirrm lib/R/library/methods/po/pl/LC_MESSAGES -%%NLS%%@dirrm lib/R/library/methods/po/pl -%%NLS%%@dirrm lib/R/library/methods/po/ko/LC_MESSAGES -%%NLS%%@dirrm lib/R/library/methods/po/ko -%%NLS%%@dirrm lib/R/library/methods/po/ja/LC_MESSAGES -%%NLS%%@dirrm lib/R/library/methods/po/ja -%%NLS%%@dirrm lib/R/library/methods/po/fr/LC_MESSAGES -%%NLS%%@dirrm lib/R/library/methods/po/fr -%%NLS%%@dirrm lib/R/library/methods/po/en@quot/LC_MESSAGES -%%NLS%%@dirrm lib/R/library/methods/po/en@quot -%%NLS%%@dirrm lib/R/library/methods/po/de/LC_MESSAGES -%%NLS%%@dirrm lib/R/library/methods/po/de -%%NLS%%@dirrm lib/R/library/methods/po/da/LC_MESSAGES -%%NLS%%@dirrm lib/R/library/methods/po/da -%%NLS%%@dirrm lib/R/library/methods/po @dirrm lib/R/library/methods/libs @dirrm lib/R/library/methods/html @dirrm lib/R/library/methods/help @@ -1745,29 +1622,6 @@ lib/R/share/texmf/tex/latex/upquote.sty @dirrm lib/R/library/lattice/R @dirrm lib/R/library/lattice/Meta @dirrm lib/R/library/lattice -%%NLS%%@dirrm lib/R/library/grid/po/zh_CN/LC_MESSAGES -%%NLS%%@dirrm lib/R/library/grid/po/zh_CN -%%NLS%%@dirrm lib/R/library/grid/po/ru/LC_MESSAGES -%%NLS%%@dirrm lib/R/library/grid/po/ru -%%NLS%%@dirrm lib/R/library/grid/po/pt_BR/LC_MESSAGES -%%NLS%%@dirrm lib/R/library/grid/po/pt_BR -%%NLS%%@dirrm lib/R/library/grid/po/pl/LC_MESSAGES -%%NLS%%@dirrm lib/R/library/grid/po/pl -%%NLS%%@dirrm lib/R/library/grid/po/ko/LC_MESSAGES -%%NLS%%@dirrm lib/R/library/grid/po/ko -%%NLS%%@dirrm lib/R/library/grid/po/ja/LC_MESSAGES -%%NLS%%@dirrm lib/R/library/grid/po/ja -%%NLS%%@dirrm lib/R/library/grid/po/it/LC_MESSAGES -%%NLS%%@dirrm lib/R/library/grid/po/it -%%NLS%%@dirrm lib/R/library/grid/po/fr/LC_MESSAGES -%%NLS%%@dirrm lib/R/library/grid/po/fr -%%NLS%%@dirrm lib/R/library/grid/po/en@quot/LC_MESSAGES -%%NLS%%@dirrm lib/R/library/grid/po/en@quot -%%NLS%%@dirrm lib/R/library/grid/po/de/LC_MESSAGES -%%NLS%%@dirrm lib/R/library/grid/po/de -%%NLS%%@dirrm lib/R/library/grid/po/da/LC_MESSAGES -%%NLS%%@dirrm lib/R/library/grid/po/da -%%NLS%%@dirrm lib/R/library/grid/po @dirrm lib/R/library/grid/libs @dirrm lib/R/library/grid/html @dirrm lib/R/library/grid/help @@ -1775,29 +1629,7 @@ lib/R/share/texmf/tex/latex/upquote.sty @dirrm lib/R/library/grid/R @dirrm lib/R/library/grid/Meta @dirrm lib/R/library/grid -%%NLS%%@dirrm lib/R/library/graphics/po/zh_CN/LC_MESSAGES -%%NLS%%@dirrm lib/R/library/graphics/po/zh_CN -%%NLS%%@dirrm lib/R/library/graphics/po/ru/LC_MESSAGES -%%NLS%%@dirrm lib/R/library/graphics/po/ru -%%NLS%%@dirrm lib/R/library/graphics/po/pt_BR/LC_MESSAGES -%%NLS%%@dirrm lib/R/library/graphics/po/pt_BR -%%NLS%%@dirrm lib/R/library/graphics/po/pl/LC_MESSAGES -%%NLS%%@dirrm lib/R/library/graphics/po/pl -%%NLS%%@dirrm lib/R/library/graphics/po/ko/LC_MESSAGES -%%NLS%%@dirrm lib/R/library/graphics/po/ko -%%NLS%%@dirrm lib/R/library/graphics/po/ja/LC_MESSAGES -%%NLS%%@dirrm lib/R/library/graphics/po/ja -%%NLS%%@dirrm lib/R/library/graphics/po/it/LC_MESSAGES -%%NLS%%@dirrm lib/R/library/graphics/po/it -%%NLS%%@dirrm lib/R/library/graphics/po/fr/LC_MESSAGES -%%NLS%%@dirrm lib/R/library/graphics/po/fr -%%NLS%%@dirrm lib/R/library/graphics/po/en@quot/LC_MESSAGES -%%NLS%%@dirrm lib/R/library/graphics/po/en@quot -%%NLS%%@dirrm lib/R/library/graphics/po/de/LC_MESSAGES -%%NLS%%@dirrm lib/R/library/graphics/po/de -%%NLS%%@dirrm lib/R/library/graphics/po/da/LC_MESSAGES -%%NLS%%@dirrm lib/R/library/graphics/po/da -%%NLS%%@dirrm lib/R/library/graphics/po +@dirrm lib/R/library/graphics/libs @dirrm lib/R/library/graphics/html @dirrm lib/R/library/graphics/help/figures @dirrm lib/R/library/graphics/help @@ -1805,36 +1637,12 @@ lib/R/share/texmf/tex/latex/upquote.sty @dirrm lib/R/library/graphics/R @dirrm lib/R/library/graphics/Meta @dirrm lib/R/library/graphics -%%NLS%%@dirrm lib/R/library/grDevices/po/zh_CN/LC_MESSAGES -%%NLS%%@dirrm lib/R/library/grDevices/po/zh_CN -%%NLS%%@dirrm lib/R/library/grDevices/po/ru/LC_MESSAGES -%%NLS%%@dirrm lib/R/library/grDevices/po/ru -%%NLS%%@dirrm lib/R/library/grDevices/po/pt_BR/LC_MESSAGES -%%NLS%%@dirrm lib/R/library/grDevices/po/pt_BR -%%NLS%%@dirrm lib/R/library/grDevices/po/pl/LC_MESSAGES -%%NLS%%@dirrm lib/R/library/grDevices/po/pl -%%NLS%%@dirrm lib/R/library/grDevices/po/ko/LC_MESSAGES -%%NLS%%@dirrm lib/R/library/grDevices/po/ko -%%NLS%%@dirrm lib/R/library/grDevices/po/ja/LC_MESSAGES -%%NLS%%@dirrm lib/R/library/grDevices/po/ja -%%NLS%%@dirrm lib/R/library/grDevices/po/it/LC_MESSAGES -%%NLS%%@dirrm lib/R/library/grDevices/po/it -%%NLS%%@dirrm lib/R/library/grDevices/po/fr/LC_MESSAGES -%%NLS%%@dirrm lib/R/library/grDevices/po/fr -%%NLS%%@dirrm lib/R/library/grDevices/po/en@quot/LC_MESSAGES -%%NLS%%@dirrm lib/R/library/grDevices/po/en@quot -%%NLS%%@dirrm lib/R/library/grDevices/po/en_GB/LC_MESSAGES -%%NLS%%@dirrm lib/R/library/grDevices/po/en_GB -%%NLS%%@dirrm lib/R/library/grDevices/po/de/LC_MESSAGES -%%NLS%%@dirrm lib/R/library/grDevices/po/de -%%NLS%%@dirrm lib/R/library/grDevices/po/da/LC_MESSAGES -%%NLS%%@dirrm lib/R/library/grDevices/po/da -%%NLS%%@dirrm lib/R/library/grDevices/po @dirrm lib/R/library/grDevices/libs @dirrm lib/R/library/grDevices/icc @dirrm lib/R/library/grDevices/html @dirrm lib/R/library/grDevices/help @dirrm lib/R/library/grDevices/enc +@dirrm lib/R/library/grDevices/demo @dirrm lib/R/library/grDevices/afm @dirrm lib/R/library/grDevices/R @dirrm lib/R/library/grDevices/Meta @@ -1860,27 +1668,6 @@ lib/R/share/texmf/tex/latex/upquote.sty @dirrm lib/R/library/datasets/data @dirrm lib/R/library/datasets/Meta @dirrm lib/R/library/datasets -%%NLS%%@dirrm lib/R/library/compiler/po/zh_CN/LC_MESSAGES -%%NLS%%@dirrm lib/R/library/compiler/po/zh_CN -%%NLS%%@dirrm lib/R/library/compiler/po/ru/LC_MESSAGES -%%NLS%%@dirrm lib/R/library/compiler/po/ru -%%NLS%%@dirrm lib/R/library/compiler/po/pt_BR/LC_MESSAGES -%%NLS%%@dirrm lib/R/library/compiler/po/pt_BR -%%NLS%%@dirrm lib/R/library/compiler/po/pl/LC_MESSAGES -%%NLS%%@dirrm lib/R/library/compiler/po/pl -%%NLS%%@dirrm lib/R/library/compiler/po/ko/LC_MESSAGES -%%NLS%%@dirrm lib/R/library/compiler/po/ko -%%NLS%%@dirrm lib/R/library/compiler/po/ja/LC_MESSAGES -%%NLS%%@dirrm lib/R/library/compiler/po/ja -%%NLS%%@dirrm lib/R/library/compiler/po/fr/LC_MESSAGES -%%NLS%%@dirrm lib/R/library/compiler/po/fr -%%NLS%%@dirrm lib/R/library/compiler/po/en@quot/LC_MESSAGES -%%NLS%%@dirrm lib/R/library/compiler/po/en@quot -%%NLS%%@dirrm lib/R/library/compiler/po/de/LC_MESSAGES -%%NLS%%@dirrm lib/R/library/compiler/po/de -%%NLS%%@dirrm lib/R/library/compiler/po/da/LC_MESSAGES -%%NLS%%@dirrm lib/R/library/compiler/po/da -%%NLS%%@dirrm lib/R/library/compiler/po @dirrm lib/R/library/compiler/html @dirrm lib/R/library/compiler/help @dirrm lib/R/library/compiler/R @@ -1907,6 +1694,8 @@ lib/R/share/texmf/tex/latex/upquote.sty @dirrm lib/R/library/cluster %%NLS%%@dirrm lib/R/library/class/po/pl/LC_MESSAGES %%NLS%%@dirrm lib/R/library/class/po/pl +%%NLS%%@dirrm lib/R/library/class/po/ko/LC_MESSAGES +%%NLS%%@dirrm lib/R/library/class/po/ko %%NLS%%@dirrm lib/R/library/class/po/fr/LC_MESSAGES %%NLS%%@dirrm lib/R/library/class/po/fr %%NLS%%@dirrm lib/R/library/class/po/en@quot/LC_MESSAGES @@ -1924,6 +1713,8 @@ lib/R/share/texmf/tex/latex/upquote.sty %%NLS%%@dirrm lib/R/library/boot/po/ru %%NLS%%@dirrm lib/R/library/boot/po/pl/LC_MESSAGES %%NLS%%@dirrm lib/R/library/boot/po/pl +%%NLS%%@dirrm lib/R/library/boot/po/ko/LC_MESSAGES +%%NLS%%@dirrm lib/R/library/boot/po/ko %%NLS%%@dirrm lib/R/library/boot/po/fr/LC_MESSAGES %%NLS%%@dirrm lib/R/library/boot/po/fr %%NLS%%@dirrm lib/R/library/boot/po/en@quot/LC_MESSAGES @@ -1937,33 +1728,6 @@ lib/R/share/texmf/tex/latex/upquote.sty @dirrm lib/R/library/boot/R @dirrm lib/R/library/boot/Meta @dirrm lib/R/library/boot -%%NLS%%@dirrm lib/R/library/base/po/zh_CN/LC_MESSAGES -%%NLS%%@dirrm lib/R/library/base/po/zh_CN -%%NLS%%@dirrm lib/R/library/base/po/tr/LC_MESSAGES -%%NLS%%@dirrm lib/R/library/base/po/tr -%%NLS%%@dirrm lib/R/library/base/po/ru/LC_MESSAGES -%%NLS%%@dirrm lib/R/library/base/po/ru -%%NLS%%@dirrm lib/R/library/base/po/pt_BR/LC_MESSAGES -%%NLS%%@dirrm lib/R/library/base/po/pt_BR -%%NLS%%@dirrm lib/R/library/base/po/pl/LC_MESSAGES -%%NLS%%@dirrm lib/R/library/base/po/pl -%%NLS%%@dirrm lib/R/library/base/po/nn/LC_MESSAGES -%%NLS%%@dirrm lib/R/library/base/po/nn -%%NLS%%@dirrm lib/R/library/base/po/ko/LC_MESSAGES -%%NLS%%@dirrm lib/R/library/base/po/ko -%%NLS%%@dirrm lib/R/library/base/po/ja/LC_MESSAGES -%%NLS%%@dirrm lib/R/library/base/po/ja -%%NLS%%@dirrm lib/R/library/base/po/it/LC_MESSAGES -%%NLS%%@dirrm lib/R/library/base/po/it -%%NLS%%@dirrm lib/R/library/base/po/fr/LC_MESSAGES -%%NLS%%@dirrm lib/R/library/base/po/fr -%%NLS%%@dirrm lib/R/library/base/po/en@quot/LC_MESSAGES -%%NLS%%@dirrm lib/R/library/base/po/en@quot -%%NLS%%@dirrm lib/R/library/base/po/de/LC_MESSAGES -%%NLS%%@dirrm lib/R/library/base/po/de -%%NLS%%@dirrm lib/R/library/base/po/da/LC_MESSAGES -%%NLS%%@dirrm lib/R/library/base/po/da -%%NLS%%@dirrm lib/R/library/base/po @dirrm lib/R/library/base/html @dirrm lib/R/library/base/help @dirrm lib/R/library/base/demo @@ -1991,6 +1755,8 @@ lib/R/share/texmf/tex/latex/upquote.sty @dirrm lib/R/library/MASS/scripts %%NLS%%@dirrm lib/R/library/MASS/po/pl/LC_MESSAGES %%NLS%%@dirrm lib/R/library/MASS/po/pl +%%NLS%%@dirrm lib/R/library/MASS/po/ko/LC_MESSAGES +%%NLS%%@dirrm lib/R/library/MASS/po/ko %%NLS%%@dirrm lib/R/library/MASS/po/fr/LC_MESSAGES %%NLS%%@dirrm lib/R/library/MASS/po/fr %%NLS%%@dirrm lib/R/library/MASS/po/en@quot/LC_MESSAGES @@ -2007,6 +1773,8 @@ lib/R/share/texmf/tex/latex/upquote.sty @dirrm lib/R/library/MASS %%NLS%%@dirrm lib/R/library/KernSmooth/po/pl/LC_MESSAGES %%NLS%%@dirrm lib/R/library/KernSmooth/po/pl +%%NLS%%@dirrm lib/R/library/KernSmooth/po/ko/LC_MESSAGES +%%NLS%%@dirrm lib/R/library/KernSmooth/po/ko %%NLS%%@dirrm lib/R/library/KernSmooth/po/en@quot/LC_MESSAGES %%NLS%%@dirrm lib/R/library/KernSmooth/po/en@quot %%NLS%%@dirrm lib/R/library/KernSmooth/po/de/LC_MESSAGES diff --git a/math/ess/Makefile b/math/ess/Makefile index 3ff619b80233..1d61e80b2167 100644 --- a/math/ess/Makefile +++ b/math/ess/Makefile @@ -3,6 +3,7 @@ PORTNAME= ess DISTVERSION= 13.05 +PORTREVISION= 1 CATEGORIES= math MASTER_SITES= http://ess.r-project.org/downloads/ess/ EXTRACT_SUFX= .tgz diff --git a/math/p5-Statistics-R/Makefile b/math/p5-Statistics-R/Makefile index cd05bd1fb8f7..77a41a40ed82 100644 --- a/math/p5-Statistics-R/Makefile +++ b/math/p5-Statistics-R/Makefile @@ -3,7 +3,7 @@ PORTNAME= Statistics-R PORTVERSION= 0.31 -PORTREVISION= 1 +PORTREVISION= 2 CATEGORIES= math perl5 MASTER_SITES= CPAN MASTER_SITE_SUBDIR= CPAN:FANGLY diff --git a/math/rkward-kde4/Makefile b/math/rkward-kde4/Makefile index 2d9a2db763f9..cefdb91b555e 100644 --- a/math/rkward-kde4/Makefile +++ b/math/rkward-kde4/Makefile @@ -3,6 +3,7 @@ PORTNAME= rkward PORTVERSION= 0.6.1 +PORTREVISION= 1 CATEGORIES= math MASTER_SITES= SF/${PORTNAME}/Current_Stable_Releases PKGNAMESUFFIX= -kde4 diff --git a/math/rkward/Makefile b/math/rkward/Makefile index 15a97e0a52f9..b66d27801400 100644 --- a/math/rkward/Makefile +++ b/math/rkward/Makefile @@ -3,7 +3,7 @@ PORTNAME= rkward DISTVERSION= 0.4.9a -PORTREVISION= 19 +PORTREVISION= 20 PORTEPOCH= 3 CATEGORIES= math MASTER_SITES= SF/${PORTNAME}/Historical_Releases/0.4.x_and_earlier/0.4.9a%20%28KDE3%29 diff --git a/math/rkward/files/patch-rkward_rbackend_rembedinternal.cpp b/math/rkward/files/patch-rkward_rbackend_rembedinternal.cpp index ff283dc0187d..bfa2c1c3020f 100644 --- a/math/rkward/files/patch-rkward_rbackend_rembedinternal.cpp +++ b/math/rkward/files/patch-rkward_rbackend_rembedinternal.cpp @@ -1,5 +1,5 @@ ---- ./rkward/rbackend/rembedinternal.cpp.orig 2008-04-10 15:19:08.000000000 +0200 -+++ ./rkward/rbackend/rembedinternal.cpp 2009-01-21 10:27:25.000000000 +0100 +--- rkward/rbackend/rembedinternal.cpp.orig 2008-04-10 09:19:08.000000000 -0400 ++++ rkward/rbackend/rembedinternal.cpp 2013-05-28 07:06:41.000000000 -0400 @@ -87,7 +87,9 @@ #include "R.h" #include "Rinternals.h" @@ -11,3 +11,29 @@ #include "R_ext/Parse.h" #ifdef R_2_4 +@@ -118,7 +120,9 @@ + + // some functions we need that are not declared + extern int Rf_initEmbeddedR(int argc, char **argv); ++#if (R_VERSION < R_Version(3,0,0)) + extern void Rf_PrintWarnings (void); ++#endif + extern int R_interrupts_pending; + #ifdef R_2_3 + extern int Rf_initialize_R(int ac, char **av); +@@ -839,6 +843,7 @@ + + UNPROTECT(1); /* pr */ + ++#if (R_VERSION < R_Version(3,0,0)) + // for safety, let's protect exp for the two print calls below. + // TODO: this is not good. It causes an additional PROTECT and UPROTECT. Need to (re-)move printing + PROTECT (exp); +@@ -849,6 +854,7 @@ + Rf_PrintWarnings (); + + UNPROTECT (1); // exp; We unprotect this, as most of the time the caller is not really interested in the result ++#endif + return exp; + } + diff --git a/math/rkward/files/patch-rkward_rbackend_rpackages_Makefile.in b/math/rkward/files/patch-rkward_rbackend_rpackages_Makefile.in new file mode 100644 index 000000000000..aa178d77df0f --- /dev/null +++ b/math/rkward/files/patch-rkward_rbackend_rpackages_Makefile.in @@ -0,0 +1,11 @@ +--- rkward/rbackend/rpackages/Makefile.in.orig 2008-04-20 14:56:59.000000000 -0400 ++++ rkward/rbackend/rpackages/Makefile.in 2013-05-28 09:56:00.000000000 -0400 +@@ -651,7 +651,7 @@ + OLDTMP=$$TMPDIR ; \ + export TMPDIR=`pwd`/tmp ; \ + mkdir -p $(DESTDIR)/$(R_LIBDIR) ; \ +- ${R_HOMEDIR}/bin/R CMD INSTALL -l $(DESTDIR)/$(R_LIBDIR) rkward ; \ ++ ${R_HOMEDIR}/bin/R CMD INSTALL -l $(DESTDIR)/$(R_LIBDIR) rkward_*.tar.gz ; \ + export TMPDIR=$$OLDTMP + uninstall: + -${R_HOMEDIR}/bin/R CMD REMOVE -l $(DESTDIR)/$(R_LIBDIR) rkward diff --git a/math/rkward/pkg-plist b/math/rkward/pkg-plist index 9104b17e4046..509516abfa1e 100644 --- a/math/rkward/pkg-plist +++ b/math/rkward/pkg-plist @@ -478,6 +478,7 @@ lib/R/library/rkward/NAMESPACE lib/R/library/rkward/Meta/Rd.rds lib/R/library/rkward/Meta/hsearch.rds lib/R/library/rkward/Meta/links.rds +lib/R/library/rkward/Meta/nsInfo.rds lib/R/library/rkward/Meta/package.rds lib/R/library/rkward/R/rkward lib/R/library/rkward/R/rkward.rdb diff --git a/math/rpy/Makefile b/math/rpy/Makefile index 2fb09b182c96..4f39edb33555 100644 --- a/math/rpy/Makefile +++ b/math/rpy/Makefile @@ -3,7 +3,7 @@ PORTNAME= rpy PORTVERSION= 1.0.3 -PORTREVISION= 27 +PORTREVISION= 28 CATEGORIES= math MASTER_SITES= SF @@ -24,7 +24,7 @@ LDFLAGS+= -L${LOCALBASE}/lib/R/modules -L${LOCALBASE}/lib/R/lib post-patch: @${REINPLACE_CMD} -e 's,^statichere ,,' ${WRKSRC}/src/rpymodule.c - @${REINPLACE_CMD} -e 's|%%LOCALBASE%%|${LOCALBASE}|g' ${WRKSRC}/setup.py + @${REINPLACE_CMD} -e 's|/usr/share|${LOCALBASE}/lib|' ${WRKSRC}/setup.py pre-configure: @(if [ ! -e ${LOCALBASE}/lib/R/lib/libR.so ] ; then \ diff --git a/math/rpy/files/patch-rpy.py b/math/rpy/files/patch-rpy.py new file mode 100644 index 000000000000..32d3b25f1b8a --- /dev/null +++ b/math/rpy/files/patch-rpy.py @@ -0,0 +1,12 @@ +--- rpy.py ++++ rpy.py +@@ -139,6 +139,7 @@ if VERBOSE: + + # Version + from rpy_version import rpy_version ++__version__ = rpy_version + + # Symbolic names for conversion modes + TOP_CONVERSION = 4 +diff --git rpy_tools.py rpy_tools.py +index f312201..6e83321 100644 diff --git a/math/rpy/files/patch-rpy_tools.py b/math/rpy/files/patch-rpy_tools.py index 09f166003c77..3371df201690 100644 --- a/math/rpy/files/patch-rpy_tools.py +++ b/math/rpy/files/patch-rpy_tools.py @@ -1,13 +1,35 @@ ---- rpy_tools.py.orig 2009-12-29 09:42:02.000000000 +0800 -+++ rpy_tools.py 2009-12-29 09:42:41.000000000 +0800 -@@ -97,8 +97,8 @@ +--- rpy_tools.py ++++ rpy_tools.py +@@ -97,8 +97,7 @@ def get_R_VERSION(RHOME=None, force_exec=False): if stat or len(output)<=0: raise RuntimeError("Couldn't execute the R interpreter" + " `%s'.\n" % rexec ) - # edd 05 Apr 2006 version = re.search("R +([0-9]\.[0-9]\.[0-9])", output) - version = re.search(" +([0-9]\.[0-9]\.[0-9])", output) -+ # edd 05 Apr 2006 version = re.search("R +([0-9]\.[0-9][0-9]\.[0-9])", output) -+ version = re.search(" +([0-9]\.[0-9][0-9]\.[0-9])", output) ++ version = re.search(" +([0-9]+\.[0-9]+\.[0-9]+)", output) if not version: raise RuntimeError("Couldn't obtain version number from output\n" "of `R --version'.\n") +@@ -143,3 +142,20 @@ def get_PYTHON_DIR(): + % PYTHON_DIR ) + + return PYTHON_DIR ++ ++def get_R_LAPACK_LIB_FLAGS(RHOME=get_R_HOME()): ++ """ ++ Determine the necessary link arguments for lapack ++ """ ++ rexec = os.path.join(RHOME, 'bin', 'R') ++ stat, output = getstatusoutput('"%s" CMD config LAPACK_LIBS' % rexec ) ++ if stat or len(output)<=0: ++ raise RuntimeError("Couldn't execute the R interpreter" + ++ " `%s'.\n" % rexec ) ++ ++ LAPACK_LIB_FLAGS = output.strip() ++ if not LAPACK_LIB_FLAGS: ++ raise RuntimeError("Couldn't obtain LAPACK_LIBS information from output\n" ++ "of `R CMD config LAPACK_LIBS'.\n") ++ ++ return LAPACK_LIB_FLAGS +diff --git setup.py setup.py +index cf0fa2e..4a1f840 100644 diff --git a/math/rpy/files/patch-setup.py b/math/rpy/files/patch-setup.py index 6cc97c1af08f..caeba282d087 100644 --- a/math/rpy/files/patch-setup.py +++ b/math/rpy/files/patch-setup.py @@ -1,13 +1,60 @@ ---- setup.py.orig 2008-07-29 22:53:21.000000000 +0200 -+++ setup.py 2008-07-29 22:54:04.000000000 +0200 -@@ -159,8 +159,8 @@ - source_files = source_files + ["src/setenv.c"] +--- setup.py ++++ setup.py +@@ -30,13 +30,14 @@ can be used for each of these R versions. + See the files INSTALL.UNIX and INSTALL.WINDOWS for more details. + """ + +-DEBUG=True ++DEBUG=False + + import os, os.path, sys, shutil, re + from distutils.core import setup, Extension + from distutils.sysconfig import * + from distutils.errors import * + import rpy_tools ++ + if sys.platform=="win32": + import rpy_wintools + +@@ -85,7 +86,7 @@ for RHOME in RHOMES: + get_config_vars()['OPT'] = '-g -Wall' + else: + # to avoid strict prototypes errors from R includes +- get_config_vars()['OPT'] = '-DNDEBUG -g -O3 -Wall' ++ get_config_vars()['OPT'] = '-DNDEBUG -O3 -Wall' + + # get the Python version + if sys.version[:3] >= '2.2': +@@ -149,22 +150,21 @@ for RHOME in RHOMES: + library_dirs= r_libs + runtime_libs = r_libs + extra_compile_args=[] +- elif sys.platform=='osf1V5': +- include_dirs = [ os.path.join(RHOME.strip(), 'include'), +- 'src' ] +- libraries=['R','Rlapack'] +- library_dirs = r_libs +- runtime_libs = r_libs +- extra_compile_args=["-shared"] +- source_files = source_files + ["src/setenv.c"] ++ else: # unix-like systems, this is known to work for Linux and Solaris include_dirs = [ os.path.join(RHOME.strip(), 'include'), -- 'src', '/usr/share/R/include' ] + 'src', '/usr/share/R/include' ] - libraries=['R','Rlapack'] -+ 'src', '%%LOCALBASE%%/lib/R/include' ] -+ libraries=['R','R'] ++ library_dirs = r_libs runtime_libs = r_libs extra_compile_args=["-shared"] + source_files = source_files + ["src/setenv.c"] ++ ++ libraries=['R'] ++ ++ # Ask R to tell us how to properly link against lapack ++ extra_compile_args += [ rpy_tools.get_R_LAPACK_LIB_FLAGS( RHOME ) ] ++ + + # Discover which array packages are present + try: +diff --git src/RPy.h src/RPy.h +index 04faf3d..614ae5a 100644 diff --git a/math/rpy/files/patch-src-RPy.h b/math/rpy/files/patch-src-RPy.h index 333d43f91776..a795ee3d31c1 100644 --- a/math/rpy/files/patch-src-RPy.h +++ b/math/rpy/files/patch-src-RPy.h @@ -1,6 +1,20 @@ ---- src/RPy.h.orig 2008-12-17 16:53:19.000000000 +0800 -+++ src/RPy.h 2008-12-17 16:53:35.000000000 +0800 -@@ -74,7 +74,7 @@ +--- src/RPy.h ++++ src/RPy.h +@@ -52,6 +52,13 @@ + #include <Rdefines.h> + #include <Rinternals.h> + #include <Rversion.h> ++ ++#if (R_VERSION >= R_Version(2,4,0)) ++#include <Rembedded.h> ++#endif ++ ++ ++ + #undef _POSIX_C_SOURCE + #include <Python.h> + #include <R_ext/Rdynload.h> +@@ -74,7 +81,7 @@ # endif #endif /* _WIN32 */ @@ -9,3 +23,5 @@ /* Missing definitions from Rinterface.h or RStartup.h */ +diff --git src/io.c src/io.c +index 6c7c31d..cb10259 100644 diff --git a/math/rpy/files/patch-src-io.c b/math/rpy/files/patch-src-io.c new file mode 100644 index 000000000000..dc09967eb6a3 --- /dev/null +++ b/math/rpy/files/patch-src-io.c @@ -0,0 +1,13 @@ +--- src/io.c ++++ src/io.c +@@ -130,7 +130,7 @@ RPy_ReadConsole(char *prompt, + PyErr_Clear(); + return 0; + } +- snprintf(buf, len, "%s", PyString_AsString(input_data)); ++ snprintf( (char*) buf, len, "%s", PyString_AsString(input_data)); + Py_DECREF(input_data); + return 1; + } +diff --git src/rpymodule.c src/rpymodule.c +index fe8b39f..fda1881 100644 diff --git a/math/rpy/files/patch-src-rpymodule.c b/math/rpy/files/patch-src-rpymodule.c new file mode 100644 index 000000000000..09f47bfb3271 --- /dev/null +++ b/math/rpy/files/patch-src-rpymodule.c @@ -0,0 +1,13 @@ +--- src/rpymodule.c ++++ src/rpymodule.c +@@ -1772,8 +1772,10 @@ start_events(void) + + void r_finalize(void) + { ++#if (R_VERSION < R_Version(2,4,0)) + unsigned char buf[1024]; + char * tmpdir; ++#endif + + R_dot_Last(); + R_RunExitFinalizers(); diff --git a/math/rpy/pkg-plist b/math/rpy/pkg-plist index 2e3ef74a3e8e..f3524efa7caf 100644 --- a/math/rpy/pkg-plist +++ b/math/rpy/pkg-plist @@ -1,4 +1,4 @@ -%%PYTHON_SITELIBDIR%%/_rpy2153.so +%%PYTHON_SITELIBDIR%%/_rpy3001.so %%PYTHON_SITELIBDIR%%/rpy.py %%PYTHON_SITELIBDIR%%/rpy.pyc %%PYTHON_SITELIBDIR%%/rpy.pyo diff --git a/math/rpy2/Makefile b/math/rpy2/Makefile index 072e45d20cb0..edd3d0bc3b96 100644 --- a/math/rpy2/Makefile +++ b/math/rpy2/Makefile @@ -3,7 +3,7 @@ PORTNAME= rpy2 PORTVERSION= 2.2.6 -PORTREVISION= 5 +PORTREVISION= 6 CATEGORIES= math MASTER_SITES= CHEESESHOP \ SF diff --git a/net/R-cran-twitteR/Makefile b/net/R-cran-twitteR/Makefile index 381e358560a3..ecca5fa17c05 100644 --- a/net/R-cran-twitteR/Makefile +++ b/net/R-cran-twitteR/Makefile @@ -3,6 +3,7 @@ PORTNAME= twitteR PORTVERSION= 1.1.6 +PORTREVISION= 1 CATEGORIES= net DISTNAME= ${PORTNAME}_${PORTVERSION} diff --git a/science/R-cran-AMORE/Makefile b/science/R-cran-AMORE/Makefile index 35d06ac5bffc..10b3a96ff70b 100644 --- a/science/R-cran-AMORE/Makefile +++ b/science/R-cran-AMORE/Makefile @@ -3,7 +3,7 @@ PORTNAME= AMORE PORTVERSION= 0.2.12 -PORTREVISION= 10 +PORTREVISION= 11 CATEGORIES= science DISTNAME= ${PORTNAME}_${PORTVERSION:C/\./-/g:C/-/\./1} diff --git a/science/R-cran-DCluster/Makefile b/science/R-cran-DCluster/Makefile index 3fd28f506c79..15b9c98d4d73 100644 --- a/science/R-cran-DCluster/Makefile +++ b/science/R-cran-DCluster/Makefile @@ -3,7 +3,7 @@ PORTNAME= DCluster DISTVERSION= 0.2-6 -PORTREVISION= 1 +PORTREVISION= 2 CATEGORIES= science DISTNAME= ${PORTNAME}_${DISTVERSION} diff --git a/science/R-cran-Epi/Makefile b/science/R-cran-Epi/Makefile index f8b3c6bb78fc..f5ea6a36a0b1 100644 --- a/science/R-cran-Epi/Makefile +++ b/science/R-cran-Epi/Makefile @@ -3,6 +3,7 @@ PORTNAME= Epi PORTVERSION= 1.1.49 +PORTREVISION= 1 CATEGORIES= science DISTNAME= ${PORTNAME}_${PORTVERSION} diff --git a/science/R-cran-bayesm/Makefile b/science/R-cran-bayesm/Makefile index 2dad766a265b..26164cdb0b45 100644 --- a/science/R-cran-bayesm/Makefile +++ b/science/R-cran-bayesm/Makefile @@ -3,7 +3,7 @@ PORTNAME= bayesm PORTVERSION= 2.2.4 -PORTREVISION= 10 +PORTREVISION= 11 CATEGORIES= science DISTNAME= ${PORTNAME}_${PORTVERSION:C/\./-/g:C/-/\./1} diff --git a/science/R-cran-e1071/Makefile b/science/R-cran-e1071/Makefile index 766a7a8bf2fa..dc7efef819e9 100644 --- a/science/R-cran-e1071/Makefile +++ b/science/R-cran-e1071/Makefile @@ -3,7 +3,7 @@ PORTNAME= e1071 DISTVERSION= 1.6-1 -PORTREVISION= 2 +PORTREVISION= 3 CATEGORIES= science DISTNAME= ${PORTNAME}_${DISTVERSION} diff --git a/science/R-cran-eco/Makefile b/science/R-cran-eco/Makefile index 4bffa271945f..d974f1f0105e 100644 --- a/science/R-cran-eco/Makefile +++ b/science/R-cran-eco/Makefile @@ -3,6 +3,7 @@ PORTNAME= eco PORTVERSION= 3.1.6 +PORTREVISION= 1 CATEGORIES= science DISTNAME= ${PORTNAME}_${PORTVERSION:C/\./-/g:C/-/\./1} diff --git a/science/R-cran-epicalc/Makefile b/science/R-cran-epicalc/Makefile index 24fc398a8986..5ef562f5eafe 100644 --- a/science/R-cran-epicalc/Makefile +++ b/science/R-cran-epicalc/Makefile @@ -3,7 +3,7 @@ PORTNAME= epicalc PORTVERSION= 2.15.1.0 -PORTREVISION= 2 +PORTREVISION= 3 CATEGORIES= science DISTNAME= ${PORTNAME}_${PORTVERSION} diff --git a/science/R-cran-snow/Makefile b/science/R-cran-snow/Makefile index 876ad86ec6ac..618c0e1d20b8 100644 --- a/science/R-cran-snow/Makefile +++ b/science/R-cran-snow/Makefile @@ -3,6 +3,7 @@ PORTNAME= snow DISTVERSION= 0.3-12 +PORTREVISION= 1 CATEGORIES= science DISTNAME= ${PORTNAME}_${DISTVERSION} diff --git a/science/R-cran-som/Makefile b/science/R-cran-som/Makefile index 9d0dbbe298bc..27e69662881b 100644 --- a/science/R-cran-som/Makefile +++ b/science/R-cran-som/Makefile @@ -3,7 +3,7 @@ PORTNAME= som DISTVERSION= 0.3-5 -PORTREVISION= 4 +PORTREVISION= 5 CATEGORIES= science DISTNAME= ${PORTNAME}_${DISTVERSION} diff --git a/science/afni/Makefile b/science/afni/Makefile index 1343a5ef859c..e490f4aee4ee 100644 --- a/science/afni/Makefile +++ b/science/afni/Makefile @@ -11,7 +11,7 @@ PORTNAME= afni PORTVERSION= 2012.04.17.2129 -PORTREVISION= 3 +PORTREVISION= 4 CATEGORIES= science biology graphics MASTER_SITES= http://personalpages.tds.net/~jwbacon/Ports/distfiles/AFNI/${PORTVERSION}/ \ http://www.acadix.biz/Ports/distfiles/AFNI/${PORTVERSION}/ diff --git a/security/R-cran-ROAuth/Makefile b/security/R-cran-ROAuth/Makefile index 0eada5323f10..da9cb9a0934b 100644 --- a/security/R-cran-ROAuth/Makefile +++ b/security/R-cran-ROAuth/Makefile @@ -3,6 +3,7 @@ PORTNAME= ROAuth PORTVERSION= 0.9.3 +PORTREVISION= 1 CATEGORIES= security DISTNAME= ${PORTNAME}_${PORTVERSION} diff --git a/security/R-cran-digest/Makefile b/security/R-cran-digest/Makefile index d7945c727c97..0d272c4a2aaf 100644 --- a/security/R-cran-digest/Makefile +++ b/security/R-cran-digest/Makefile @@ -3,7 +3,7 @@ PORTNAME= digest PORTVERSION= 0.6.3 -PORTREVISION= 1 +PORTREVISION= 2 CATEGORIES= security DISTNAME= ${PORTNAME}_${PORTVERSION} diff --git a/textproc/R-cran-R2HTML/Makefile b/textproc/R-cran-R2HTML/Makefile index ea00b8c75746..7c67cf69fdc2 100644 --- a/textproc/R-cran-R2HTML/Makefile +++ b/textproc/R-cran-R2HTML/Makefile @@ -3,6 +3,7 @@ PORTNAME= R2HTML PORTVERSION= 2.2.1 +PORTREVISION= 1 CATEGORIES= textproc DISTNAME= ${PORTNAME}_${PORTVERSION} diff --git a/textproc/R-cran-XML/Makefile b/textproc/R-cran-XML/Makefile index 71dc6d3f5a07..044f5640e110 100644 --- a/textproc/R-cran-XML/Makefile +++ b/textproc/R-cran-XML/Makefile @@ -3,6 +3,7 @@ PORTNAME= XML DISTVERSION= 3.96-1.1 +PORTREVISION= 1 CATEGORIES= textproc DISTNAME= ${PORTNAME}_${DISTVERSION} diff --git a/textproc/R-cran-stringr/Makefile b/textproc/R-cran-stringr/Makefile index e13e60f6d854..13b4e3371582 100644 --- a/textproc/R-cran-stringr/Makefile +++ b/textproc/R-cran-stringr/Makefile @@ -3,7 +3,7 @@ PORTNAME= stringr PORTVERSION= 0.6.2 -PORTREVISION= 2 +PORTREVISION= 3 CATEGORIES= textproc DISTNAME= ${PORTNAME}_${PORTVERSION} diff --git a/textproc/R-cran-xtable/Makefile b/textproc/R-cran-xtable/Makefile index 9481dc205a2d..db3599e65340 100644 --- a/textproc/R-cran-xtable/Makefile +++ b/textproc/R-cran-xtable/Makefile @@ -3,7 +3,7 @@ PORTNAME= xtable DISTVERSION= 1.7-1 -PORTREVISION= 1 +PORTREVISION= 2 CATEGORIES= textproc DISTNAME= ${PORTNAME}_${DISTVERSION} diff --git a/www/R-cran-RgoogleMaps/Makefile b/www/R-cran-RgoogleMaps/Makefile index 00735e807723..d5cdab7d4aa0 100644 --- a/www/R-cran-RgoogleMaps/Makefile +++ b/www/R-cran-RgoogleMaps/Makefile @@ -3,6 +3,7 @@ PORTNAME= RgoogleMaps PORTVERSION= 1.2.0.3 +PORTREVISION= 1 CATEGORIES= www DISTNAME= ${PORTNAME}_${PORTVERSION} diff --git a/www/R-cran-Rpad/Makefile b/www/R-cran-Rpad/Makefile index 3dedaa0e2c06..121831b628fa 100644 --- a/www/R-cran-Rpad/Makefile +++ b/www/R-cran-Rpad/Makefile @@ -3,7 +3,7 @@ PORTNAME= Rpad PORTVERSION= 1.3.0 -PORTREVISION= 8 +PORTREVISION= 9 CATEGORIES= www DISTNAME= ${PORTNAME}_${PORTVERSION} diff --git a/www/R-cran-httpuv/Makefile b/www/R-cran-httpuv/Makefile index 3e4469581c41..4f7eb87fd3fc 100644 --- a/www/R-cran-httpuv/Makefile +++ b/www/R-cran-httpuv/Makefile @@ -3,6 +3,7 @@ PORTNAME= httpuv PORTVERSION= 1.0.5 +PORTREVISION= 1 CATEGORIES= www DISTNAME= ${PORTNAME}_${PORTVERSION} diff --git a/www/R-cran-scrapeR/Makefile b/www/R-cran-scrapeR/Makefile index fbc615bf63d3..f98935dd0f1d 100644 --- a/www/R-cran-scrapeR/Makefile +++ b/www/R-cran-scrapeR/Makefile @@ -3,7 +3,7 @@ PORTNAME= scrapeR PORTVERSION= 0.1.6 -PORTREVISION= 8 +PORTREVISION= 9 CATEGORIES= www DISTNAME= ${PORTNAME}_${PORTVERSION} diff --git a/www/R-cran-shiny/Makefile b/www/R-cran-shiny/Makefile index c7a0e4cb0add..ce63f2280d77 100644 --- a/www/R-cran-shiny/Makefile +++ b/www/R-cran-shiny/Makefile @@ -3,7 +3,7 @@ PORTNAME= shiny PORTVERSION= 0.5.0 -PORTREVISION= 1 +PORTREVISION= 2 CATEGORIES= www DISTNAME= ${PORTNAME}_${PORTVERSION} |