Re: [R-SIG-Mac] adjusting .libPaths
That's it! There was a .Renviron file in my home directory with the one
line
R_LIBS_USER="/Users/ken/Library/R/4.1/library"
so I changed it to
R_LIBS_USER="/Users/ken/Library/R/x86_64/4.2/library"
and now I get in the Rgui, R terminal and Rstudio
libPaths()
[1] "/Users/ken/Library/R/x86_64/4.2/library"
[2] "/Library/Frameworks/R.framework/Versions/4.2/Resources/library"
which is what I expected to have in the first place.
Thank you, Duncan.
best,
--
Kenneth Knoblauch
Inserm U1208
Stem-cell and Brain Research Institute
18 avenue du Doyen Lépine
69500 Bron
France
tel: +33 (0)4 72 91 34 77
fax: +33 (0)4 72 91 34 61
portable: +33 (0)6 84 10 64 10
http://www.sbri.fr/user/1453
On 2022-04-28 16:26, Duncan Murdoch wrote:
On 28/04/2022 9:44 a.m., Kenneth Knoblauch wrote:
Hi,
In R 4.2, when I look at .libPaths() from within the standard R gui,
I
see:
.libPaths()
[1] "/Users/ken/Library/R/x86_64/4.2/library"
[2] "/Users/ken/Library/R/4.1/library"
[3] "/Library/Frameworks/R.framework/Versions/4.2/Resources/library"
From a terminal, I get
.libPaths()
[1] "/Users/ken/Library/R/4.1/library"
[2] "/Library/Frameworks/R.framework/Versions/4.2/Resources/library"
The old 4.1 directory, I suspect, should not be there. From
Sys.getenv(), I see
R_LIBS /Users/ken/Library/R/x86_64/4.2/library
R_LIBS_SITE
/Library/Frameworks/R.framework/Resources/site-library
R_LIBS_USER /Users/ken/Library/R/4.1/library
and the system Renviron file contains
uc7131:Resources ken$ grep R_LIBS etc/Renviron
R_LIBS_USER=${R_LIBS_USER:-'%U'}
R_LIBS_SITE=${R_LIBS_SITE:-'%S'}
but I wouldn't know what to adjust these to, to fix this (if I even
should).
In Rstudio (which is not the problem of this list), I also get
.libPaths()
[1] "/Users/ken/Library/R/4.1/library"
[2] "/Library/Frameworks/R.framework/Versions/4.2/Resources/library"
and I would guess the 4.1 entry is why Rstudio bombs when I try to
execute any graphics.
I would be grateful for any suggestions as to how to fix this.
I'd guess the 41 isn't coming from the system file, but from a user
file
on your account or in the directory where you start Rgui. Running
getwd() as the first command might find that dir, as long as some
profile code hasn't changed it.
The filename might be ".Renviron" rather than "Renviron"
Duncan Murdoch
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[R-SIG-Mac] compilation problem
Hi, When compiling packages with C/Fortran code, I'm frequently getting the following sort of error at the stage of testing if package can be installed from temporary location: ** testing if installed package can be loaded from temporary location Error: package or namespace load failed for 'akima' in dyn.load(file, DLLpath = DLLpath, ...): unable to load shared object '/Users/ken/Library/R/x86_64/4.2/library/00LOCK-akima/00new/akima/libs/akima.so': dlopen(/Users/ken/Library/R/x86_64/4.2/library/00LOCK-akima/00new/akima/libs/akima.so, 6): Symbol not found: ___addtf3 Referenced from: /usr/local/lib/libquadmath.0.dylib Expected in: /usr/local/lib/libgcc_s_x86_64.1.dylib in /usr/local/lib/libquadmath.0.dylib Error: loading failed Execution halted ERROR: loading failed Any suggestions about how to fix this? If it is a PATH problem, how do I set that so that it is correct when I start up R? Thank you. best, Ken sessionInfo() R version 4.2.0 (2022-04-22) Platform: x86_64-apple-darwin17.0 (64-bit) Running under: macOS Catalina 10.15.7 Matrix products: default BLAS: /Library/Frameworks/R.framework/Versions/4.2/Resources/lib/libRblas.0.dylib LAPACK: /Library/Frameworks/R.framework/Versions/4.2/Resources/lib/libRlapack.dylib locale: [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8 attached base packages: [1] stats graphics grDevices utils datasets methods base loaded via a namespace (and not attached): [1] compiler_4.2.0 tools_4.2.0 Sys.getenv() . . . PATH /usr/bin:/bin:/usr/sbin:/sbin:/usr/local/bin . . . -- Kenneth Knoblauch Inserm U1208 Stem-cell and Brain Research Institute 18 avenue du Doyen Lépine 69500 Bron France tel: +33 (0)4 72 91 34 77 fax: +33 (0)4 72 91 34 61 portable: +33 (0)6 84 10 64 10 http://www.sbri.fr/user/1453 ___ R-SIG-Mac mailing list R-SIG-Mac@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-mac
[R-SIG-Mac] binaries for R 4.3 x86_64
Hi, I am upgrading to R 4.3. and trying to upgrade the packages. I had to upgrade to macOS 12 first because I was at 10 and my 2017 Intel Mac Air doesn't seem to be able to run later versions. I was looking at the Mac binaries at the R for mac OS page and it looks like both links big-sur-x86_64 and big-sur-arm64 lead to a page with header: Index of /bin/macosx/big-sur-arm64 Is this just a heading error or is there a misdirect in the link? The formalities: sessionInfo() R version 4.3.0 (2023-04-21) Platform: x86_64-apple-darwin20 (64-bit) Running under: macOS Monterey 12.6.5 Matrix products: default BLAS: /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/lib/libRblas.0.dylib LAPACK: /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/lib/libRlapack.dylib; LAPACK version 3.11.0 locale: [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8 time zone: Europe/Paris tzcode source: internal attached base packages: [1] stats graphics grDevices utils datasets methods base loaded via a namespace (and not attached): [1] compiler_4.3.0 > capabilities() jpeg pngtiff tcltk X11aqua http/ftp TRUETRUETRUETRUETRUETRUE TRUE sockets libxmlfifo cledit iconv NLS Rprof TRUE FALSETRUETRUETRUETRUE TRUE profmem cairo ICU long.double libcurl TRUETRUETRUETRUETRUE Thank you. best, Ken ___ Kenneth Knoblauch Inserm U1208 Stem-cell and Brain Research Institute 18 avenue du Doyen Lépine 69500 Bron France tel: +33 (0)4 72 91 34 77 fax: +33 (0)4 72 91 34 61 portable: +33 (0)6 84 10 64 10 https://sbri.fr/public-profile/63/single-member/ ___ R-SIG-Mac mailing list R-SIG-Mac@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-mac
Re: [R-SIG-Mac] binaries for R 4.3 x86_64
Thank you Uwe for the rapid response, I tried: install.packages(p42[3], .libPaths()[1], repos = "https://cran.r-project.org/bin/macosx/big-sur-x86_64/;, type = "mac.binary") Warning: unable to access index for repository https://cran.r-project.org/bin/macosx/big-sur-x86_64/bin/macosx/contrib/4.3: cannot open URL 'https://cran.r-project.org/bin/macosx/big-sur-x86_64/bin/macosx/contrib/4.3/PACKAGES' and install.packages(p42[3], .libPaths()[1], repos = "https://cran.r-project.org/bin/macosx/big-sur-x86_64/contrib/4.3;, type = "mac.binary") Warning: unable to access index for repository https://cran.r-project.org/bin/macosx/big-sur-x86_64/contrib/4.3/bin/macosx/contrib/4.3: cannot open URL 'https://cran.r-project.org/bin/macosx/big-sur-x86_64/contrib/4.3/bin/macosx/contrib/4.3/PACKAGES' and install.packages(p42, .libPaths()[1], repos = "https://cran.r-project.org;, type = "mac.binary") Warning: unable to access index for repository https://cran.r-project.org/bin/macosx/contrib/4.3: cannot open URL 'https://cran.r-project.org/bin/macosx/contrib/4.3/PACKAGES' where p42 was a character vector of the package names that I had installed under 4.2 Any guidance would be greatly appreciated. Thank you, in advance. best, Ken ___ Kenneth Knoblauch Inserm U1208 Stem-cell and Brain Research Institute 18 avenue du Doyen Lépine 69500 Bron France tel: +33 (0)4 72 91 34 77 fax: +33 (0)4 72 91 34 61 portable: +33 (0)6 84 10 64 10 https://sbri.fr/public-profile/63/single-member/ De : Uwe Ligges Envoyé : lundi 24 avril 2023 14:51 À : Kenneth Knoblauch; r-sig-mac@r-project.org Objet : Re: [R-SIG-Mac] binaries for R 4.3 x86_64 On 24.04.2023 14:41, Kenneth Knoblauch wrote: > Hi, > > I am upgrading to R 4.3. and trying to upgrade the packages. I had to > upgrade to macOS 12 first because I was at 10 and my 2017 Intel Mac Air > doesn't seem to be able to run later versions. I was looking at the Mac > binaries at the R for mac OS page and it looks like both links > > big-sur-x86_64 and big-sur-arm64 lead to a page with header: > > Index of /bin/macosx/big-sur-arm64 > > Is this just a heading error or is there a misdirect in the link? Misdirect, simply replace arm64 by x86_64 in the link for now. I am sure Simon will fix it soon, too. Best, Uwe Ligges > > The formalities: > > sessionInfo() > R version 4.3.0 (2023-04-21) > Platform: x86_64-apple-darwin20 (64-bit) > Running under: macOS Monterey 12.6.5 > > Matrix products: default > BLAS: > /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/lib/libRblas.0.dylib > LAPACK: > /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/lib/libRlapack.dylib; > LAPACK version 3.11.0 > > locale: > [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8 > > time zone: Europe/Paris > tzcode source: internal > > attached base packages: > [1] stats graphics grDevices utils datasets methods base > > loaded via a namespace (and not attached): > [1] compiler_4.3.0 >> capabilities() > jpeg png tiff tcltk X11 aqua >http/ftp > TRUE TRUE TRUE TRUE TRUE TRUE > TRUE > sockets libxml fifo cledit iconv NLS > Rprof > TRUE FALSE TRUE TRUE TRUE TRUE > TRUE > profmem cairo ICU long.double libcurl > TRUE TRUE TRUE TRUE TRUE > > Thank you. > > best, > > Ken > > > ___ > Kenneth Knoblauch > Inserm U1208 > Stem-cell and Brain Research Institute > 18 avenue du Doyen Lépine > 69500 Bron > France > tel: +33 (0)4 72 91 34 77 > fax: +33 (0)4 72 91 34 61 > portable: +33 (0)6 84 10 64 10 > https://sbri.fr/public-profile/63/single-member/ > > ___ > R-SIG-Mac mailing list > R-SIG-Mac@r-project.org > https://stat.ethz.ch/mailman/listinfo/r-sig-mac ___ R-SIG-Mac mailing list R-SIG-Mac@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-mac
Re: [R-SIG-Mac] binaries for R 4.3 x86_64
Actually, I was able to update everything from source. I initially didn't think that would work because of the need to update Xcode and gfortran, but it all worked and none of that was necessary. Thanks. best, Ken ___ Kenneth Knoblauch Inserm U1208 Stem-cell and Brain Research Institute 18 avenue du Doyen Lépine 69500 Bron France tel: +33 (0)4 72 91 34 77 fax: +33 (0)4 72 91 34 61 portable: +33 (0)6 84 10 64 10 https://sbri.fr/public-profile/63/single-member/ De : Kenneth Knoblauch Envoyé : lundi 24 avril 2023 15:12 À : Uwe Ligges; r-sig-mac@r-project.org Objet : RE: [R-SIG-Mac] binaries for R 4.3 x86_64 Thank you Uwe for the rapid response, I tried: install.packages(p42[3], .libPaths()[1], repos = "https://cran.r-project.org/bin/macosx/big-sur-x86_64/;, type = "mac.binary") Warning: unable to access index for repository https://cran.r-project.org/bin/macosx/big-sur-x86_64/bin/macosx/contrib/4.3: cannot open URL 'https://cran.r-project.org/bin/macosx/big-sur-x86_64/bin/macosx/contrib/4.3/PACKAGES' and install.packages(p42[3], .libPaths()[1], repos = "https://cran.r-project.org/bin/macosx/big-sur-x86_64/contrib/4.3;, type = "mac.binary") Warning: unable to access index for repository https://cran.r-project.org/bin/macosx/big-sur-x86_64/contrib/4.3/bin/macosx/contrib/4.3: cannot open URL 'https://cran.r-project.org/bin/macosx/big-sur-x86_64/contrib/4.3/bin/macosx/contrib/4.3/PACKAGES' and install.packages(p42, .libPaths()[1], repos = "https://cran.r-project.org;, type = "mac.binary") Warning: unable to access index for repository https://cran.r-project.org/bin/macosx/contrib/4.3: cannot open URL 'https://cran.r-project.org/bin/macosx/contrib/4.3/PACKAGES' where p42 was a character vector of the package names that I had installed under 4.2 Any guidance would be greatly appreciated. Thank you, in advance. best, Ken ___ Kenneth Knoblauch Inserm U1208 Stem-cell and Brain Research Institute 18 avenue du Doyen Lépine 69500 Bron France tel: +33 (0)4 72 91 34 77 fax: +33 (0)4 72 91 34 61 portable: +33 (0)6 84 10 64 10 https://sbri.fr/public-profile/63/single-member/ De : Uwe Ligges Envoyé : lundi 24 avril 2023 14:51 À : Kenneth Knoblauch; r-sig-mac@r-project.org Objet : Re: [R-SIG-Mac] binaries for R 4.3 x86_64 On 24.04.2023 14:41, Kenneth Knoblauch wrote: > Hi, > > I am upgrading to R 4.3. and trying to upgrade the packages. I had to > upgrade to macOS 12 first because I was at 10 and my 2017 Intel Mac Air > doesn't seem to be able to run later versions. I was looking at the Mac > binaries at the R for mac OS page and it looks like both links > > big-sur-x86_64 and big-sur-arm64 lead to a page with header: > > Index of /bin/macosx/big-sur-arm64 > > Is this just a heading error or is there a misdirect in the link? Misdirect, simply replace arm64 by x86_64 in the link for now. I am sure Simon will fix it soon, too. Best, Uwe Ligges > > The formalities: > > sessionInfo() > R version 4.3.0 (2023-04-21) > Platform: x86_64-apple-darwin20 (64-bit) > Running under: macOS Monterey 12.6.5 > > Matrix products: default > BLAS: > /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/lib/libRblas.0.dylib > LAPACK: > /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/lib/libRlapack.dylib; > LAPACK version 3.11.0 > > locale: > [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8 > > time zone: Europe/Paris > tzcode source: internal > > attached base packages: > [1] stats graphics grDevices utils datasets methods base > > loaded via a namespace (and not attached): > [1] compiler_4.3.0 >> capabilities() > jpeg png tiff tcltk X11 aqua >http/ftp > TRUE TRUE TRUE TRUE TRUE TRUE > TRUE > sockets libxml fifo cledit iconv NLS > Rprof > TRUE FALSE TRUE TRUE TRUE TRUE > TRUE > profmem cairo ICU long.double libcurl > TRUE TRUE TRUE TRUE TRUE > > Thank you. > > best, > > Ken > > > ___ > Kenneth Knoblauch > Inserm U1208 > Stem-cell and Brain Research Institute > 18 avenue du Doyen Lépine > 69500 Bron > France > tel: +33 (0)4 72 91 34 77 > fax: +33 (0)4 72 91 34 61 > portable: +33 (0)6 84 10 64 10 > https://sbri.fr/public-profile/63/single-member/ > > ___ > R-SIG-Mac mailing list > R-SIG-Mac@r-project.org > https://stat.ethz.ch/mailman/listinfo/r-sig-mac ___ R-SIG-Mac mailing list R-SIG-Mac@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-mac
Re: [R-SIG-Mac] binaries for R 4.3 x86_64
Simon, Thank you. Ken Kenneth Knoblauch Inserm U1208 Stem-cell and Brain Research Institute 18 avenue du Doyen Lépine 69500 Bron France tel: +33 (0)4 72 91 34 77 fax: +33 (0)4 72 91 34 61 portable: +33 (0)6 84 10 64 10 http<http://www.sbri.fr/user/1453>s://sbri.fr/public-profile/63/single-member/ On 24 Apr 2023, at 23:27, Simon Urbanek wrote: This has been fixed a while time ago so I suspect the culprit are outdated mirrors. If in doubt, please use https://mac.R-project.org/bin/macosx which is the most up-to-date. Cheers, Simon On Apr 25, 2023, at 12:51 AM, Uwe Ligges wrote: On 24.04.2023 14:41, Kenneth Knoblauch wrote: Hi, I am upgrading to R 4.3. and trying to upgrade the packages. I had to upgrade to macOS 12 first because I was at 10 and my 2017 Intel Mac Air doesn't seem to be able to run later versions. I was looking at the Mac binaries at the R for mac OS page and it looks like both links big-sur-x86_64 and big-sur-arm64 lead to a page with header: Index of /bin/macosx/big-sur-arm64 Is this just a heading error or is there a misdirect in the link? Misdirect, simply replace arm64 by x86_64 in the link for now. I am sure Simon will fix it soon, too. Best, Uwe Ligges The formalities: sessionInfo() R version 4.3.0 (2023-04-21) Platform: x86_64-apple-darwin20 (64-bit) Running under: macOS Monterey 12.6.5 Matrix products: default BLAS: /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/lib/libRblas.0.dylib LAPACK: /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/lib/libRlapack.dylib; LAPACK version 3.11.0 locale: [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8 time zone: Europe/Paris tzcode source: internal attached base packages: [1] stats graphics grDevices utils datasets methods base loaded via a namespace (and not attached): [1] compiler_4.3.0 capabilities() jpeg pngtiff tcltk X11aqua http/ftp TRUETRUETRUETRUETRUETRUE TRUE sockets libxmlfifo cledit iconv NLS Rprof TRUE FALSETRUETRUETRUETRUE TRUE profmem cairo ICU long.double libcurl TRUETRUETRUETRUETRUE Thank you. best, Ken ___ Kenneth Knoblauch Inserm U1208 Stem-cell and Brain Research Institute 18 avenue du Doyen Lépine 69500 Bron France tel: +33 (0)4 72 91 34 77 fax: +33 (0)4 72 91 34 61 portable: +33 (0)6 84 10 64 10 https://sbri.fr/public-profile/63/single-member/ ___ R-SIG-Mac mailing list R-SIG-Mac@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-mac ___ R-SIG-Mac mailing list R-SIG-Mac@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-mac [[alternative HTML version deleted]] ___ R-SIG-Mac mailing list R-SIG-Mac@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-mac
