Wednesday, August 03, 2022

UPDATE: math/R

Dear useRs,
Dear Brian,

update math/R 4.1.2 -> 4.2.1

- Sync math/rstudio patch as SO_VERSION is bumped (symbols added and removed)

- There is now a (multiple) warning in the build:

Warning message:
In normalizePath("~") :
path[1]="/R-4.2.1_writes_to_HOME": No such file or directory

The cause is likely that the _pbuild user has its home directory set
to /nonexistent. It tried to manually set HOME="$WRKDIR" in
CONFIGURE_ENV and MAKE_ENV but without success (either not picked up
or makes no difference).

However, R runs fine for me and I could not identify any problems
later on. So I did not investigate further.

OK?

Best regards,
Ingo

Index: R/Makefile
===================================================================
RCS file: /cvs/ports/math/R/Makefile,v
retrieving revision 1.126
diff -u -p -r1.126 Makefile
--- R/Makefile 25 Jul 2022 06:11:05 -0000 1.126
+++ R/Makefile 3 Aug 2022 11:49:55 -0000
@@ -1,9 +1,9 @@
COMMENT= powerful math/statistics/graphics language
-DISTNAME= R-4.1.2
+DISTNAME= R-4.2.1

# When bumping SO_VERSION, adjust
# math/rstudio/patches/patch-src_cpp_core_r_util_REnvironmentPosix_cpp
-SO_VERSION= 38.0
+SO_VERSION= 39.0
.for _lib in R Rblas Rlapack
SHARED_LIBS += ${_lib} ${SO_VERSION}
.endfor
Index: R/distinfo
===================================================================
RCS file: /cvs/ports/math/R/distinfo,v
retrieving revision 1.55
diff -u -p -r1.55 distinfo
--- R/distinfo 4 Nov 2021 07:57:06 -0000 1.55
+++ R/distinfo 3 Aug 2022 11:49:55 -0000
@@ -1,2 +1,2 @@
-SHA256 (R-4.1.2.tar.gz) = IDYiXp9yB9TOCX5Ulyrs2qi0DX2ZEc0mSR+sWg+rOK8=
-SIZE (R-4.1.2.tar.gz) = 34009074
+SHA256 (R-4.2.1.tar.gz) = TVLbSG0nhI5UYT1O6XetlS7AjOF4B+G1JbEM1ENsZD8=
+SIZE (R-4.2.1.tar.gz) = 37601544
Index: R/pkg/PLIST
===================================================================
RCS file: /cvs/ports/math/R/pkg/PLIST,v
retrieving revision 1.50
diff -u -p -r1.50 PLIST
--- R/pkg/PLIST 11 Mar 2022 19:36:11 -0000 1.50
+++ R/pkg/PLIST 3 Aug 2022 11:49:56 -0000
@@ -62,7 +62,6 @@ lib/R/include/R_ext/Parse.h
lib/R/include/R_ext/Print.h
lib/R/include/R_ext/PrtUtil.h
lib/R/include/R_ext/QuartzDevice.h
-lib/R/include/R_ext/R-ftp-http.h
lib/R/include/R_ext/RS.h
lib/R/include/R_ext/RStartup.h
lib/R/include/R_ext/Rallocators.h
@@ -82,7 +81,6 @@ lib/R/include/Rinterface.h
lib/R/include/Rinternals.h
lib/R/include/Rmath.h
lib/R/include/Rversion.h
-lib/R/include/S.h
lib/R/lib/
@lib lib/R/lib/libR.so.${LIBR_VERSION}
@lib lib/R/lib/libRblas.so.${LIBRblas_VERSION}
@@ -1023,10 +1021,6 @@ lib/R/library/mgcv/po/fr/
lib/R/library/mgcv/po/fr/LC_MESSAGES/
lib/R/library/mgcv/po/fr/LC_MESSAGES/R-mgcv.mo
lib/R/library/mgcv/po/fr/LC_MESSAGES/mgcv.mo
-lib/R/library/mgcv/po/it/
-lib/R/library/mgcv/po/it/LC_MESSAGES/
-lib/R/library/mgcv/po/it/LC_MESSAGES/R-mgcv.mo
-lib/R/library/mgcv/po/it/LC_MESSAGES/mgcv.mo
lib/R/library/mgcv/po/ko/
lib/R/library/mgcv/po/ko/LC_MESSAGES/
lib/R/library/mgcv/po/ko/LC_MESSAGES/R-mgcv.mo
@@ -1039,7 +1033,6 @@ lib/R/library/nlme/
lib/R/library/nlme/CITATION
lib/R/library/nlme/DESCRIPTION
lib/R/library/nlme/INDEX
-lib/R/library/nlme/LICENCE
lib/R/library/nlme/Meta/
lib/R/library/nlme/Meta/Rd.rds
lib/R/library/nlme/Meta/data.rds
@@ -1774,9 +1767,13 @@ lib/R/library/translations/lt/LC_MESSAGE
lib/R/library/translations/lt/LC_MESSAGES/R-grDevices.mo
lib/R/library/translations/lt/LC_MESSAGES/R-graphics.mo
lib/R/library/translations/lt/LC_MESSAGES/R-grid.mo
+lib/R/library/translations/lt/LC_MESSAGES/R-methods.mo
lib/R/library/translations/lt/LC_MESSAGES/R-parallel.mo
+lib/R/library/translations/lt/LC_MESSAGES/R-splines.mo
+lib/R/library/translations/lt/LC_MESSAGES/R-stats.mo
lib/R/library/translations/lt/LC_MESSAGES/R-stats4.mo
lib/R/library/translations/lt/LC_MESSAGES/R-tcltk.mo
+lib/R/library/translations/lt/LC_MESSAGES/R-tools.mo
lib/R/library/translations/lt/LC_MESSAGES/R-utils.mo
lib/R/library/translations/lt/LC_MESSAGES/R.mo
lib/R/library/translations/lt/LC_MESSAGES/RGui.mo
@@ -1788,6 +1785,7 @@ lib/R/library/translations/lt/LC_MESSAGE
lib/R/library/translations/lt/LC_MESSAGES/splines.mo
lib/R/library/translations/lt/LC_MESSAGES/stats.mo
lib/R/library/translations/lt/LC_MESSAGES/tcltk.mo
+lib/R/library/translations/lt/LC_MESSAGES/tools.mo
lib/R/library/translations/lt/LC_MESSAGES/utils.mo
lib/R/library/translations/nn/
lib/R/library/translations/nn/LC_MESSAGES/
@@ -1916,11 +1914,13 @@ lib/R/library/translations/zh_TW/LC_MESS
lib/R/library/translations/zh_TW/LC_MESSAGES/R-grDevices.mo
lib/R/library/translations/zh_TW/LC_MESSAGES/R-graphics.mo
lib/R/library/translations/zh_TW/LC_MESSAGES/R-grid.mo
+lib/R/library/translations/zh_TW/LC_MESSAGES/R-methods.mo
lib/R/library/translations/zh_TW/LC_MESSAGES/R-parallel.mo
lib/R/library/translations/zh_TW/LC_MESSAGES/R-splines.mo
lib/R/library/translations/zh_TW/LC_MESSAGES/R-stats.mo
lib/R/library/translations/zh_TW/LC_MESSAGES/R-stats4.mo
lib/R/library/translations/zh_TW/LC_MESSAGES/R-tcltk.mo
+lib/R/library/translations/zh_TW/LC_MESSAGES/R-tools.mo
lib/R/library/translations/zh_TW/LC_MESSAGES/R-utils.mo
lib/R/library/translations/zh_TW/LC_MESSAGES/R.mo
lib/R/library/translations/zh_TW/LC_MESSAGES/RGui.mo
@@ -2057,10 +2057,80 @@ share/doc/R/html/SearchOn.html
share/doc/R/html/about.html
share/doc/R/html/favicon.ico
share/doc/R/html/index.html
+share/doc/R/html/katex/
+share/doc/R/html/katex-config.js
+share/doc/R/html/katex/LICENSE
+share/doc/R/html/katex/README.md
+share/doc/R/html/katex/fonts/
+share/doc/R/html/katex/fonts/KaTeX_AMS-Regular.ttf
+share/doc/R/html/katex/fonts/KaTeX_AMS-Regular.woff
+share/doc/R/html/katex/fonts/KaTeX_AMS-Regular.woff2
+share/doc/R/html/katex/fonts/KaTeX_Caligraphic-Bold.ttf
+share/doc/R/html/katex/fonts/KaTeX_Caligraphic-Bold.woff
+share/doc/R/html/katex/fonts/KaTeX_Caligraphic-Bold.woff2
+share/doc/R/html/katex/fonts/KaTeX_Caligraphic-Regular.ttf
+share/doc/R/html/katex/fonts/KaTeX_Caligraphic-Regular.woff
+share/doc/R/html/katex/fonts/KaTeX_Caligraphic-Regular.woff2
+share/doc/R/html/katex/fonts/KaTeX_Fraktur-Bold.ttf
+share/doc/R/html/katex/fonts/KaTeX_Fraktur-Bold.woff
+share/doc/R/html/katex/fonts/KaTeX_Fraktur-Bold.woff2
+share/doc/R/html/katex/fonts/KaTeX_Fraktur-Regular.ttf
+share/doc/R/html/katex/fonts/KaTeX_Fraktur-Regular.woff
+share/doc/R/html/katex/fonts/KaTeX_Fraktur-Regular.woff2
+share/doc/R/html/katex/fonts/KaTeX_Main-Bold.ttf
+share/doc/R/html/katex/fonts/KaTeX_Main-Bold.woff
+share/doc/R/html/katex/fonts/KaTeX_Main-Bold.woff2
+share/doc/R/html/katex/fonts/KaTeX_Main-BoldItalic.ttf
+share/doc/R/html/katex/fonts/KaTeX_Main-BoldItalic.woff
+share/doc/R/html/katex/fonts/KaTeX_Main-BoldItalic.woff2
+share/doc/R/html/katex/fonts/KaTeX_Main-Italic.ttf
+share/doc/R/html/katex/fonts/KaTeX_Main-Italic.woff
+share/doc/R/html/katex/fonts/KaTeX_Main-Italic.woff2
+share/doc/R/html/katex/fonts/KaTeX_Main-Regular.ttf
+share/doc/R/html/katex/fonts/KaTeX_Main-Regular.woff
+share/doc/R/html/katex/fonts/KaTeX_Main-Regular.woff2
+share/doc/R/html/katex/fonts/KaTeX_Math-BoldItalic.ttf
+share/doc/R/html/katex/fonts/KaTeX_Math-BoldItalic.woff
+share/doc/R/html/katex/fonts/KaTeX_Math-BoldItalic.woff2
+share/doc/R/html/katex/fonts/KaTeX_Math-Italic.ttf
+share/doc/R/html/katex/fonts/KaTeX_Math-Italic.woff
+share/doc/R/html/katex/fonts/KaTeX_Math-Italic.woff2
+share/doc/R/html/katex/fonts/KaTeX_SansSerif-Bold.ttf
+share/doc/R/html/katex/fonts/KaTeX_SansSerif-Bold.woff
+share/doc/R/html/katex/fonts/KaTeX_SansSerif-Bold.woff2
+share/doc/R/html/katex/fonts/KaTeX_SansSerif-Italic.ttf
+share/doc/R/html/katex/fonts/KaTeX_SansSerif-Italic.woff
+share/doc/R/html/katex/fonts/KaTeX_SansSerif-Italic.woff2
+share/doc/R/html/katex/fonts/KaTeX_SansSerif-Regular.ttf
+share/doc/R/html/katex/fonts/KaTeX_SansSerif-Regular.woff
+share/doc/R/html/katex/fonts/KaTeX_SansSerif-Regular.woff2
+share/doc/R/html/katex/fonts/KaTeX_Script-Regular.ttf
+share/doc/R/html/katex/fonts/KaTeX_Script-Regular.woff
+share/doc/R/html/katex/fonts/KaTeX_Script-Regular.woff2
+share/doc/R/html/katex/fonts/KaTeX_Size1-Regular.ttf
+share/doc/R/html/katex/fonts/KaTeX_Size1-Regular.woff
+share/doc/R/html/katex/fonts/KaTeX_Size1-Regular.woff2
+share/doc/R/html/katex/fonts/KaTeX_Size2-Regular.ttf
+share/doc/R/html/katex/fonts/KaTeX_Size2-Regular.woff
+share/doc/R/html/katex/fonts/KaTeX_Size2-Regular.woff2
+share/doc/R/html/katex/fonts/KaTeX_Size3-Regular.ttf
+share/doc/R/html/katex/fonts/KaTeX_Size3-Regular.woff
+share/doc/R/html/katex/fonts/KaTeX_Size3-Regular.woff2
+share/doc/R/html/katex/fonts/KaTeX_Size4-Regular.ttf
+share/doc/R/html/katex/fonts/KaTeX_Size4-Regular.woff
+share/doc/R/html/katex/fonts/KaTeX_Size4-Regular.woff2
+share/doc/R/html/katex/fonts/KaTeX_Typewriter-Regular.ttf
+share/doc/R/html/katex/fonts/KaTeX_Typewriter-Regular.woff
+share/doc/R/html/katex/fonts/KaTeX_Typewriter-Regular.woff2
+share/doc/R/html/katex/katex.css
+share/doc/R/html/katex/katex.js
share/doc/R/html/left.jpg
share/doc/R/html/logo.jpg
+share/doc/R/html/mathjax-config.js
share/doc/R/html/packages-head-utf8.html
share/doc/R/html/packages.html
+share/doc/R/html/prism.css
+share/doc/R/html/prism.js
share/doc/R/html/resources.html
share/doc/R/html/right.jpg
share/doc/R/html/up.jpg
@@ -2090,9 +2160,5 @@ share/texmf-local/tex/latex/
share/texmf-local/tex/latex/Rd.sty
share/texmf-local/tex/latex/Sweave.sty
share/texmf-local/tex/latex/jss.cls
-share/texmf-local/tex/latex/omsaer.fd
-share/texmf-local/tex/latex/omsaett.fd
share/texmf-local/tex/latex/omscmtt.fd
-share/texmf-local/tex/latex/ts1aer.fd
-share/texmf-local/tex/latex/ts1aett.fd
@tag mktexlsr-local
Index: rstudio/Makefile
===================================================================
RCS file: /cvs/ports/math/rstudio/Makefile,v
retrieving revision 1.10
diff -u -p -r1.10 Makefile
--- rstudio/Makefile 14 Jul 2022 02:02:48 -0000 1.10
+++ rstudio/Makefile 3 Aug 2022 11:49:57 -0000
@@ -10,7 +10,7 @@ ONLY_FOR_ARCHS = ${LP64_ARCHS}
V = 1.3.959
COMMENT = Integrated Development Environment (IDE) for R
PKGNAME = rstudio-${V}
-REVISION = 6
+REVISION = 7
CATEGORIES = math x11

HOMEPAGE = https://www.rstudio.com/
Index: rstudio/patches/patch-src_cpp_core_r_util_REnvironmentPosix_cpp
===================================================================
RCS file: /cvs/ports/math/rstudio/patches/patch-src_cpp_core_r_util_REnvironmentPosix_cpp,v
retrieving revision 1.3
diff -u -p -r1.3 patch-src_cpp_core_r_util_REnvironmentPosix_cpp
--- rstudio/patches/patch-src_cpp_core_r_util_REnvironmentPosix_cpp 14 Jul 2022 02:02:49 -0000 1.3
+++ rstudio/patches/patch-src_cpp_core_r_util_REnvironmentPosix_cpp 3 Aug 2022 11:49:57 -0000
@@ -8,7 +8,7 @@ Index: src/cpp/core/r_util/REnvironmentP
#else

-#define kLibRFileName "libR.so"
-+#define kLibRFileName "libR.so.38.0"
++#define kLibRFileName "libR.so.39.0"
#define kLibraryPathEnvVariable "LD_LIBRARY_PATH"

FilePath systemDefaultRScript(std::string* pErrMsg)

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