Re: [R-SIG-Mac] pdflatex not found! Not building PDF manual.
Hi, Marc: That's what I needed. Thanks. Spencer Graves On 2/27/24 3:05 PM, Marc Schwartz wrote: Dennis, Do you have a TeX installation on your Mac? pdflatex is typically installed with TeX, which for macOS is usually via MacTeX: https://tug.org/mactex/ Once you have that installed, you should be good to go, but if you are currently running an interactive R session, you will likely need to exit that, and then after installing MacTex, restart your R session. You will also end up with a TeX folder in your Applications folder, where supporting apps will reside, including the TeX Live utility, which can be used to update the TeX installation periodically. Regards, Marc Schwartz -Original Message- From: R-SIG-Mac mailto:r-sig-mac-boun...@r-project.org>> on behalf of Spencer Graves mailto:spencer.gra...@prodsyse.com>> Date: Tuesday, February 27, 2024 at 2:02 PM To: r-sig-mac mailto:r-sig-mac@r-project.org>> Subject: [R-SIG-Mac] pdflatex not found! Not building PDF manual. Hello: Running "devtools::check_win_devel()", I got, "pdflatex not found! Not building PDF manual." "sessionInfo()" below. Suggestions? Thanks, Spencer Graves sessionInfo() R version 4.3.2 (2023-10-31) Platform: aarch64-apple-darwin20 (64-bit) Running under: macOS Sonoma 14.3.1 Matrix products: default BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib LAPACK: /Library/Frameworks/R.framework/Versions/4.3-arm64/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: America/Chicago tzcode source: internal attached base packages: [1] stats graphics grDevices utils datasets methods base loaded via a namespace (and not attached): [1] miniUI_0.1.1.1 compiler_4.3.2 promises_1.2.1 Rcpp_1.0.12 [5] stringr_1.5.1 callr_3.7.3 later_1.3.2 fastmap_1.1.1 [9] mime_0.12 R6_2.5.1 curl_5.2.0 htmlwidgets_1.6.4 [13] tibble_3.2.1 desc_1.4.3 profvis_0.3.8 shiny_1.8.0 [17] pillar_1.9.0 rlang_1.1.3 utf8_1.2.4 cachem_1.0.8 [21] stringi_1.8.3 httpuv_1.6.14 fs_1.6.3 pkgload_1.3.4 [25] memoise_2.0.1 cli_3.6.2 magrittr_2.0.3 ps_1.7.6 [29] processx_3.8.3 digest_0.6.34 rstudioapi_0.15.0 xtable_1.8-4 [33] remotes_2.4.2.1 devtools_2.4.5 lifecycle_1.0.4 vctrs_0.6.5 [37] glue_1.7.0 urlchecker_1.0.1 sessioninfo_1.2.2 pkgbuild_1.4.3 [41] fansi_1.0.6 purrr_1.0.2 pkgconfig_2.0.3 tools_4.3.2 [45] usethis_2.2.3 ellipsis_0.3.2 htmltools_0.5.7 ___ R-SIG-Mac mailing list R-SIG-Mac@r-project.org <mailto:R-SIG-Mac@r-project.org> https://stat.ethz.ch/mailman/listinfo/r-sig-mac <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
[R-SIG-Mac] pdflatex not found! Not building PDF manual.
Hello: Running "devtools::check_win_devel()", I got, "pdflatex not found! Not building PDF manual." "sessionInfo()" below. Suggestions? Thanks, Spencer Graves sessionInfo() R version 4.3.2 (2023-10-31) Platform: aarch64-apple-darwin20 (64-bit) Running under: macOS Sonoma 14.3.1 Matrix products: default BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib LAPACK: /Library/Frameworks/R.framework/Versions/4.3-arm64/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: America/Chicago tzcode source: internal attached base packages: [1] stats graphics grDevices utils datasets methods base loaded via a namespace (and not attached): [1] miniUI_0.1.1.1compiler_4.3.2promises_1.2.1Rcpp_1.0.12 [5] stringr_1.5.1 callr_3.7.3 later_1.3.2 fastmap_1.1.1 [9] mime_0.12 R6_2.5.1 curl_5.2.0 htmlwidgets_1.6.4 [13] tibble_3.2.1 desc_1.4.3profvis_0.3.8 shiny_1.8.0 [17] pillar_1.9.0 rlang_1.1.3 utf8_1.2.4cachem_1.0.8 [21] stringi_1.8.3 httpuv_1.6.14 fs_1.6.3 pkgload_1.3.4 [25] memoise_2.0.1 cli_3.6.2 magrittr_2.0.3ps_1.7.6 [29] processx_3.8.3digest_0.6.34 rstudioapi_0.15.0 xtable_1.8-4 [33] remotes_2.4.2.1 devtools_2.4.5lifecycle_1.0.4 vctrs_0.6.5 [37] glue_1.7.0urlchecker_1.0.1 sessioninfo_1.2.2 pkgbuild_1.4.3 [41] fansi_1.0.6 purrr_1.0.2 pkgconfig_2.0.3 tools_4.3.2 [45] usethis_2.2.3 ellipsis_0.3.2htmltools_0.5.7 > ___ R-SIG-Mac mailing list R-SIG-Mac@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-mac
Re: [R-SIG-Mac] gfortran: command not found
Dear Prof. Ripley et al.: On 7/8/23 1:16 AM, Prof Brian Ripley wrote: On 08/07/2023 00:41, Spencer Graves wrote: Hello, Simon Urbanek and Professor Ripley: On 7/7/23 4:21 AM, Simon Urbanek wrote: On Jul 7, 2023, at 6:54 PM, Prof Brian Ripley wrote: An alternative is not to have gfortran on the path and use a personal Makevars file, as documented at https://cran.r-project.org/doc/manuals/r-devel/R-admin.html#macOS-packages . Reasons to do it that way include a) GCC builds have included other compilers including gcc in the same directory as gfortran, and I have been caught in the past by badly-written software looking for gcc as a C compiler and finding that one rather than Apple's gcc which is a wrapper for clang. (The current gfortran distribution only includes x86_64-apple-darwin20.0-gcc and similar.) b) If the gfortran you have installed differs from that used to build R, you may need to set FLIBS, and this has happened as different CRAN distributions have been built with different versions of gfortran. When I do want gfortran on the path, for example to build other software, I do symlink it to somewhere on my path. I would prefer if Simon continues to give the full path as FC in etc/Makeconf: anyone who wants a different compiler can use a personal Makevars. (Continues at least for arm64, and I would prefer consistency.) I agree - it wasn't entirely intentional (it's really historical), but then there was request for a PATH-less gfortran settings. After this discussion I agree that it's not a good idea since the instructions on CRAN should be fully self-sufficient *and* we want to avoid other incompatible Fortran compilers. (I have trouble reaching the x86_64 build machine from home right now, so I'll change it on Monday). Might it be feasible and appropriate for me to try to do this on my 2014 MacBook Pro running macOS 11.7.8? I ask, because I have so far not been able to parse the instructions in the link Prof. Ripley provided above. I found a ".r" subdirectory in my default directory, but its contents seems to be only "crashpad_database". I did not see anything that looked to me like, "HOME/.R/Makevars-R_PLATFORM". ??? You need to create the file (which is called ~/.R/Makevars in the section I referred you to). Using a case-insenstive file system does not help (I had no idea what created ~/.r/crashpad_database, but Googling suggests RStudio). (If you did not have ~/.r, you would need mkdir ~/.R in a Terminal.) Then use your favourite editor to create a file ~/.r/Makevars containing the single line FC=/opt/gfortran/bin/gfortran The only issue is if you ever install a new gfortran you will need to edit/remove this file -- it is easily forgotten. As Simon says he is changing this soon, I would make a note to remove the file when you update R. For now, I've added a file "~/.r/Makevars" containing this single line and deleted the corresponding reference from "/etc/paths". I rebooted and confirmed that it works. Thanks very much. Spencer Graves ___ R-SIG-Mac mailing list R-SIG-Mac@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-mac
Re: [R-SIG-Mac] gfortran: command not found
Hello, Simon Urbanek and Professor Ripley:
On 7/7/23 4:21 AM, Simon Urbanek wrote:
On Jul 7, 2023, at 6:54 PM, Prof Brian Ripley wrote:
An alternative is not to have gfortran on the path and use a personal Makevars
file, as documented at
https://cran.r-project.org/doc/manuals/r-devel/R-admin.html#macOS-packages .
Reasons to do it that way include
a) GCC builds have included other compilers including gcc in the same directory
as gfortran, and I have been caught in the past by badly-written software
looking for gcc as a C compiler and finding that one rather than Apple's gcc
which is a wrapper for clang. (The current gfortran distribution only includes
x86_64-apple-darwin20.0-gcc and similar.)
b) If the gfortran you have installed differs from that used to build R, you
may need to set FLIBS, and this has happened as different CRAN distributions
have been built with different versions of gfortran.
When I do want gfortran on the path, for example to build other software, I do
symlink it to somewhere on my path.
I would prefer if Simon continues to give the full path as FC in etc/Makeconf:
anyone who wants a different compiler can use a personal Makevars. (Continues
at least for arm64, and I would prefer consistency.)
I agree - it wasn't entirely intentional (it's really historical), but then
there was request for a PATH-less gfortran settings. After this discussion I
agree that it's not a good idea since the instructions on CRAN should be fully
self-sufficient *and* we want to avoid other incompatible Fortran compilers. (I
have trouble reaching the x86_64 build machine from home right now, so I'll
change it on Monday).
Might it be feasible and appropriate for me to try to do this on my
2014 MacBook Pro running macOS 11.7.8?
I ask, because I have so far not been able to parse the instructions
in the link Prof. Ripley provided above. I found a ".r" subdirectory in
my default directory, but its contents seems to be only
"crashpad_database". I did not see anything that looked to me like,
"HOME/.R/Makevars-R_PLATFORM". ???
Thanks,
Spencer Graves
Thanks,
Simon
On 07/07/2023 00:07, Simon Urbanek wrote:
On 7/07/2023, at 10:15 AM, Spencer Graves wrote:
Hi, Simon:
Thanks for this. I have more questions:
On 7/6/23 4:52 PM, Simon Urbanek wrote:
In the shell:
PATH=/opt/gfortran/bin:$PATH R CMD INSTALL ...
Please excuse my ignorance, but I don't understand this. I previously tried
"PATH=/bin:/sbin:/user/bin:/user/sbin:/system/Library/ export PATH",
recommended on a page associated with support.apple.com, as mentioned below. That did
not seem to work for me.
That one sets the specified fixed path and then exports it. Setting a fixed
PATH by hand is typically a bad idea since it removes all existing entries -
and the one you listed didn't even have gfortran on it. Exporting is another
alternative if you want to set the PATH for all subsequent commands.
The line I sent just prepends the /opt/gfortran/bin to the PATH for the one R
CMD command, but doesn't affect anything else. I would recommend reading a
basic tutorial on unix shell if you really want to know more (actually a good
idea if you ever want to use the Terminal and not kill your machine).
How is this different? What did I do wrong before that this would
fix? [Or feel free to ignore this question: My immediate problem seems to be
fixed, and I'm not eager to do more experimentation with this now ;-]
in R if using install.packages()
Sys.setenv(PATH=paste0("/opt/gfortran/bin:", Sys.getenv("PATH")))
If I set this in RStudio, will it affect what I do in "Terminal" on
my Mac and vice versa?
No, it is only valid for the current R session (and I don't know about RStudio
- it's not R so sometimes R rules don't apply), that's why I said it's for the
case where you run install.packages() in the R session.
Note that another alternative is to simply symlink gfortran to your
/usr/local/bin since that is on the PATH on macOS by default, i.e., you only
need to run this in the Terminal once (requires admin access):
sudo ln -sfn /opt/gfortran/bin/gfortran /usr/local/bin/gfortran
Cheers,
Simon
This looks like a potentially similar thing to do from what I did. Is the
effect of this different? If so, how? [Again, please feel free to ignore this question.
I'm not eager to practice my "do-it-myself lobotomy" skills ;-]
Thanks,
Spencer Graves>
On Jul 7, 2023, at 5:58 AM, Spencer Graves wrote:
1. I need to apologize to Simon: I failed to see his reply to the original
post. Then I found the instructions and installed gfortran-12.2-universal.pkg,
as indicated there, but it still didn't work.
2. I'm not finding clear instructions on how to update the path on macOS 11.7.8, which
is the latest ve
Re: [R-SIG-Mac] gfortran: command not found
Hi, Simon:
Thanks for this. I have more questions:
On 7/6/23 4:52 PM, Simon Urbanek wrote:
In the shell:
PATH=/opt/gfortran/bin:$PATH R CMD INSTALL ...
Please excuse my ignorance, but I don't understand this. I
previously tried "PATH=/bin:/sbin:/user/bin:/user/sbin:/system/Library/
export PATH", recommended on a page associated with support.apple.com,
as mentioned below. That did not seem to work for me.
How is this different? What did I do wrong before that this would
fix? [Or feel free to ignore this question: My immediate problem seems
to be fixed, and I'm not eager to do more experimentation with this now
;-]
in R if using install.packages()
Sys.setenv(PATH=paste0("/opt/gfortran/bin:", Sys.getenv("PATH")))
If I set this in RStudio, will it affect what I do in "Terminal" on
my Mac and vice versa?
This looks like a potentially similar thing to do from what I did.
Is the effect of this different? If so, how? [Again, please feel free
to ignore this question. I'm not eager to practice my "do-it-myself
lobotomy" skills ;-]
Thanks,
Spencer Graves>
On Jul 7, 2023, at 5:58 AM, Spencer Graves wrote:
1. I need to apologize to Simon: I failed to see his reply to the original
post. Then I found the instructions and installed gfortran-12.2-universal.pkg,
as indicated there, but it still didn't work.
2. I'm not finding clear instructions on how to update the path on macOS 11.7.8, which
is the latest version available for my 2014 MacBook Pro with a 2.8 GHz Quad-Core Intel
Core i7. I found several pages with differing instructions. I found one in
"support.apple.com" that recommended something that didn't work.[2]
Further suggestions?
Thanks again very much.
Spencer Graves
[2] "support.apple.com" recommended "PATH=/bin:/sbin:/user/bin:/user/sbin:/system/Library/ export PATH", then "env". I
did "env" to get the current path, than appended ":/opt/gfortran/bin" to that and executed the revised
"PATH=...:/opt/gfortran/bin export PATH". However, when I checked with "env" again, the change was not displayed. I rebooted
with the same result.
https://support.apple.com/guide/terminal/use-environment-variables-apd382cc5fa-4f58-4449-b20a-41c53c006f8f/mac
On 7/6/23 11:01 AM, Simon Urbanek wrote:
AFACT he didn't say so, there was no response, just double-posting of the same
question after is was answered.
The installer says:
The resulting compiler will live in /opt/gfortran and can be called with
/opt/gfortran/bin/gfortran
so it's advisable to have /opt/gfortran/bin on the PATH.
(Side note: the arm64 build of R uses the full path, but some people have been
objecting to that since they wanted to use other compilers for the legacy Intel
builds, but as I suspected that causes other issues, so I'll change that for
the next release).
Cheers,
Simon
On Jul 6, 2023, at 11:45 PM, Peter Dalgaard mailto:pda...@gmail.com>> wrote:
AFAICT, Spencer followed the implied instructions and it still didn't work.
There may also be a PATH issue when upgrading to 4.3.x, /usr/local ->
/opt/R/ Does gfortran 12.2 install to /opt/R/.../bin ?
-pd
On 6 Jul 2023, at 07:42 , Simon Urbanek mailto:simon.urba...@r-project.org>> wrote:
Already answered to you and on R-pkg-devel [9 mins after you posted there - now
more than 5h ago...]:
To quote from the page you downloaded R from:
This release uses Xcode 14.2/14.3 and GNU Fortran 12.2. If you wish to compile R packages which
contain Fortran code, you may need to download the corresponding GNU Fortran compiler from
https://mac.R-project.org/tools <https://mac.R-project.org/tools>
<https://mac.r-project.org/tools <https://mac.r-project.org/tools>>.
On Jul 6, 2023, at 5:16 PM, Spencer Graves mailto:spencer.gra...@prodsyse.com>> wrote:
Hello, All:
"R CMD check KFAS" under macOS 11.7.8 (the latest version that will run on my aging
Mac) complains "gfortran: command not found".
I just upgraded to R 4.3.1 and installed "gfortran-12.2-universal.pkg" per
"https://cran.r-project.org/bin/macosx/tools/
<https://cran.r-project.org/bin/macosx/tools/>". I expected this to solve the problem. It
didn't.
Suggestions?
Thanks,
Spencer Graves
p.s. This is my fork of KFAS, available at "https://github.com/sbgraves237/KFAS
<https://github.com/sbgraves237/KFAS>". "sessionInfo()" appears below.
##
sessionInfo()
R version 4.3.1 (2023-06-16)
Platform: x86_64-apple-darwin20 (64-bit)
Running under: macOS Big Sur 11.7.8
Matrix products: default
BLAS:
/System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
LAPACK:
/Library/Framework
Re: [R-SIG-Mac] gfortran: command not found
Hi, Peter et al.:
On 7/6/23 1:15 PM, Peter Dalgaard wrote:
I think the cleanest way is to diddle the /etc/paths.d structure. I have
PeterDaardsiMac:R pd$ ls /etc/paths.d
40-XQuartz R TeX clang8 gfortran
PeterDaardsiMac:R pd$ cat /etc/paths.d/gfortran
/usr/local/gfortran/bin
PeterDaardsiMac:R pd$ cat /etc/paths
/usr/local/bin
/usr/bin
/bin
/usr/sbin
/sbin
and the latter would want to be /opt/gfortran/bin for 12.2 (I still have 8.2
for now).
I could not figure out how "to diddle the /etc/paths.d structure",
but I was successful by appending "/opt/gfortran/bin" to etc/paths using
"sudo vi etc/paths". It didn't work immediately nor after I exited and
restarted Terminal, but it did after I rebooted.
There's till a lot I do not understand about this.
readLines('/etc/paths') now returns a character vector of length 8, with
the last string being the one I appended. Meanwhile, "echo $PATH" at a
prompt returned a path with 13 components with "/opt/gfortran/bin" being
number 11, and 'Sys.getenv("PATH")' returned a path with 18 components,
with "/opt/gfortran/bin" being number 12.
Anyway, thanks again to Simon and Peter.
Best Wishes,
Spencer Graves
Two things to note:
1. The directories in paths.d/* are added to those in /etc/paths in
alphabetical order, so careful with older versions in /usr/local/bin.
2. You (probably) need to logout and back in for the changes to take effect in
your Terminal windows.
Alternatively, you can twiddle the shell startup files (~/.profile /etc/profile
/etc/bashrc ) directly. The trouble I have with that, is that I never feel
sure that I am doing it in the right place.
- Peter D.
On 6 Jul 2023, at 19:58 , Spencer Graves wrote:
1. I need to apologize to Simon: I failed to see his reply to the original
post. Then I found the instructions and installed gfortran-12.2-universal.pkg,
as indicated there, but it still didn't work.
2. I'm not finding clear instructions on how to update the path on macOS 11.7.8, which
is the latest version available for my 2014 MacBook Pro with a 2.8 GHz Quad-Core Intel
Core i7. I found several pages with differing instructions. I found one in
"support.apple.com" that recommended something that didn't work.[2]
Further suggestions?
Thanks again very much.
Spencer Graves
[2] "support.apple.com" recommended "PATH=/bin:/sbin:/user/bin:/user/sbin:/system/Library/ export PATH", then "env". I
did "env" to get the current path, than appended ":/opt/gfortran/bin" to that and executed the revised
"PATH=...:/opt/gfortran/bin export PATH". However, when I checked with "env" again, the change was not displayed. I rebooted
with the same result.
https://support.apple.com/guide/terminal/use-environment-variables-apd382cc5fa-4f58-4449-b20a-41c53c006f8f/mac
On 7/6/23 11:01 AM, Simon Urbanek wrote:
AFACT he didn't say so, there was no response, just double-posting of the same
question after is was answered.
The installer says:
The resulting compiler will live in /opt/gfortran and can be called with
/opt/gfortran/bin/gfortran
so it's advisable to have /opt/gfortran/bin on the PATH.
(Side note: the arm64 build of R uses the full path, but some people have been
objecting to that since they wanted to use other compilers for the legacy Intel
builds, but as I suspected that causes other issues, so I'll change that for
the next release).
Cheers,
Simon
On Jul 6, 2023, at 11:45 PM, Peter Dalgaard mailto:pda...@gmail.com>> wrote:
AFAICT, Spencer followed the implied instructions and it still didn't work.
There may also be a PATH issue when upgrading to 4.3.x, /usr/local ->
/opt/R/ Does gfortran 12.2 install to /opt/R/.../bin ?
-pd
On 6 Jul 2023, at 07:42 , Simon Urbanek mailto:simon.urba...@r-project.org>> wrote:
Already answered to you and on R-pkg-devel [9 mins after you posted there - now
more than 5h ago...]:
To quote from the page you downloaded R from:
This release uses Xcode 14.2/14.3 and GNU Fortran 12.2. If you wish to compile R packages which
contain Fortran code, you may need to download the corresponding GNU Fortran compiler from
https://mac.R-project.org/tools <https://mac.R-project.org/tools>
<https://mac.r-project.org/tools <https://mac.r-project.org/tools>>.
On Jul 6, 2023, at 5:16 PM, Spencer Graves mailto:spencer.gra...@prodsyse.com>> wrote:
Hello, All:
"R CMD check KFAS" under macOS 11.7.8 (the latest version that will run on my aging
Mac) complains "gfortran: command not found".
I just upgraded to R 4.3.1 and installed "gfortran-12.2-universal.pkg" per
"https://cran.r-project.org/bin/macosx/tools/<https://cran.r-project.org/bin/m
Re: [R-SIG-Mac] gfortran: command not found
1. I need to apologize to Simon: I failed to see his reply to the
original post. Then I found the instructions and installed
gfortran-12.2-universal.pkg, as indicated there, but it still didn't work.
2. I'm not finding clear instructions on how to update the path on
macOS 11.7.8, which is the latest version available for my 2014 MacBook
Pro with a 2.8 GHz Quad-Core Intel Core i7. I found several pages with
differing instructions. I found one in "support.apple.com" that
recommended something that didn't work.[2]
Further suggestions?
Thanks again very much.
Spencer Graves
[2] "support.apple.com" recommended
"PATH=/bin:/sbin:/user/bin:/user/sbin:/system/Library/ export PATH",
then "env". I did "env" to get the current path, than appended
":/opt/gfortran/bin" to that and executed the revised
"PATH=...:/opt/gfortran/bin export PATH". However, when I checked with
"env" again, the change was not displayed. I rebooted with the same
result.
https://support.apple.com/guide/terminal/use-environment-variables-apd382cc5fa-4f58-4449-b20a-41c53c006f8f/mac
On 7/6/23 11:01 AM, Simon Urbanek wrote:
AFACT he didn't say so, there was no response, just double-posting of
the same question after is was answered.
The installer says:
The resulting compiler will live in /opt/gfortran and can be called with
/opt/gfortran/bin/gfortran
so it's advisable to have /opt/gfortran/bin on the PATH.
(Side note: the arm64 build of R uses the full path, but some people
have been objecting to that since they wanted to use other compilers for
the legacy Intel builds, but as I suspected that causes other issues, so
I'll change that for the next release).
Cheers,
Simon
On Jul 6, 2023, at 11:45 PM, Peter Dalgaard <mailto:pda...@gmail.com>> wrote:
AFAICT, Spencer followed the implied instructions and it still didn't
work.
There may also be a PATH issue when upgrading to 4.3.x, /usr/local ->
/opt/R/ Does gfortran 12.2 install to /opt/R/.../bin ?
-pd
On 6 Jul 2023, at 07:42 , Simon Urbanek <mailto:simon.urba...@r-project.org>> wrote:
Already answered to you and on R-pkg-devel [9 mins after you posted
there - now more than 5h ago...]:
To quote from the page you downloaded R from:
This release uses Xcode 14.2/14.3 and GNU Fortran 12.2. If you wish
to compile R packages which contain Fortran code, you may need to
download the corresponding GNU Fortran compiler from
https://mac.R-project.org/tools <https://mac.R-project.org/tools>
<https://mac.r-project.org/tools <https://mac.r-project.org/tools>>.
On Jul 6, 2023, at 5:16 PM, Spencer Graves
mailto:spencer.gra...@prodsyse.com>>
wrote:
Hello, All:
"R CMD check KFAS" under macOS 11.7.8 (the latest version that will
run on my aging Mac) complains "gfortran: command not found".
I just upgraded to R 4.3.1 and installed
"gfortran-12.2-universal.pkg" per
"https://cran.r-project.org/bin/macosx/tools/
<https://cran.r-project.org/bin/macosx/tools/>". I expected this to
solve the problem. It didn't.
Suggestions?
Thanks,
Spencer Graves
p.s. This is my fork of KFAS, available at
"https://github.com/sbgraves237/KFAS
<https://github.com/sbgraves237/KFAS>". "sessionInfo()" appears below.
##
sessionInfo()
R version 4.3.1 (2023-06-16)
Platform: x86_64-apple-darwin20 (64-bit)
Running under: macOS Big Sur 11.7.8
Matrix products: default
BLAS:
/System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.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: America/Chicago
tzcode source: internal
attached base packages:
[1] stats graphics grDevices utils datasets methods base
loaded via a namespace (and not attached):
[1] compiler_4.3.1 R6_2.5.1 magrittr_2.0.3 cli_3.6.1
[5] tools_4.3.1 glue_1.6.2 rstudioapi_0.14 roxygen2_7.2.3
[9] xml2_1.3.4 vctrs_0.6.2 stringi_1.7.12 knitr_1.42
[13] xfun_0.39 stringr_1.5.0 lifecycle_1.0.3 rlang_1.1.1
[17] purrr_1.0.1
___
R-SIG-Mac mailing list
R-SIG-Mac@r-project.org <mailto: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 <mailto:R-SIG-Mac@r-project.org>
https://stat.ethz.ch/mailman/listinfo/r-sig-mac
--
Peter Dalgaard, Professor,
Center for Statistics, Copenhagen Business School
Solbjerg Plads 3, 2000 Frederiksberg, Denmark
Phone: (+45)38153501
Office: A 4.23
Email: pd@c
Re: [R-SIG-Mac] gfortran: command not found
Hi, Peter et al.:
On 7/6/23 6:45 AM, Peter Dalgaard wrote:
AFAICT, Spencer followed the implied instructions and it still didn't work.
There may also be a PATH issue when upgrading to 4.3.x, /usr/local ->
/opt/R/ Does gfortran 12.2 install to /opt/R/.../bin ?
The default install went to "/opt/gfortran", and gcc is in "/usr/bin".
What should I do to fix this?
I downloaded and reinstalled "gfortran-12.2-universal.pkg". I did NOT
see an option to install it anyplace else.
Thanks,
Spencer Graves
-pd
On 6 Jul 2023, at 07:42 , Simon Urbanek wrote:
Already answered to you and on R-pkg-devel [9 mins after you posted there - now
more than 5h ago...]:
To quote from the page you downloaded R from:
This release uses Xcode 14.2/14.3 and GNU Fortran 12.2. If you wish to compile R
packages which contain Fortran code, you may need to download the corresponding GNU
Fortran compiler from https://mac.R-project.org/tools
<https://mac.r-project.org/tools>.
On Jul 6, 2023, at 5:16 PM, Spencer Graves wrote:
Hello, All:
"R CMD check KFAS" under macOS 11.7.8 (the latest version that will run on my
aging Mac) complains "gfortran: command not found".
I just upgraded to R 4.3.1 and installed "gfortran-12.2-universal.pkg" per
"https://cran.r-project.org/bin/macosx/tools/;. I expected this to solve the problem.
It didn't.
Suggestions?
Thanks,
Spencer Graves
p.s. This is my fork of KFAS, available at "https://github.com/sbgraves237/KFAS;.
"sessionInfo()" appears below.
##
sessionInfo()
R version 4.3.1 (2023-06-16)
Platform: x86_64-apple-darwin20 (64-bit)
Running under: macOS Big Sur 11.7.8
Matrix products: default
BLAS:
/System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.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: America/Chicago
tzcode source: internal
attached base packages:
[1] stats graphics grDevices utils datasets methods base
loaded via a namespace (and not attached):
[1] compiler_4.3.1 R6_2.5.1magrittr_2.0.3 cli_3.6.1
[5] tools_4.3.1 glue_1.6.2 rstudioapi_0.14 roxygen2_7.2.3
[9] xml2_1.3.4 vctrs_0.6.2 stringi_1.7.12 knitr_1.42
[13] xfun_0.39 stringr_1.5.0 lifecycle_1.0.3 rlang_1.1.1
[17] purrr_1.0.1
___
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
___
R-SIG-Mac mailing list
R-SIG-Mac@r-project.org
https://stat.ethz.ch/mailman/listinfo/r-sig-mac
[R-SIG-Mac] gfortran: command not found
Hello, All:
"R CMD check KFAS" under macOS 11.7.8 (the latest version that will
run on my aging Mac) complains "gfortran: command not found".
I just upgraded to R 4.3.1 and installed
"gfortran-12.2-universal.pkg" per
"https://cran.r-project.org/bin/macosx/tools/;. I expected this to
solve the problem. It didn't.
Suggestions?
Thanks,
Spencer Graves
p.s. This is my fork of KFAS, available at
"https://github.com/sbgraves237/KFAS;. "sessionInfo()" appears below.
##
sessionInfo()
R version 4.3.1 (2023-06-16)
Platform: x86_64-apple-darwin20 (64-bit)
Running under: macOS Big Sur 11.7.8
Matrix products: default
BLAS:
/System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.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: America/Chicago
tzcode source: internal
attached base packages:
[1] stats graphics grDevices utils datasets methods base
loaded via a namespace (and not attached):
[1] compiler_4.3.1 R6_2.5.1magrittr_2.0.3 cli_3.6.1
[5] tools_4.3.1 glue_1.6.2 rstudioapi_0.14 roxygen2_7.2.3
[9] xml2_1.3.4 vctrs_0.6.2 stringi_1.7.12 knitr_1.42
[13] xfun_0.39 stringr_1.5.0 lifecycle_1.0.3 rlang_1.1.1
[17] purrr_1.0.1
>
___
R-SIG-Mac mailing list
R-SIG-Mac@r-project.org
https://stat.ethz.ch/mailman/listinfo/r-sig-mac
Re: [R-SIG-Mac] macOS may not give R much time in a long compute
On 2/18/23 4:34 PM, Simon Urbanek wrote: On Feb 19, 2023, at 3:50 AM, Spencer Graves wrote: On 2/18/23 6:40 AM, Prof Brian Ripley wrote: Are you using R.app (you failed to say)? I'm "using the newest version of RStudio" [Version 2022.12.0+353 (2022.12.0+353)]. This means I am running R.app? No, it means you're not using R, so please ask RStudio support since that is not under R's control (since RStudio is a web server there are many ways how this could matter). Cheers, Simon PS: that made me think - if R is embedded in another application we should probably include that information in sessionInfo() to avoid confusion of R with other tools. Agreed. Thanks for all you do to help make it easier for people everywhere to understand the information available to them. Spencer Graves ___ R-SIG-Mac mailing list R-SIG-Mac@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-mac
Re: [R-SIG-Mac] macOS may not give R much time in a long compute
On 2/18/23 6:40 AM, Prof Brian Ripley wrote:
Are you using R.app (you failed to say)?
I'm "using the newest version of RStudio" [Version 2022.12.0+353
(2022.12.0+353)]. This means I am running R.app?
If so, have you acted on the documentation about 'app nap'? E.g. §4.1
of the R-admin manual.
Thanks for the term "app nap" and the reference to §4.1 of the
R-admin manual. I had not previously heard of "app nap", but that
sounds like what I've encountered, and that section of the manual
suggests that if I encounter this problem again, I can open a terminal
and enter:
defaults write org.R-project.R NSAppSleepDisabled -bool YES
Will it take effect immediately? Or will I need to restart R?
I've changed the code since I reported this problem, and I have not
encountered this problem since. I'm not sure, but when I noticed this
problem, I may have had "if(max(et3i)>1800)" [progress report every 30
minutes] instead of "if(max(et3i)>180)" [progress report every 3
minutes].[*] With luck, this change may fix this problem. If yes,
might you have any idea what the threshold might be?
Thanks very much.
Spencer Graves
[*] I'm not sure what threshold I was using when I encountered this
problem: 180 or 1800 seconds. I foolishly didn't save the output that
included lines like the following:
iscan = 22992 ; et3i = 180 26 104
iscan = 32124 ; et3i = 22 1 180
On 18/02/2023 12:31, Spencer Graves wrote:
Hello:
During a long compute (in a while loop), I've asked R to report
progress via:
# Progress report every 3 minutes
et3i <- proc.time()-startT3i
if(max(et3i)>180){
startT3i <- proc.time()
cat('iscan = ', iscan3, '; et3i = ',
round(et3i[1:3]), '\n')
}
When it's running properly, I get something like the following:
iscan = 22992 ; et3i = 180 26 104
However if I leave my computer running unattended, I can get
reports like the following:
iscan = 32124 ; et3i = 22 1 180
Evidently, macOS 11.7.4 decided NOT to give time to R.
Suggestions?
Thanks,
Spencer Graves
sessionInfo()
R version 4.2.2 (2022-10-31)
Platform: x86_64-apple-darwin17.0 (64-bit)
Running under: macOS Big Sur 11.7.4
Matrix products: default
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_4.2.2 tools_4.2.2 knitr_1.42 xfun_0.37
>
___
R-SIG-Mac mailing list
R-SIG-Mac@r-project.org
https://stat.ethz.ch/mailman/listinfo/r-sig-mac
[R-SIG-Mac] macOS may not give R much time in a long compute
Hello:
During a long compute (in a while loop), I've asked R to report
progress via:
# Progress report every 3 minutes
et3i <- proc.time()-startT3i
if(max(et3i)>180){
startT3i <- proc.time()
cat('iscan = ', iscan3, '; et3i = ',
round(et3i[1:3]), '\n')
}
When it's running properly, I get something like the following:
iscan = 22992 ; et3i = 180 26 104
However if I leave my computer running unattended, I can get reports
like the following:
iscan = 32124 ; et3i = 22 1 180
Evidently, macOS 11.7.4 decided NOT to give time to R.
Suggestions?
Thanks,
Spencer Graves
sessionInfo()
R version 4.2.2 (2022-10-31)
Platform: x86_64-apple-darwin17.0 (64-bit)
Running under: macOS Big Sur 11.7.4
Matrix products: default
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_4.2.2 tools_4.2.2knitr_1.42 xfun_0.37
>
___
R-SIG-Mac mailing list
R-SIG-Mac@r-project.org
https://stat.ethz.ch/mailman/listinfo/r-sig-mac
Re: [R-SIG-Mac] sessionInfo on Monterey
I updated yesterday to macOS Big Sur 11.5.2,
sessionInfo()
R version 4.1.0 (2021-05-18)
Platform: x86_64-apple-darwin17.0 (64-bit)
Running under: macOS Big Sur 10.16
I just upgraded to 4.1.1 with the same results:
> sessionInfo()
R version 4.1.1 (2021-08-10)
Platform: x86_64-apple-darwin17.0 (64-bit)
Running under: macOS Big Sur 10.16
Hope this helps.
Spencer Graves
On 8/28/21 7:36 AM, peter dalgaard wrote:
Odd indeed. A local build of mine has
sessionInfo()
R version 4.1.0 Patched (2021-05-25 r80389)
Platform: x86_64-apple-darwin20.5.0 (64-bit)
Running under: macOS Big Sur 11.5.2
(Obvsly not up-to-the minute, and my build tools are likely not either on this
machine...)
- pd
On 28 Aug 2021, at 08:00 , Bob Rudis wrote:
arm64:
R version 4.1.1 Patched (2021-08-13 r80752)
Platform: aarch64-apple-darwin20 (64-bit)
Running under: macOS Monterey 12.0
x86_64:
R version 4.1.1 Patched (2021-08-10 r80733)
Platform: x86_64-apple-darwin17.0 (64-bit)
Running under: macOS Big Sur 10.16
On Fri, Aug 27, 2021 at 3:42 AM Prof Brian Ripley wrote:
One oddity is that the CRAN Intel binary build of R (or any other built
under 10.x) when run on Big Sur reports
sessionInfo()
R version 4.1.1 (2021-08-10)
Platform: x86_64-apple-darwin17.0 (64-bit)
Running under: macOS Big Sur 10.16
...
because the system call used reports '10.16'.
If anyone running a beta of Monterey has the CRAN binary installed, for
completeness I would appreciate seeing what is reported.
--
Brian D. Ripley, rip...@stats.ox.ac.uk
Emeritus Professor of Applied Statistics, University of Oxford
___
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
___
R-SIG-Mac mailing list
R-SIG-Mac@r-project.org
https://stat.ethz.ch/mailman/listinfo/r-sig-mac
Re: [R-SIG-Mac] In svg("tst.svg") : failed to load cairo DLL
THANKS, Prof. Ripley. That fixed the problem. Spencer Graves
[please excuse a problem with delayed detection of an error with
autocomplete.]
On 8/7/21 12:05 AM, Prof Brian Ripley wrote:
Install (or re-install) XQuartz. As the R-admin manual §4 says
Various parts of the build require XQuartz to be installed: see
https://www.xquartz.org/releases. These include the tcltk package and
the X11 device: attempting to use these without XQuartz will if possible
remind you. This is also needed for some builds of the
cairographics-based devices (which are not often used on macOS) such as
png(type = "cairo").
svg() is a cairographics-based device .
On 06/08/2021 22:12, Spencer Graves wrote:
Hello:
In R 4.1.0 under macOS 11.4, 'svg("tst.svg")' says, "failed to
load cairo DLL".
This works fine under Windows 10. (I tested under RStudio
1.4.1106, R terminal and R Console all with the same results.)
The first time I try "svg('tst.svg')" in a new R session, I get
a longer message; see below for that and for sessionInfo(). When I
repeat "svg('tst.svg')", I get only "failed to load cairo DLL".
Suggestions?
Thanks,
Spencer Graves
svg('tst.svg')
Warning messages:
1: In grSoftVersion() :
unable to load shared object
'/Library/Frameworks/R.framework/Resources/modules//R_X11.so':
dlopen(/Library/Frameworks/R.framework/Resources/modules//R_X11.so,
6): Library not loaded: /opt/X11/lib/libSM.6.dylib
Referenced from:
/Library/Frameworks/R.framework/Versions/4.1/Resources/modules/R_X11.so
Reason: image not found
2: In cairoVersion() :
unable to load shared object
'/Library/Frameworks/R.framework/Resources/library/grDevices/libs//cairo.so':
dlopen(/Library/Frameworks/R.framework/Resources/library/grDevices/libs//cairo.so,
6): Library not loaded: /opt/X11/lib/libXrender.1.dylib
Referenced from:
/Library/Frameworks/R.framework/Versions/4.1/Resources/library/grDevices/libs/cairo.so
Reason: image not found
3: In svg("tst.svg") : failed to load cairo DLL
> sessionInfo()
R version 4.1.0 (2021-05-18)
Platform: x86_64-apple-darwin17.0 (64-bit)
Running under: macOS Big Sur 10.16
Matrix products: default
LAPACK:
/Library/Frameworks/R.framework/Versions/4.1/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_4.1.0 tools_4.1.0
>
___
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] In svg("tst.svg") : failed to load cairo DLL
This, Prof. Ripley. That fixed the problem. Spencer Graves
On 8/7/21 12:05 AM, Prof Brian Ripley wrote:
Install (or re-install) XQuartz. As the R-admin manual §4 says
Various parts of the build require XQuartz to be installed: see
https://www.xquartz.org/releases. These include the tcltk package and
the X11 device: attempting to use these without XQuartz will if possible
remind you. This is also needed for some builds of the
cairographics-based devices (which are not often used on macOS) such as
png(type = "cairo").
svg() is a cairographics-based device .
On 06/08/2021 22:12, Spencer Graves wrote:
Hello:
In R 4.1.0 under macOS 11.4, 'svg("tst.svg")' says, "failed to
load cairo DLL".
This works fine under Windows 10. (I tested under RStudio
1.4.1106, R terminal and R Console all with the same results.)
The first time I try "svg('tst.svg')" in a new R session, I get
a longer message; see below for that and for sessionInfo(). When I
repeat "svg('tst.svg')", I get only "failed to load cairo DLL".
Suggestions?
Thanks,
Spencer Graves
svg('tst.svg')
Warning messages:
1: In grSoftVersion() :
unable to load shared object
'/Library/Frameworks/R.framework/Resources/modules//R_X11.so':
dlopen(/Library/Frameworks/R.framework/Resources/modules//R_X11.so,
6): Library not loaded: /opt/X11/lib/libSM.6.dylib
Referenced from:
/Library/Frameworks/R.framework/Versions/4.1/Resources/modules/R_X11.so
Reason: image not found
2: In cairoVersion() :
unable to load shared object
'/Library/Frameworks/R.framework/Resources/library/grDevices/libs//cairo.so':
dlopen(/Library/Frameworks/R.framework/Resources/library/grDevices/libs//cairo.so,
6): Library not loaded: /opt/X11/lib/libXrender.1.dylib
Referenced from:
/Library/Frameworks/R.framework/Versions/4.1/Resources/library/grDevices/libs/cairo.so
Reason: image not found
3: In svg("tst.svg") : failed to load cairo DLL
> sessionInfo()
R version 4.1.0 (2021-05-18)
Platform: x86_64-apple-darwin17.0 (64-bit)
Running under: macOS Big Sur 10.16
Matrix products: default
LAPACK:
/Library/Frameworks/R.framework/Versions/4.1/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_4.1.0 tools_4.1.0
>
___
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
[R-SIG-Mac] In svg("tst.svg") : failed to load cairo DLL
Hello:
In R 4.1.0 under macOS 11.4, 'svg("tst.svg")' says, "failed to load
cairo DLL".
This works fine under Windows 10. (I tested under RStudio 1.4.1106,
R terminal and R Console all with the same results.)
The first time I try "svg('tst.svg')" in a new R session, I get a
longer message; see below for that and for sessionInfo(). When I
repeat "svg('tst.svg')", I get only "failed to load cairo DLL".
Suggestions?
Thanks,
Spencer Graves
svg('tst.svg')
Warning messages:
1: In grSoftVersion() :
unable to load shared object
'/Library/Frameworks/R.framework/Resources/modules//R_X11.so':
dlopen(/Library/Frameworks/R.framework/Resources/modules//R_X11.so,
6): Library not loaded: /opt/X11/lib/libSM.6.dylib
Referenced from:
/Library/Frameworks/R.framework/Versions/4.1/Resources/modules/R_X11.so
Reason: image not found
2: In cairoVersion() :
unable to load shared object
'/Library/Frameworks/R.framework/Resources/library/grDevices/libs//cairo.so':
dlopen(/Library/Frameworks/R.framework/Resources/library/grDevices/libs//cairo.so,
6): Library not loaded: /opt/X11/lib/libXrender.1.dylib
Referenced from:
/Library/Frameworks/R.framework/Versions/4.1/Resources/library/grDevices/libs/cairo.so
Reason: image not found
3: In svg("tst.svg") : failed to load cairo DLL
> sessionInfo()
R version 4.1.0 (2021-05-18)
Platform: x86_64-apple-darwin17.0 (64-bit)
Running under: macOS Big Sur 10.16
Matrix products: default
LAPACK:
/Library/Frameworks/R.framework/Versions/4.1/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_4.1.0 tools_4.1.0
>
___
R-SIG-Mac mailing list
R-SIG-Mac@r-project.org
https://stat.ethz.ch/mailman/listinfo/r-sig-mac
Re: [R-SIG-Mac] [BULK] Re: INSTALL R 4.0.2
unless, of course, the segfault is part of the exam ;-) On 2020-12-03 15:59, Simon Urbanek wrote: R 4.0.2 and 4.0.3 are binary compatible and the latter fixes a rather important segfault on macOS, so I would not recommend anyone using R 4.0.2 on macOS ... On 4/12/2020, at 3:19 AM, Spencer Graves wrote: If R 4.0.3 will do, that's easy to find via Google. If you absolutely need R 4.0.2, that's much less obvious. sg On 2020-12-03 07:08, Dr Eberhard W Lisse wrote: You are most welcome. The answer to your question lies probably also in Google. el On 03/12/2020 14:52, Giuseppe Sant wrote: That’s the right way to motivate me. Will let you know about the results. Last thing, because of the unkind comment can you help me solving one thing but radiant? I downloaded the packages thank opened it but in Basics->Prob calculator the layout is incomplete. I can only see the graphic, not the data over it. You know why? Il giorno 3 dic 2020, alle ore 13:41, Dr Eberhard W Lisse ha scritto: Guiseppe, if you can't google, I do not see a bright future for your exam. el On 03/12/2020 14:37, Giuseppe Sant wrote: Hi, I’m a student and I really need to install version of R 4.0.2 as soon as possible because I have an important exam that could change my career. I’m texting just to have the link to download that version. Really thankful, Giuseppe Santangelo. [...] ___ 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] INSTALL R 4.0.2
If R 4.0.3 will do, that's easy to find via Google. If you absolutely need R 4.0.2, that's much less obvious. sg On 2020-12-03 07:08, Dr Eberhard W Lisse wrote: You are most welcome. The answer to your question lies probably also in Google. el On 03/12/2020 14:52, Giuseppe Sant wrote: That’s the right way to motivate me. Will let you know about the results. Last thing, because of the unkind comment can you help me solving one thing but radiant? I downloaded the packages thank opened it but in Basics->Prob calculator the layout is incomplete. I can only see the graphic, not the data over it. You know why? Il giorno 3 dic 2020, alle ore 13:41, Dr Eberhard W Lisse ha scritto: Guiseppe, if you can't google, I do not see a bright future for your exam. el On 03/12/2020 14:37, Giuseppe Sant wrote: Hi, I’m a student and I really need to install version of R 4.0.2 as soon as possible because I have an important exam that could change my career. I’m texting just to have the link to download that version. Really thankful, Giuseppe Santangelo. [...] ___ R-SIG-Mac mailing list R-SIG-Mac@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-mac
Re: [R-SIG-Mac] Problems with R and Big Sur
Sorry: Typo: I tried "sudo xcode-select --install" and got the same error. This was in Terminal where "The default interactive shell is now zsh." It's not critical, because "I was able to update Xcode from App Store." Thanks for the reply. sg On 2020-12-02 11:48, Dr Eberhard W Lisse wrote: sudo xcode-select --install el On 2020-12-02 18:52 , Spencer Graves wrote: $ clang --version Apple clang version 11.0.3 (clang-1103.0.32.59) Target: x86_64-apple-darwin20.1.0 Thread model: posix InstalledDir: /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin ** "sudo rm -rf /Library/Developer/CommandLineTools" deleted "CommandLineTools". Then "sudo xcode-select —install" gave me "invalid argument '—install'". "sudo xcode-select —install" gave me the same. ** Fortunately, I was able to update Xcode from App Store. Now I get: $ clang --version Apple clang version 12.0.0 (clang-1200.0.32.27) Target: x86_64-apple-darwin20.1.0 Thread model: posix InstalledDir: /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin If you also have a problem with "sudo xcode-select —install", you might try the App Store. Thanks, Spencer On 2020-12-02 08:18, Gilberto Camara wrote: For me, it worked as follows sudo rm -rf /Library/Developer/CommandLineTools sudo xcode-select —install Best Gilberto On 2 Dec 2020, at 15:15, Spencer Graves wrote: What should I do to "make sure to have installed the latest version of Apple's development environment, including version 12.0 of the compiler"? Thanks, Spencer Graves On 2020-12-02 07:36, GilbertoCamara wrote: Dear all, I am running R 4.0.3 on BigSur without major performance issues. I am using RStudio instead of the R GUI. I had to build all spatial packages (rgdal, sf, terra and raster) from source using the Apple clang version 12.0.0 compiler. I also had to build GDAL from scratch, since neither the “homebrew” version nor the “kyngchaos” version work well with BigSur. If anyone is building packages from source, please make sure to have installed the latest version of Apple’s development environment, including version 12.0 of the compiler as earlier versions do not work well in BigSur. Best Gilberto === Prof Dr Gilberto Camara Secretariat Director GEO - Group on Earth Observations On 2 Dec 2020, at 14:15, Bob Rudis wrote: After a bit of git and google poking it seems this is happening to users of MacVim (https://github.com/macvim-dev/macvim/issues/1114) and a few other FOSS projects. In various GH issues (like that one) the issue claims to be resolved by using the latest Xcode & SDK but that’s not likely to be a solution for R GUI (which I’m assuming you're using and where this error is coming up). Some of the threads I saw made it seem like it was happening especially on Touch Bar-equipped MacBook Pros (but that’s not confirmed). When I try R GUI on Big Sur (on the new M1 Mini) — either just plain R scripts or plotting — I do not see this, nor do I see this on my Intel MacBook Pro (both are on the latest Big Sur beta and R 4.0.3). On Dec 2, 2020 at 7:53:26 AM, Spencer Graves wrote: I didn't get this with R 4.0.3 under macOS Big Sur 11.0.1 with "time R CMD build" / check. I have not tried it under RStudio. sg On 2020-12-02 05:01, Dr Eberhard W Lisse wrote: I don't get this in 4.0.3 (using the command line version of R) and I don't get this in RStudio 1.3.1093 either. I use the homebrew versions without the R GUI even installed. I am sure more detail will be helpful to the developers. el On 02/12/2020 11:09, Maria-Angeles Casares-de-Cal via R-SIG-Mac wrote: To those in charge of R for Mac OS X: I have installed the new Big Sur operating system and now I always get a warning similar to: 2020-12-02 09:52:00.647 R[703:11786] Warning: Expected min height of view: () to be less than or equal to 30 but got a height of 32.00. This error will be logged once per view in violation. and the computer becomes very slow. Can I do something to fix it, or will we have to wait for an R update? Thank you very much for your attention. Sincerely, María-Ángeles Casares-de-Cal [...] ___ 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 ___ R-SIG-Mac mailing list R-SIG-Mac@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-mac
Re: [R-SIG-Mac] Problems with R and Big Sur
$ clang --version Apple clang version 11.0.3 (clang-1103.0.32.59) Target: x86_64-apple-darwin20.1.0 Thread model: posix InstalledDir: /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin ** "sudo rm -rf /Library/Developer/CommandLineTools" deleted "CommandLineTools". Then "sudo xcode-select —install" gave me "invalid argument '—install'". "sudo xcode-select —install" gave me the same. ** Fortunately, I was able to update Xcode from App Store. Now I get: $ clang --version Apple clang version 12.0.0 (clang-1200.0.32.27) Target: x86_64-apple-darwin20.1.0 Thread model: posix InstalledDir: /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin If you also have a problem with "sudo xcode-select —install", you might try the App Store. Thanks, Spencer On 2020-12-02 08:18, Gilberto Camara wrote: For me, it worked as follows sudo rm -rf /Library/Developer/CommandLineTools sudo xcode-select —install Best Gilberto On 2 Dec 2020, at 15:15, Spencer Graves wrote: What should I do to "make sure to have installed the latest version of Apple's development environment, including version 12.0 of the compiler"? Thanks, Spencer Graves On 2020-12-02 07:36, GilbertoCamara wrote: Dear all, I am running R 4.0.3 on BigSur without major performance issues. I am using RStudio instead of the R GUI. I had to build all spatial packages (rgdal, sf, terra and raster) from source using the Apple clang version 12.0.0 compiler. I also had to build GDAL from scratch, since neither the “homebrew” version nor the “kyngchaos” version work well with BigSur. If anyone is building packages from source, please make sure to have installed the latest version of Apple’s development environment, including version 12.0 of the compiler as earlier versions do not work well in BigSur. Best Gilberto === Prof Dr Gilberto Camara Secretariat Director GEO - Group on Earth Observations On 2 Dec 2020, at 14:15, Bob Rudis wrote: After a bit of git and google poking it seems this is happening to users of MacVim (https://github.com/macvim-dev/macvim/issues/1114) and a few other FOSS projects. In various GH issues (like that one) the issue claims to be resolved by using the latest Xcode & SDK but that’s not likely to be a solution for R GUI (which I’m assuming you're using and where this error is coming up). Some of the threads I saw made it seem like it was happening especially on Touch Bar-equipped MacBook Pros (but that’s not confirmed). When I try R GUI on Big Sur (on the new M1 Mini) — either just plain R scripts or plotting — I do not see this, nor do I see this on my Intel MacBook Pro (both are on the latest Big Sur beta and R 4.0.3). On Dec 2, 2020 at 7:53:26 AM, Spencer Graves wrote: I didn't get this with R 4.0.3 under macOS Big Sur 11.0.1 with "time R CMD build" / check. I have not tried it under RStudio. sg On 2020-12-02 05:01, Dr Eberhard W Lisse wrote: I don't get this in 4.0.3 (using the command line version of R) and I don't get this in RStudio 1.3.1093 either. I use the homebrew versions without the R GUI even installed. I am sure more detail will be helpful to the developers. el On 02/12/2020 11:09, Maria-Angeles Casares-de-Cal via R-SIG-Mac wrote: To those in charge of R for Mac OS X: I have installed the new Big Sur operating system and now I always get a warning similar to: 2020-12-02 09:52:00.647 R[703:11786] Warning: Expected min height of view: () to be less than or equal to 30 but got a height of 32.00. This error will be logged once per view in violation. and the computer becomes very slow. Can I do something to fix it, or will we have to wait for an R update? Thank you very much for your attention. Sincerely, María-Ángeles Casares-de-Cal [...] ___ 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 ___ 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] Problems with R and Big Sur
What should I do to "make sure to have installed the latest version
of Apple's development environment, including version 12.0 of the
compiler"?
Thanks,
Spencer Graves
On 2020-12-02 07:36, GilbertoCamara wrote:
Dear all,
I am running R 4.0.3 on BigSur without major performance issues. I am using
RStudio instead of the R GUI.
I had to build all spatial packages (rgdal, sf, terra and raster) from source
using the Apple clang version 12.0.0 compiler. I also had to build GDAL from
scratch, since neither the “homebrew” version nor the “kyngchaos” version work
well with BigSur.
If anyone is building packages from source, please make sure to have installed
the latest version of Apple’s development environment, including version 12.0
of the compiler as earlier versions do not work well in BigSur.
Best
Gilberto
===
Prof Dr Gilberto Camara
Secretariat Director
GEO - Group on Earth Observations
On 2 Dec 2020, at 14:15, Bob Rudis wrote:
After a bit of git and google poking it seems this is happening to users
of MacVim (https://github.com/macvim-dev/macvim/issues/1114) and a few
other FOSS projects.
In various GH issues (like that one) the issue claims to be resolved by
using the latest Xcode & SDK but that’s not likely to be a solution for R
GUI (which I’m assuming you're using and where this error is coming up).
Some of the threads I saw made it seem like it was happening especially on
Touch Bar-equipped MacBook Pros (but that’s not confirmed).
When I try R GUI on Big Sur (on the new M1 Mini) — either just plain R
scripts or plotting — I do not see this, nor do I see this on my Intel
MacBook Pro (both are on the latest Big Sur beta and R 4.0.3).
On Dec 2, 2020 at 7:53:26 AM, Spencer Graves
wrote:
I didn't get this with R 4.0.3 under macOS Big Sur 11.0.1 with "time
R CMD build" / check. I have not tried it under RStudio.
sg
On 2020-12-02 05:01, Dr Eberhard W Lisse wrote:
I don't get this in 4.0.3 (using the command line version of R) and I
don't get this in RStudio 1.3.1093 either. I use the homebrew versions
without the R GUI even installed.
I am sure more detail will be helpful to the developers.
el
On 02/12/2020 11:09, Maria-Angeles Casares-de-Cal via R-SIG-Mac wrote:
To those in charge of R for Mac OS X:
I have installed the new Big Sur operating system and now I always get
a warning similar to:
2020-12-02 09:52:00.647 R[703:11786] Warning: Expected min height of
view: () to be less than
or equal to 30 but got a height of 32.00. This error will be
logged once per view in violation.
and the computer becomes very slow.
Can I do something to fix it, or will we have to wait for an R update?
Thank you very much for your attention.
Sincerely,
María-Ángeles Casares-de-Cal
[...]
___
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
___
R-SIG-Mac mailing list
R-SIG-Mac@r-project.org
https://stat.ethz.ch/mailman/listinfo/r-sig-mac
Re: [R-SIG-Mac] Problems with R and Big Sur
I didn't get this with R 4.0.3 under macOS Big Sur 11.0.1 with "time R CMD build" / check. I have not tried it under RStudio. sg On 2020-12-02 05:01, Dr Eberhard W Lisse wrote: I don't get this in 4.0.3 (using the command line version of R) and I don't get this in RStudio 1.3.1093 either. I use the homebrew versions without the R GUI even installed. I am sure more detail will be helpful to the developers. el On 02/12/2020 11:09, Maria-Angeles Casares-de-Cal via R-SIG-Mac wrote: To those in charge of R for Mac OS X: I have installed the new Big Sur operating system and now I always get a warning similar to: 2020-12-02 09:52:00.647 R[703:11786] Warning: Expected min height of view: () to be less than or equal to 30 but got a height of 32.00. This error will be logged once per view in violation. and the computer becomes very slow. Can I do something to fix it, or will we have to wait for an R update? Thank you very much for your attention. Sincerely, María-Ángeles Casares-de-Cal [...] ___ R-SIG-Mac mailing list R-SIG-Mac@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-mac
Re: [R-SIG-Mac] Catalina Crashes R
I have 10.15.4, and I don't notice any serious problems. I just
did "install.packages('KernSmooth')" and "help(pac='KernSmooth')" to
look at the DESCRIPTION file, without a problem.
Spencer Graves
On 2020-05-21 09:49, Joseph Vanterpool wrote:
Hello,
Yesterday, I started using the John Hopkins course that includes R training. I
currently have a Mac with Catalina (Version 10.15.4).
For simple examples, they have you install and load KernSmooth to view the
copyright date. The first time I tried this, the installation was fine, but
loading didn’t work. I tried a second time and it worked.
I noticed on the forum that other people had similar problems, though were
further along in their use of R. Have these problems been resolved?
Thanks,
Joseph
___
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] obsolete LaTeX software in "R CMD check" on Mac?
I did more tidying. "ls -l /usr/local/bin/" contained 854 objects before I did "rm" on 451 that were alias for objects in "/usr/local/texlive/2016". After I did that, "ls -l /usr/local/bin/" contained 403 = 854-451 objects. Thanks again to Ken Beath, Peter Dalgaard, Eberhard W Lisse, Berend Hasselman, marc Schwartz, Adrian Dușa, and everyone else who took the time to consider the question. This had been a problem for me since at least early February. It's good to have it fixed. Spencer Graves On 2020-05-17 02:11, peter dalgaard wrote: So you should be set. Anything more is just tidying. I have two of the three programs mentioned in /library/TeX xindy.mem nowhere in sight, but they are pretty obscure. -pd On 17 May 2020, at 05:18 , Spencer Graves wrote: I did "which" for all 451 executables found by "ls -l /usr/local/bin | grep 'texlive/20' > texlive_20.txt". All but 3 of them were found in "/Library/TeX/texbin/". The 3 not found were lua2dox_filter, pdfatfi, and xindy.mem. In particular, a2ping was found there. Anything else? Thanks again. Spencer Graves ___ R-SIG-Mac mailing list R-SIG-Mac@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-mac
Re: [R-SIG-Mac] obsolete LaTeX software in "R CMD check" on Mac?
On 2020-05-15 03:34, peter dalgaard wrote:
On 15 May 2020, at 06:04 , Spencer Graves wrote:
Hi, Peter et al.:
I'm still overwhelmed.
To limit changes to things I think I understand, my '/usr/local/texlive'
directory contains subdirectories 2014, 2015, 2016, 2020, and texmf-local.
From your comments, I gather that the following would be wise:
sudo rm -r /usr/local/texlive/2014
sudo rm -r /usr/local/texlive/2015
sudo rm -r /usr/local/texlive/2016
I did this, and "R CMD check Ecfun_0.2-4.tar.gz" still ran to completion
without errors.
I don't understand "ls -l /usr/local/bin | grep 'texlive/2016' | awk '{print $9}'",
but I did "ls -l /usr/local/bin | grep 'texlive/20' > texlive_20.txt" and examined
texlive_20.txt in R. I found it contained 451 lines like the following:
lrwxr-xr-x 1 sbgraves admin48 Jan 13 17:42 a2ping ->
/usr/local/texlive/2016/bin/x86_64-darwin/a2ping
Yup, upgrades until 2016 likely overwrote earlier links to 2015, 2014,..
The awk thing just reduces the above to the 9th field (i.e. "a2ping"), so you
could in principle save the list to a file, say remove.me, and then
for i in `cat remove.me` ; do rm /usr/local/bin/$i ; done
(with a sudo somewhere, and do check carefully...)
All had "2016". I'm inferring from your comments that if anything I do calls any of those 451
operations like "a2ping", I will get "not found". If I get that, I gather I'm supposed to
"sudo rm /usr/local/bin/a2ping" and hope that solves the problem.
Yep. That should solve things, provided there's an a2ping in /Library/TeX/texbin
I did "which" for all 451 executables found by "ls -l
/usr/local/bin | grep 'texlive/20' > texlive_20.txt". All but 3 of them
were found in "/Library/TeX/texbin/". The 3 not found were
lua2dox_filter, pdfatfi, and xindy.mem. In particular, a2ping was found
there.
Anything else?
Thanks again.
Spencer Graves
___
R-SIG-Mac mailing list
R-SIG-Mac@r-project.org
https://stat.ethz.ch/mailman/listinfo/r-sig-mac
Re: [R-SIG-Mac] obsolete LaTeX software in "R CMD check" on Mac?
Hi, Peter et al.:
I'm still overwhelmed.
To limit changes to things I think I understand, my
'/usr/local/texlive' directory contains subdirectories 2014, 2015, 2016,
2020, and texmf-local. From your comments, I gather that the following
would be wise:
sudo rm -r /usr/local/texlive/2014
sudo rm -r /usr/local/texlive/2015
sudo rm -r /usr/local/texlive/2016
I did this, and "R CMD check Ecfun_0.2-4.tar.gz" still ran to
completion without errors.
I don't understand "ls -l /usr/local/bin | grep 'texlive/2016' |
awk '{print $9}'", but I did "ls -l /usr/local/bin | grep 'texlive/20' >
texlive_20.txt" and examined texlive_20.txt in R. I found it contained
451 lines like the following:
lrwxr-xr-x 1 sbgraves admin 48 Jan 13 17:42 a2ping ->
/usr/local/texlive/2016/bin/x86_64-darwin/a2ping
All had "2016". I'm inferring from your comments that if
anything I do calls any of those 451 operations like "a2ping", I will
get "not found". If I get that, I gather I'm supposed to "sudo rm
/usr/local/bin/a2ping" and hope that solves the problem.
???
Thanks very much.
Spencer Graves
On 2020-05-14 02:51, peter dalgaard wrote:
Well, you solved the immediate problem. However, you could get in trouble later
with other tools from the 2016 TeXlive set, which seems to be what you have
lingering.
There doesn't seem to be an uninstaller that removes the symlinks on Mac. So...
Either: (a) remove all links manually plus the entire /usr/local/texlive/2016
tree.
Or: (b) ensure that the current TeXlive stuff is found ahead of /usr/local/bin
(a) is a bit painful when it comes to the symlinks. There are likely around 450
of them. Of course, only a handful are ever used, so once
/usr/local/texlive/2016 is gone, you just get a 'not found' type error and can
remove the offending link one at a time. It is possible to automate it, but a
bit dangerous if you get it wrong... Something like
ls -l /usr/local/bin | grep 'texlive/2016' | awk '{print $9}'
should give you a list. (...which with a bit of diligence, you can have removed
in one swoop, but...)
(b) is more expedient (but leaves the mess in /usr/local/bin): edit /etc/paths
with, like,
sudo nano /etc/paths
insert /Library/TeX/texbin at the top and save. Then, for good measure
sudo rm /etc/paths.d/TeX
so that it isn't in $PATH twice.
-pd
On 14 May 2020, at 01:21 , Spencer Graves wrote:
Hi, Eberhard:
Please excuse: I've already solved this problem. "sudo rm
/usr/local/bin/pdflatex" did the trick.
You may be right that I should reformat my hard drive and restore from my
TimeMachine. However, that sounds too much like "do-it-yourself lobotomy" to
me. I don't plan to try that right now.
Thanks again for your suggestions.
Spencer
On 2020-05-13 18:16, Dr Eberhard W Lisse wrote:
Spencer,
If you just google
https://www.google.com/search?q=uninstallpkg
the first link coming up is the right one. But see below.
Do you have a ~/Downloads directory? Did you look in there?
So the removing of /usr/local/bin/pdflatex did not remove the old 2019
version. Which is why I proposed uninstallPKG to get rid of all the old
crud.
To be honest, I reckon you should run TimeMachine and then re-install
Catalina after reformatting your hard disk, restore your home directory
and then carefully (step by step) install the Xcode Command Lime Tools,
homebrew, MacTeX and R, which will give you a known state.
I like to have a consistent, known state, with only one (the latest if
possible) version of everything and if possible via the Software Update
or a package manager (homebrew).
homebrew has what is called Casks, which installs proper MacApps (often
from the original developers’ site). I check regularly whether there
are (new) casks for apps I have manually installed which I then install
(overwrite) so a
brew upgrade
brew cask upgrade
will sort me out
btw, I just looked and
brew cask install uninstallpkg
will do the deed nicely.
el
On 2020-05-13 23:31 , Spencer Graves wrote:
Thank you all for your comments on this. I'm overwhelmed, not
just with the volume of the discussion, but my own ignorance of the
standard command line protocols.
After trying some but on all of Eberhard Lisse's and Peter
Dalgaard's suggestions below, the problem disappeard after I executed
"sudo rm /usr/local/bin/pdflatex". I tested "R CMD check
Ecfun_0.2-4.tar.gz" right before I did that, and the problem was still
there. It disappeared right after I did that.
Lisse's "UninstallPKG" might have been more graceful, but I
couldn't find the key to that padlock, so I used something that seems
more like boltcutters instead -- and it worked.
Thanks again,
Spencer Graves
On
Re: [R-SIG-Mac] obsolete LaTeX software in "R CMD check" on Mac?
Hi, Eberhard:
Please excuse: I've already solved this problem. "sudo rm
/usr/local/bin/pdflatex" did the trick.
You may be right that I should reformat my hard drive and
restore from my TimeMachine. However, that sounds too much like
"do-it-yourself lobotomy" to me. I don't plan to try that right now.
Thanks again for your suggestions.
Spencer
On 2020-05-13 18:16, Dr Eberhard W Lisse wrote:
Spencer,
If you just google
https://www.google.com/search?q=uninstallpkg
the first link coming up is the right one. But see below.
Do you have a ~/Downloads directory? Did you look in there?
So the removing of /usr/local/bin/pdflatex did not remove the old 2019
version. Which is why I proposed uninstallPKG to get rid of all the old
crud.
To be honest, I reckon you should run TimeMachine and then re-install
Catalina after reformatting your hard disk, restore your home directory
and then carefully (step by step) install the Xcode Command Lime Tools,
homebrew, MacTeX and R, which will give you a known state.
I like to have a consistent, known state, with only one (the latest if
possible) version of everything and if possible via the Software Update
or a package manager (homebrew).
homebrew has what is called Casks, which installs proper MacApps (often
from the original developers’ site). I check regularly whether there
are (new) casks for apps I have manually installed which I then install
(overwrite) so a
brew upgrade
brew cask upgrade
will sort me out
btw, I just looked and
brew cask install uninstallpkg
will do the deed nicely.
el
On 2020-05-13 23:31 , Spencer Graves wrote:
Thank you all for your comments on this. I'm overwhelmed, not
just with the volume of the discussion, but my own ignorance of the
standard command line protocols.
After trying some but on all of Eberhard Lisse's and Peter
Dalgaard's suggestions below, the problem disappeard after I executed
"sudo rm /usr/local/bin/pdflatex". I tested "R CMD check
Ecfun_0.2-4.tar.gz" right before I did that, and the problem was still
there. It disappeared right after I did that.
Lisse's "UninstallPKG" might have been more graceful, but I
couldn't find the key to that padlock, so I used something that seems
more like boltcutters instead -- and it worked.
Thanks again,
Spencer Graves
On 2020-05-13 09:57, Dr Eberhard W Lisse wrote:
Peter,
as far as I understand this the idea is to make the binaries of whatever
MacTeX you use available in
/Library/TeX/texbin
Finder says this was installed yesterday, presumably when I
installed MacTex.
so that it survives the (annual) upgrade of MacTeX or a switch from the
Basic to the Big MacTeX or whatever.
I would personally not remove the pdflatex, but find something like
UninstallPKG
How do I find something like "UninstallPKG"?
and then locate MacTeX in there and remove that (all
versions, so all old crud goes away.
If you, like me, use MacTeXBasic you can do something like
I don't think I'm using MacTexBasic, but I'm not a big LaTeX user,
beyond trying to make RMarkdown work these days (and having used LaTeX
when writing "Functional Data Analysis with R and Matlab with Ramsay and
Hooker over a decade ago).
if [ ! -x /usr/local/bin/gawk ]
I don't seem to have gawk installed, at least not there, and
"gawk" at a Terminal prompt returned, "-bash: gawk: command not found".
then
brew install gawk
I did that, and it seemed to work. It started "Updating
Homebrew..." and ended 'For compilers to find readline you may need to
set: export LDFLAGS="-L/usr/local/opt/readline/lib"; export
CPPFLAGS="-I/usr/local/opt/readline/include"'.
fi
tlmgr list --only-installed \
| gawk '{gsub(/:/, ""); print $2}' \
> ~/Downloads/texlive.$(date +%Y-%m-%d).installed.txt
I tried that. It executed quickly with no output.
before uninstalling the old packages,
I don't know what to uninstall nor how to do it nor how to even
find what I should uninstall, other than ask here (or maybe at
tex.stackexchange, as Dirk Eddelbuettel had suggested).
then you install the latest and
greatest MacTeXBasic
I installed MacTex yesterday, as I indicated earlier in this
thread. That may not be enough, but I will skip that for the moment.
and run something like
tlmgr update --self
I did this in /Library/TeX/texbin as follows:
texbin sbgraves$ tlmgr update --self
tlmgr: Local TeX Live (2019) is older than remote repository (2020).
Cross release updates are only supported with
update-tlmgr-latest(.sh/.exe) --update
See https://tug.org/texlive/upgrade.html for details.
That link starts with, "By default, please get the new TL by doing
a
Re: [R-SIG-Mac] obsolete LaTeX software in "R CMD check" on Mac?
Thank you all for your comments on this. I'm overwhelmed, not
just with the volume of the discussion, but my own ignorance of the
standard command line protocols.
After trying some but on all of Eberhard Lisse's and Peter
Dalgaard's suggestions below, the problem disappeard after I executed
"sudo rm /usr/local/bin/pdflatex". I tested "R CMD check
Ecfun_0.2-4.tar.gz" right before I did that, and the problem was still
there. It disappeared right after I did that.
Lisse's "UninstallPKG" might have been more graceful, but I
couldn't find the key to that padlock, so I used something that seems
more like boltcutters instead -- and it worked.
Thanks again,
Spencer Graves
On 2020-05-13 09:57, Dr Eberhard W Lisse wrote:
Peter,
as far as I understand this the idea is to make the binaries of whatever
MacTeX you use available in
/Library/TeX/texbin
Finder says this was installed yesterday, presumably when I
installed MacTex.
so that it survives the (annual) upgrade of MacTeX or a switch from the
Basic to the Big MacTeX or whatever.
I would personally not remove the pdflatex, but find something like
UninstallPKG
How do I find something like "UninstallPKG"?
and then locate MacTeX in there and remove that (all
versions, so all old crud goes away.
If you, like me, use MacTeXBasic you can do something like
I don't think I'm using MacTexBasic, but I'm not a big LaTeX
user, beyond trying to make RMarkdown work these days (and having used
LaTeX when writing "Functional Data Analysis with R and Matlab with
Ramsay and Hooker over a decade ago).
if [ ! -x /usr/local/bin/gawk ]
I don't seem to have gawk installed, at least not there, and
"gawk" at a Terminal prompt returned, "-bash: gawk: command not found".
then
brew install gawk
I did that, and it seemed to work. It started "Updating
Homebrew..." and ended 'For compilers to find readline you may need to
set: export LDFLAGS="-L/usr/local/opt/readline/lib"; export
CPPFLAGS="-I/usr/local/opt/readline/include"'.
fi
tlmgr list --only-installed \
| gawk '{gsub(/:/, ""); print $2}' \
> ~/Downloads/texlive.$(date +%Y-%m-%d).installed.txt
I tried that. It executed quickly with no output.
before uninstalling the old packages,
I don't know what to uninstall nor how to do it nor how to even
find what I should uninstall, other than ask here (or maybe at
tex.stackexchange, as Dirk Eddelbuettel had suggested).
then you install the latest and
greatest MacTeXBasic
I installed MacTex yesterday, as I indicated earlier in this
thread. That may not be enough, but I will skip that for the moment.
and run something like
tlmgr update --self
I did this in /Library/TeX/texbin as follows:
texbin sbgraves$ tlmgr update --self
tlmgr: Local TeX Live (2019) is older than remote repository (2020).
Cross release updates are only supported with
update-tlmgr-latest(.sh/.exe) --update
See https://tug.org/texlive/upgrade.html for details.
That link starts with, "By default, please get the new TL by
doing a new installation instead of proceeding here." Clicking "here"
took me to where I was yesterday, when I installed MacTex-2020, which
seems to have gone into "/user/local/texlive/2020". I also found under
"/user/local/texlive" subdirectories for 2014, and 2016 but not 2019.
tlmgr install $(cat ~/Downloads/texlive.$(date +%Y-%m-%d).installed.txt)
This gave me the same message as "tlmgr update --self".
and, perhaps
perl -i -p \
-e 's+\$SELFAUTOPARENT/+/usr/local/texlive/+' \
/usr/local/texlive/2020basic/texmf.cnf
texhash
I have "/user/local/texlive/2020" but not "2020basic", as I
indicated above. I think I'll skip this for the moment.
:-)-O
Nowadays, you can just
sudo rm -rf /usr/local/texlive/2019basic
and if you use homebrew you might have /usr/local owned by yourself so
you don't need the sudo.
Time Machine is your friend (as I just noticed) :-)-O
el
On 13/05/2020 15:34, peter dalgaard wrote:
Hmm, like Eberhard, I'm not too sure this is right.
A look at ls -l /usr/local/bin should be informative though.
ls -l /usr/local/bin
total 460456
lrwxr-xr-x 1 root wheel 66 Nov 26 2018 2to3 ->
../../../Library/Frameworks/Python.framework/Versions/3.7/bin/2to3
lrwxr-xr-x 1 sbgraves wheel 70 Jun 8 2016 2to3-3.5 ->
../../../Library/Frameworks/Python.framework/Versions/3.5/bin/2to3-3.5
lrwxr-xr-x 1 root wheel 70 Nov 26 2018 2to3-3.7 ->
../../../Library/Frameworks/Python.framework/Versions/3.7/bin/2to3-3.7
lrwx
Re: [R-SIG-Mac] obsolete LaTeX software in "R CMD check" on Mac?
Hi, Peter et al.:
It looks like you've properly diagnosed my problem. How do I fix
it?
"which pdflatex" and "echo $PATH" are as follows:
$ which pdflatex
/usr/local/bin/pdflatex
$ echo $PATH
/Library/Frameworks/Python.framework/Versions/3.7/bin:/Users/sbgraves/anaconda3/bin:/Library/Frameworks/Python.framework/Versions/3.7/bin:/opt/local/bin:/opt/local/sbin:/Users/sbgraves/anaconda/bin:/Library/Frameworks/Python.framework/Versions/3.5/bin:/usr/local/bin:/usr/bin:/bin:/usr/sbin:/sbin:/Library/TeX/texbin:/opt/X11/bin:/usr/local/git/bin
I do find "/Library/TeX/texbin/pdflatex" on my hard drive, but
"which pdflatex" doesn't find it.
Thanks,
Spencer Graves
On 2020-05-13 01:31, peter dalgaard wrote:
You typically need to ensure that you have the right TeX installation in your
PATH (and not an older one earlier in the path). You should see something like
this
Peters-MacBook-Air:BUILD pd$ which pdflatex
/Library/TeX/texbin/pdflatex
Peters-MacBook-Air:BUILD pd$ pdflatex -version
pdfTeX 3.14159265-2.6-1.40.20 (TeX Live 2019)
kpathsea version 6.3.1
Peters-MacBook-Air:BUILD pd$ echo $PATH
/usr/local/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/gfortran/bin:/usr/local/clang8/bin:/Library/TeX/texbin:/opt/X11/bin
(Notice that if I had older TeX stuff in /usr/local, I could be in similar
trouble...)
-pd
On 13 May 2020, at 06:15 , Spencer Graves wrote:
Hi, Ken et al.:
Thanks for the info. I tried to do what you suggested but still have
the problem.
Specifically, a web search for TexLive 2020 led me to "https://tug.org/texlive/;. That invited me to download and install
MacTex 2020 from "https://tug.org/mactex/mactex-download.html;, which I did. Everything seemed to go smoothly, but when I ran
"R CMD build Ecfun" and "R CMD check Ecfun_0.2-4.tar.gz", I got the same error. This is running those commands in a
Terminal. When I invoked "r" there just now and requested "sessionInfo()", I got the following:
R version 4.0.0 (2020-04-24)
Platform: x86_64-apple-darwin17.0 (64-bit)
Running under: macOS Catalina 10.15.4
Matrix products: default
BLAS: /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libRblas.dylib
LAPACK:
/Library/Frameworks/R.framework/Versions/4.0/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_4.0.0
Might you have other suggestions?
Thanks very much for eliminating one possible source of this problem.
Spencer Graves
On 2020-05-12 20:12, Ken Beath wrote:
Your package passes checks on my machine perfectly. It has R 4.0.0 with RStudio
and TexLive 2020 with updates to a week or two ago.
Ken
On 13 May 2020, at 8:17 am, Spencer Graves wrote:
Hello, All:
Might "R CMD check" on Mac use obsolete LaTeX software?
I ask, because "R CMD check" on my Mac started reporting LaTeX
errors on *.Rd files that previously passed "R CMD check" without
problems. Dirk Eddelbuettel recommended I ask tex.stackexchange about
that. I did that and got the following:
* "In a current tex system \textasciigrave should work with
your families - they don't have the glyph but latex will fall back
without error. In older systems it could give an error."
See:
https://tex.stackexchange.com/questions/543783/package-textcomp-error-symbol-textasciigrave-not-provided
Comments?
Thanks,
Spencer Graves
p.s. An earlier post on this issue to r-pkg-devel is copied below.
Forwarded Message
Subject: [R-pkg-devel] Error: Symbol \textasciigrave not provided by
(textcomp)
Date: Sun, 16 Feb 2020 14:21:17 -0600
From: Spencer Graves
To: r-package-de...@r-project.org
Hello, All:
"R CMD check Ecfun_0.2-4.tar.gz" ends with 8 repetitions of the
following:
! Package textcomp Error: Symbol \textasciigrave not provided by
(textcomp)font family zi4 in TS1 encoding.
(textcomp)Default family used instead.
See the textcomp package documentation for explanation.
* checking PDF version of manual without hyperrefs or index ... ERROR
* DONE
This is using R 3.6.2 under macOS 10.15.3 applied to the current
development version of"https://github.com/sbgraves237/Ecfun;. Travis
CI reported that the build passed; see
"https://travis-ci.org/sbgraves237/Ecfun/builds/650505913?utm_medium=notification_source=email;.
This looks to me like it's complaining about the use of the back
tick character ("`", below "~" on the top left key on a standard
American English keyboard), which I assume is equivalent to
"\te
Re: [R-SIG-Mac] obsolete LaTeX software in "R CMD check" on Mac?
Hi, Ken et al.:
Thanks for the info. I tried to do what you suggested but still
have the problem.
Specifically, a web search for TexLive 2020 led me to
"https://tug.org/texlive/". That invited me to download and install
MacTex 2020 from "https://tug.org/mactex/mactex-download.html;, which I
did. Everything seemed to go smoothly, but when I ran "R CMD build
Ecfun" and "R CMD check Ecfun_0.2-4.tar.gz", I got the same error. This
is running those commands in a Terminal. When I invoked "r" there just
now and requested "sessionInfo()", I got the following:
R version 4.0.0 (2020-04-24)
Platform: x86_64-apple-darwin17.0 (64-bit)
Running under: macOS Catalina 10.15.4
Matrix products: default
BLAS:
/Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libRblas.dylib
LAPACK:
/Library/Frameworks/R.framework/Versions/4.0/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_4.0.0
Might you have other suggestions?
Thanks very much for eliminating one possible source of this
problem.
Spencer Graves
On 2020-05-12 20:12, Ken Beath wrote:
Your package passes checks on my machine perfectly. It has R 4.0.0 with RStudio
and TexLive 2020 with updates to a week or two ago.
Ken
On 13 May 2020, at 8:17 am, Spencer Graves wrote:
Hello, All:
Might "R CMD check" on Mac use obsolete LaTeX software?
I ask, because "R CMD check" on my Mac started reporting LaTeX
errors on *.Rd files that previously passed "R CMD check" without
problems. Dirk Eddelbuettel recommended I ask tex.stackexchange about
that. I did that and got the following:
* "In a current tex system \textasciigrave should work with
your families - they don't have the glyph but latex will fall back
without error. In older systems it could give an error."
See:
https://tex.stackexchange.com/questions/543783/package-textcomp-error-symbol-textasciigrave-not-provided
Comments?
Thanks,
Spencer Graves
p.s. An earlier post on this issue to r-pkg-devel is copied below.
Forwarded Message
Subject:[R-pkg-devel] Error: Symbol \textasciigrave not provided by
(textcomp)
Date: Sun, 16 Feb 2020 14:21:17 -0600
From: Spencer Graves
To: r-package-de...@r-project.org
Hello, All:
"R CMD check Ecfun_0.2-4.tar.gz" ends with 8 repetitions of the
following:
! Package textcomp Error: Symbol \textasciigrave not provided by
(textcomp)font family zi4 in TS1 encoding.
(textcomp)Default family used instead.
See the textcomp package documentation for explanation.
* checking PDF version of manual without hyperrefs or index ... ERROR
* DONE
This is using R 3.6.2 under macOS 10.15.3 applied to the current
development version of"https://github.com/sbgraves237/Ecfun;. Travis
CI reported that the build passed; see
"https://travis-ci.org/sbgraves237/Ecfun/builds/650505913?utm_medium=notification_source=email;.
This looks to me like it's complaining about the use of the back
tick character ("`", below "~" on the top left key on a standard
American English keyboard), which I assume is equivalent to
"\textasciigrave" in certain contexts.
Six out of those 8 repetitions occur in the examples sections of
files "grepNonStandardCharacters.Rd", "subNonStandardCharacters.Rd", and
"subNonStandardNames.Rd". Those functions were written to fix parsing
errors with names like "Raúl" that had been mangled by different
software before I could get it into R.
After a day's work failed to produce a work around, I decided to
ask this group.
What do you suggest?
Thanks,
Spencer Graves
__
r-package-de...@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-package-devel
[[alternative HTML version deleted]]
___
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
[R-SIG-Mac] obsolete LaTeX software in "R CMD check" on Mac?
Hello, All:
Might "R CMD check" on Mac use obsolete LaTeX software?
I ask, because "R CMD check" on my Mac started reporting LaTeX
errors on *.Rd files that previously passed "R CMD check" without
problems. Dirk Eddelbuettel recommended I ask tex.stackexchange about
that. I did that and got the following:
* "In a current tex system \textasciigrave should work with
your families - they don't have the glyph but latex will fall back
without error. In older systems it could give an error."
See:
https://tex.stackexchange.com/questions/543783/package-textcomp-error-symbol-textasciigrave-not-provided
Comments?
Thanks,
Spencer Graves
p.s. An earlier post on this issue to r-pkg-devel is copied below.
Forwarded Message
Subject:[R-pkg-devel] Error: Symbol \textasciigrave not provided by
(textcomp)
Date: Sun, 16 Feb 2020 14:21:17 -0600
From: Spencer Graves
To: r-package-de...@r-project.org
Hello, All:
"R CMD check Ecfun_0.2-4.tar.gz" ends with 8 repetitions of the
following:
! Package textcomp Error: Symbol \textasciigrave not provided by
(textcomp) font family zi4 in TS1 encoding.
(textcomp) Default family used instead.
See the textcomp package documentation for explanation.
* checking PDF version of manual without hyperrefs or index ... ERROR
* DONE
This is using R 3.6.2 under macOS 10.15.3 applied to the current
development version of "https://github.com/sbgraves237/Ecfun". Travis
CI reported that the build passed; see
"https://travis-ci.org/sbgraves237/Ecfun/builds/650505913?utm_medium=notification_source=email;.
This looks to me like it's complaining about the use of the back
tick character ("`", below "~" on the top left key on a standard
American English keyboard), which I assume is equivalent to
"\textasciigrave" in certain contexts.
Six out of those 8 repetitions occur in the examples sections of
files "grepNonStandardCharacters.Rd", "subNonStandardCharacters.Rd", and
"subNonStandardNames.Rd". Those functions were written to fix parsing
errors with names like "Raúl" that had been mangled by different
software before I could get it into R.
After a day's work failed to produce a work around, I decided to
ask this group.
What do you suggest?
Thanks,
Spencer Graves
__
r-package-de...@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-package-devel
[[alternative HTML version deleted]]
___
R-SIG-Mac mailing list
R-SIG-Mac@r-project.org
https://stat.ethz.ch/mailman/listinfo/r-sig-mac
Re: [R-SIG-Mac] Please test R 4.0.0 pre-releases!
Is there a procedure for dual install, e.g., so I could run "R4 CMD check", etc.? Please excuse if this has already been answered. Thanks, Spencer Graves On 2020-04-02 02:50, Rainer M Krug wrote: On 1 Apr 2020, at 16:07, Patrick Schratz wrote: The same goes here regarding support. I am (co-)maintaining a package on ropensci focusing on provider-agnostic CI approaches for R (tic) and have quite some experience with all the little culprits there. Since you mentioned Travis: Be aware that the R community is (slowly but actively) moving away from Travis for a few reasons. Also on GitHub Actions you can only build on 10.15 (Catalina) right now. So where is the R community moving too? Rainer Best, Patrick On 1. Apr 2020, 15:41 +0200, Bob Rudis , wrote: I shall pile on with an additional offer of assistance, Simon and a huge #ty for this and all the work you do. On Apr 1, 2020, at 09:30, Balamuta, James Joseph wrote: Simon, Thanks for the overview! A few quick questions: 1. Compiler-wise, the external clang compiler requirement was removed and, so, there is no guarantee of OpenMP on macOS again? 2. Why was 10.13 chosen as the oldest system instead of 10.14 given the new push for increased security by Apple? 3. How likely is the oldest system requirement to be bumped in a patch release? Also, if you need help with mac-builder, Travis, or GitHub Actions, I'm more than happy to help! Best, JJB On 3/31/20, 11:59 PM, "R-SIG-Mac on behalf of Simon Urbanek" wrote: Dear Mac users, R 4.0.0 will be using an entirely new toolchain, entirely new build system on entirely new macOS version and hardware. Therefore I would like to ask you kindly to test the binaries from https://mac.R-project.org before the release as much as you can. Raising any issues after the release is too late! So please, please, test the pre-releases. Report any issues either directly to me or this mailing list. The nightly builds are signed, but not necessarily notarized. However, the build fulfils Apple's conditions and is known to pass notarization (in fact the the package available for download today is actually notarized) so it should be a good test for the release which will be notarized and should work on Catalina. For those that want to replicate our setup - technical details: we are now building with macOS 10.13 (High Sierra) as target (i.e. the oldest supported system), regular Apple Xcode/command line tools and GNU Fortran 8.2. R builds are running on macOS 10.15 (Catalina) with Xcode 11.4 using macOS 10.13 target. Packages are built on macOS 10.13 VMs with just Apple command line tools (this should make it easy to replicate the setup using Travis, for example). All 3rd party libraries that CRAN uses are available in http://mac.r-project.org/libs-4/ The new R build system is in https://svn.r-project.org/R-dev-web/trunk/QA/Simon/R4 Packages build system has not changed and is in https://svn.r-project.org/R-dev-web/trunk/QA/Simon/packages We also plan to have a mac-builder available with similar function as the win-builder where pre-submission tests can be performed and potentially a Travis template. Please test R pre-releases and provide feedback! Thanks, Simon ___ 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 ___ 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 -- Rainer M. Krug, PhD (Conservation Ecology, SUN), MSc (Conservation Biology, UCT), Dipl. Phys. (Germany) Orcid ID: -0002-7490-0066 Department of Evolutionary Biology and Environmental Studies University of Zürich Office Y34-J-74 Winterthurerstrasse 190 8075 Zürich Switzerland Office: +41 (0)44 635 47 64 Cell: +41 (0)78 630 66 57 email: rainer.k...@uzh.ch rai...@krugs.de Skype: RMkrug PGP: 0x0F52F982 [[alternative HTML version deleted]] ___ 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
[R-SIG-Mac] dir only shows some of what's there
Hello, All: What can cause "dir" to list only 3 of 18 files in a certain directory? I'm working with Jim Ramsay trying to migrate the fda package to GitHub. The current status is at "https://github.com/JamesRamsay5/fda-revision". The "data" subdirectory there contains only 3 files; there should be 18. I have all 18 in a local directory on my MacBook Pro running 10.15.3. I can see them in Finder, but I'm unable to get R to see more than those three. I do "(wd0 <- getwd())" and get: [1] "/Users/sbgraves/Documents/current/R/fda" Finder shows that this has subdirectories "data" and "fda2020-03-11/fda/data" both with 18 files and "fda-revision/fda/data" with only 3. The latter is a current clone of "https://github.com/JamesRamsay5/fda-revision". I copied files yesterday into "fda-revision/fda/R" and "fda-revision/fda/demo" without problems. However, over the past few hours, I've been unable to copy a file one of the remaining 15 files from "fda2020-03-11/fda/data" into "fda-revision/fda/data". In R I tried the following: > (fda511old.data <- file.path(wd0, 'fda2020-03-11', + 'fda', 'data')) [1] "/Users/sbgraves/Documents/current/R/fda/fda2020-03-11/fda/data" > dir(fda511old.data) [1] "gait.rda" "melanoma.rda" "nondurables.rda" > > (fdaRev.data <- file.path(wd0, 'fda-revision', + 'data')) [1] "/Users/sbgraves/Documents/current/R/fda/fda-revision/data" > dir(fdaRev.data) [1] "gait.rda" "melanoma.rda" "nondurables.rda" I checked "data info" on all 3 "data" directories. The two with 18 files show 18 items while the one with 3 shows only 3. "data info" for all three say "You can read and write". Suggestions? Thanks, Spencer Graves > sessionInfo() R version 3.6.3 (2020-02-29) Platform: x86_64-apple-darwin15.6.0 (64-bit) Running under: macOS Catalina 10.15.3 Matrix products: default BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib LAPACK: /Library/Frameworks/R.framework/Versions/3.6/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 [6] methods base loaded via a namespace (and not attached): [1] compiler_3.6.3 tools_3.6.3 ___ R-SIG-Mac mailing list R-SIG-Mac@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-mac
Re: [R-SIG-Mac] Using R on MacOS Catalina.....
I haven't followed this entire thread, but I'm running macOS 10.15.2 Catalina on a 2014 MacBookPro, and I haven't had problems downloading the latest version of R. Roughly a month ago, I clicked "R-3.6.2.pkg" on "https://cloud.r-project.org/bin/macosx/". It downloaded to my "Downloads" directory. Then I double-clicked on it, and it opened. I can't remember, but I may have had to click and drag the icon to the "Applications" folder. And I may have had to enter my password to assure macOS that it was OK to run that application. I may have had problems with this a few years ago, but I haven't had a problem recently. However, I may misunderstand your question. Spencer Graves On 2020-01-28 23:58, Patrick Schratz wrote: Why not use the official installer and adjust the installation path? https://cran.r-project.org/bin/macosx/ Also allows multiple versions being installed, all from the CLI (but I guess guess it's a normal desktop machine and you can just use the gui installer). 256GB is a normal size for a disk, don't see the problem. 90% of all macs probably don't have more. Homebrew R differs slightly from the official R installer and might cause problems in some cases. Matthias Krawutschke schrieb am Di., 28. Jan. 2020, 20:15: Thank you so much for you assistance. My problem is not solved, because I must install R, etc. on a different Volume like SYS-Volume & I can´t find this option under "homebrew". Best regards from Berlin, Germany Herzlichst grüßt Sie das HPC - Team Matthias Krawutschke Universität Potsdam ZIM - Zentrum für Informationstechnologie und Medienmanagement Team High-Performance-Computing Campus Am Neuen Palais: Am Neuen Palais 10 | 14469 Potsdam Tel: +49 331 977-, Fax: +49 331 977-1750 Internet: http://www.uni-potsdam.de/zim -Ursprüngliche Nachricht- Von: Dr Eberhard W Lisse Gesendet: Dienstag, 28. Januar 2020 11:09 An: Byron Ellis ; Matthias Krawutschke < krawutsc...@uni-potsdam.de> Cc: e...@lisse.na; R-SIG-Mac@r-project.org Betreff: Re: [R-SIG-Mac] Using R on MacOS Catalina. For me it usually had to resort to the latter when there were connectivity issues (more common in Namibia than in Potsdam :-)-O). And maybe once or twice when I wanted to try something special. It also has a 'cask' option with which it installs apps so I do brew install r brew cask install rstudio All in all rock solid. el On 28/01/2020 11:43, Byron Ellis wrote: Homebrew is Linux-style packaging for OS X. Think of it as an equivalent to apt-get—either it will retrieve a binary or it will attempt to build one. ___ 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 ___ R-SIG-Mac mailing list R-SIG-Mac@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-mac
Re: [R-SIG-Mac] Finding "bash" and "mv" on my hard drive?
> Sys.which(c("bash", "mv"))
bash mv
"/bin/bash" "/bin/mv"
Thanks.
It answers the question I asked, but sadly doesn't solve the
problem.
Thanks again,
Spencer Graves
On 2020-01-17 17:28, Bert Gunter wrote:
> As a minor note, Sys.which is vectorized, so
> Sys.which(c("bash", "mv"))
> will do.
>
>
> Bert Gunter
>
> "The trouble with having an open mind is that people keep coming along
> and sticking things into it."
> -- Opus (aka Berkeley Breathed in his "Bloom County" comic strip )
>
>
> On Fri, Jan 17, 2020 at 3:20 PM Bob Rudis <mailto:b...@rud.is>> wrote:
>
> R does not ship bash or bin with the program distribution on macOS. It
> uses the ones that come along for the ride with the system (which will
> be interesting when Apple removes bash completely in 10.16).
>
> If you've used MacPorts or Homebrew, you may have installed version of
> those shells/tools there which R is picking up.
>
> This:
>
> sapply(c("bash", "mv"), Sys.which)
>
> should tell you where R is picking up those binaries.
>
> -boB
>
> On Fri, Jan 17, 2020 at 6:01 PM Spencer Graves
> mailto:spencer.gra...@prodsyse.com>>
> wrote:
> >
> > Hello:
> >
> >
> > How can I find the version of "bash" and "mv" that are
> used by "R
> > CMD check" under macOS 10.15.2 Catalina?
> >
> >
> > I ask, because my "Bitdefender for Mac" has been
> interrupting "R
> > CMD check" for a couple of years now, saying, "Bitdefender Safe
> Files
> > blocked a new process, bash, from accessing your protected
> files." Each
> > time it happens, Bitdefender allows me to tell it to "Remember this
> > action: For 5 minutes" or "For this time only" or to "Keep
> blocking".
> > Their "Safe Files" feature allows me to give access to certain
> > applications. I've already "allowed" 36 different applications
> using
> > that feature, including "/bin/bash", "/bin/mv",
> > "/Library/Frameworks/R.framework/Versions/3.6/Resources/exec/R",
> and two
> > different versions of "git". I'm not sure, but I believe that
> "R CMD
> > check" uses versions of "bash" and "mv" different from
> "/bin/bash" and
> > "/bin/mv".
> >
> >
> > Thanks,
> > Spencer Graves
> >
> > ___
> > R-SIG-Mac mailing list
> > R-SIG-Mac@r-project.org <mailto: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 <mailto: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
[R-SIG-Mac] Finding "bash" and "mv" on my hard drive?
Hello: How can I find the version of "bash" and "mv" that are used by "R CMD check" under macOS 10.15.2 Catalina? I ask, because my "Bitdefender for Mac" has been interrupting "R CMD check" for a couple of years now, saying, "Bitdefender Safe Files blocked a new process, bash, from accessing your protected files." Each time it happens, Bitdefender allows me to tell it to "Remember this action: For 5 minutes" or "For this time only" or to "Keep blocking". Their "Safe Files" feature allows me to give access to certain applications. I've already "allowed" 36 different applications using that feature, including "/bin/bash", "/bin/mv", "/Library/Frameworks/R.framework/Versions/3.6/Resources/exec/R", and two different versions of "git". I'm not sure, but I believe that "R CMD check" uses versions of "bash" and "mv" different from "/bin/bash" and "/bin/mv". Thanks, Spencer Graves ___ R-SIG-Mac mailing list R-SIG-Mac@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-mac
Re: [R-SIG-Mac] R CMD build "cannot open compressed file" with R 3.6.2
Thanks to Jeff Newmiller for his reply. He was correct. My Bitdefender internet security automatically upgraded itself and started blocking R in ways it had not before. Please excuse me for taking the time of this list with this issue (and for my delay in sending this "issue resolution" email). Spencer Graves On 2019-12-25 13:18, Spencer Graves wrote: On 2019-12-25 12:02, Jeff Newmiller wrote: "Permission denied" suggests that this is not related to R. Perhaps you ran R with elevated permissions yesterday? On December 25, 2019 8:37:36 AM PST, Spencer Graves wrote: Hello, All: I just upgraded to R 3.6.2 and suddenly got, "cannot open compressed file" with "R CMD build" of a package that I built yesterday with R 3.6.1, and I don't recall having gotten an error message with 3.6.1. What do you suggest I do to get around this? Thanks, Spencer Graves $ R CMD build Ecfun * checking for file ‘Ecfun/DESCRIPTION’ ... OK * preparing ‘Ecfun’: * checking DESCRIPTION meta-information ... OK * installing the package to build vignettes * creating vignettes ... OK * checking for LF line-endings in source and make files and shell scripts * checking for empty or unneeded directories * building ‘Ecfun_0.2-2.tar.gz’ Warning in gzfile(tarfile, "wb", compression = compression_level) : cannot open compressed file '/Users/sbgraves/Documents/current/R/Ecfun_0.2-2.tar.gz', probable reason 'Permission denied' Error in gzfile(tarfile, "wb", compression = compression_level) : cannot open the connection Execution halted $ r sessionInfo() R version 3.6.2 (2019-12-12) Platform: x86_64-apple-darwin15.6.0 (64-bit) Running under: macOS Catalina 10.15.2 Matrix products: default BLAS: /Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libRblas.0.dylib LAPACK: /Library/Frameworks/R.framework/Versions/3.6/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_3.6.2 ___ 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
[R-SIG-Mac] R CMD build "cannot open compressed file" with R 3.6.2
Hello, All: I just upgraded to R 3.6.2 and suddenly got, "cannot open compressed file" with "R CMD build" of a package that I built yesterday with R 3.6.1, and I don't recall having gotten an error message with 3.6.1. What do you suggest I do to get around this? Thanks, Spencer Graves $ R CMD build Ecfun * checking for file ‘Ecfun/DESCRIPTION’ ... OK * preparing ‘Ecfun’: * checking DESCRIPTION meta-information ... OK * installing the package to build vignettes * creating vignettes ... OK * checking for LF line-endings in source and make files and shell scripts * checking for empty or unneeded directories * building ‘Ecfun_0.2-2.tar.gz’ Warning in gzfile(tarfile, "wb", compression = compression_level) : cannot open compressed file '/Users/sbgraves/Documents/current/R/Ecfun_0.2-2.tar.gz', probable reason 'Permission denied' Error in gzfile(tarfile, "wb", compression = compression_level) : cannot open the connection Execution halted $ r >sessionInfo() R version 3.6.2 (2019-12-12) Platform: x86_64-apple-darwin15.6.0 (64-bit) Running under: macOS Catalina 10.15.2 Matrix products: default BLAS: /Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libRblas.0.dylib LAPACK: /Library/Frameworks/R.framework/Versions/3.6/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_3.6.2 > ___ R-SIG-Mac mailing list R-SIG-Mac@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-mac
Re: [R-SIG-Mac] Installing the "jpeg" package?
On 2019-11-02 01:51, David Winsemius wrote: On 11/1/19 8:03 PM, Spencer Graves wrote: Hello, All: How can I get the dev files for libjpeg installed under macOS 10.15.1 Catalina? You probably have the right tools, but it wouldn't hurt to check: https://cran.r-project.org/bin/macosx/tools/ And have you installed the libjpeg library from the /libs/ directory? http://mac.r-project.org/libs/ The directions for installation from a Terminal session are at the bottom of the page. I have not updated to Catalina, but the error message suggested that jpeglib.h could not be found. Thanks or the reply. I tried to (re)install both the tools and libjpeg with apparent success. However, when I tried "install.packages()" again, I got the same error message as before. Other thoughts, e.g., diagnostic tests? Thanks again. Spencer Graves Hope this helps; David Simon Urbanek, the maintainer for the "jpeg" package, said I need them to install the "jpeg" package from sources. I'm unable to get that package to install either as a binary or from sources; see below. Suggestions? Thanks, Spencer Graves > update.packages() jpeg : Version 0.1-8 installed in /Library/Frameworks/R.framework/Versions/3.6/Resources/library Version 0.1-8.1 available at https://cran.rstudio.com Update? (Yes/no/cancel) y There is a binary version available but the source version is later: binary source needs_compilation jpeg 0.1-8 0.1-8.1 TRUE Do you want to install from sources the package which needs compilation? (Yes/no/cancel) y installing the source package ‘jpeg’ trying URL 'https://cran.rstudio.com/src/contrib/jpeg_0.1-8.1.tar.gz' Content type 'application/x-gzip' length 18116 bytes (17 KB) == downloaded 17 KB * installing *source* package ‘jpeg’ ... ** package ‘jpeg’ successfully unpacked and MD5 sums checked ** using staged installation ** libs clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c read.c -o read.o In file included from read.c:1: ./rjcommon.h:11:10: fatal error: 'jpeglib.h' file not found #include ^~~ 1 error generated. make: *** [read.o] Error 1 ERROR: compilation failed for package ‘jpeg’ * removing ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library/jpeg’ * restoring previous ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library/jpeg’ The downloaded source packages are in ‘/private/var/folders/mh/mrm_14nx19g13lsnj9zmvwjrgn/T/Rtmp8GMSE7/downloaded_packages’ Warning message: In install.packages(update[instlib == l, "Package"], l, repos = repos, : installation of package ‘jpeg’ had non-zero exit status > update.packages() jpeg : Version 0.1-8 installed in /Library/Frameworks/R.framework/Versions/3.6/Resources/library Version 0.1-8.1 available at https://cran.rstudio.com Update? (Yes/no/cancel) y There is a binary version available but the source version is later: binary source needs_compilation jpeg 0.1-8 0.1-8.1 TRUE Do you want to install from sources the package which needs compilation? (Yes/no/cancel) n trying URL 'https://cran.rstudio.com/bin/macosx/el-capitan/contrib/3.6/jpeg_0.1-8.tgz' Content type 'application/x-gzip' length 389601 bytes (380 KB) == downloaded 380 KB The downloaded binary packages are in /var/folders/mh/mrm_14nx19g13lsnj9zmvwjrgn/T//Rtmp8GMSE7/downloaded_packages > sessionInfo() R version 3.6.1 (2019-07-05) Platform: x86_64-apple-darwin15.6.0 (64-bit) Running under: macOS Catalina 10.15.1 Matrix products: default BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib LAPACK: /Library/Frameworks/R.framework/Versions/3.6/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 [6] methods base other attached packages: [1] bssm_0.1.8 loaded via a namespace (and not attached): [1] Rcpp_1.0.2 lattice_0.20-38 assertthat_0.2.1 [4] dplyr_0.8.3 crayon_1.3.4 R6_2.4.0 [7] grid_3.6.1 gtable_0.3.0 magrittr_1.5 [10] coda_0.19-3 scales_1.0.0 ggplot2_3.2.1 [13] pillar_1.4.2 rlang_0.4.1 lazyeval_0.2.2 [16] rstudioapi_0.10 diagis_0.1.3-1 tools_3.6.1 [19] glue_1.3.1 purrr_0.3.3 munsell_0.5.0 [22] compiler_3.6.1 pkgconfig_2.0.3 colorspace_1.4-1 [25] tidyselect_0.2.5 gridExtra_2.3 tibble_2.1.3 ___ R-SIG-Mac mailing list R-SIG-Mac@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-mac
[R-SIG-Mac] Installing the "jpeg" package?
Hello, All: How can I get the dev files for libjpeg installed under macOS 10.15.1 Catalina? Simon Urbanek, the maintainer for the "jpeg" package, said I need them to install the "jpeg" package from sources. I'm unable to get that package to install either as a binary or from sources; see below. Suggestions? Thanks, Spencer Graves > update.packages() jpeg : Version 0.1-8 installed in /Library/Frameworks/R.framework/Versions/3.6/Resources/library Version 0.1-8.1 available at https://cran.rstudio.com Update? (Yes/no/cancel) y There is a binary version available but the source version is later: binary source needs_compilation jpeg 0.1-8 0.1-8.1 TRUE Do you want to install from sources the package which needs compilation? (Yes/no/cancel) y installing the source package ‘jpeg’ trying URL 'https://cran.rstudio.com/src/contrib/jpeg_0.1-8.1.tar.gz' Content type 'application/x-gzip' length 18116 bytes (17 KB) == downloaded 17 KB * installing *source* package ‘jpeg’ ... ** package ‘jpeg’ successfully unpacked and MD5 sums checked ** using staged installation ** libs clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c read.c -o read.o In file included from read.c:1: ./rjcommon.h:11:10: fatal error: 'jpeglib.h' file not found #include ^~~ 1 error generated. make: *** [read.o] Error 1 ERROR: compilation failed for package ‘jpeg’ * removing ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library/jpeg’ * restoring previous ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library/jpeg’ The downloaded source packages are in ‘/private/var/folders/mh/mrm_14nx19g13lsnj9zmvwjrgn/T/Rtmp8GMSE7/downloaded_packages’ Warning message: In install.packages(update[instlib == l, "Package"], l, repos = repos, : installation of package ‘jpeg’ had non-zero exit status > update.packages() jpeg : Version 0.1-8 installed in /Library/Frameworks/R.framework/Versions/3.6/Resources/library Version 0.1-8.1 available at https://cran.rstudio.com Update? (Yes/no/cancel) y There is a binary version available but the source version is later: binary source needs_compilation jpeg 0.1-8 0.1-8.1 TRUE Do you want to install from sources the package which needs compilation? (Yes/no/cancel) n trying URL 'https://cran.rstudio.com/bin/macosx/el-capitan/contrib/3.6/jpeg_0.1-8.tgz' Content type 'application/x-gzip' length 389601 bytes (380 KB) == downloaded 380 KB The downloaded binary packages are in /var/folders/mh/mrm_14nx19g13lsnj9zmvwjrgn/T//Rtmp8GMSE7/downloaded_packages > sessionInfo() R version 3.6.1 (2019-07-05) Platform: x86_64-apple-darwin15.6.0 (64-bit) Running under: macOS Catalina 10.15.1 Matrix products: default BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib LAPACK: /Library/Frameworks/R.framework/Versions/3.6/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 [6] methods base other attached packages: [1] bssm_0.1.8 loaded via a namespace (and not attached): [1] Rcpp_1.0.2 lattice_0.20-38 assertthat_0.2.1 [4] dplyr_0.8.3 crayon_1.3.4 R6_2.4.0 [7] grid_3.6.1 gtable_0.3.0 magrittr_1.5 [10] coda_0.19-3 scales_1.0.0 ggplot2_3.2.1 [13] pillar_1.4.2 rlang_0.4.1 lazyeval_0.2.2 [16] rstudioapi_0.10 diagis_0.1.3-1 tools_3.6.1 [19] glue_1.3.1 purrr_0.3.3 munsell_0.5.0 [22] compiler_3.6.1 pkgconfig_2.0.3 colorspace_1.4-1 [25] tidyselect_0.2.5 gridExtra_2.3 tibble_2.1.3 ___ R-SIG-Mac mailing list R-SIG-Mac@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-mac
Re: [R-SIG-Mac] update.packages() cannot install from source
Thanks to James Joseph Balamuta and Eberhard W. Lisse. I followed the 2-step procedure outlined by Balamuta, and it fixed the problem for all but the jpeg package. I will write the maintainer of that package. (The one-step would probably have worked, but I didn't try it.) Thanks again, Spencer Graves On 2019-10-29 16:12, Balamuta, James Joseph wrote: Greetings and Salutations, Note that Xcode Command Line Tools is not the same as Xcode IDE. In fact, only Xcode CLI Tools are required, which are light-weight compared to the IDE. Regarding your error, this is symptomatic of an Xcode update tied to an OS point-release. Note in the session information 10.15.1 (the .1 being the bump) R version 3.6.1 (2019-07-05) Platform: x86_64-apple-darwin15.6.0 (64-bit) Running under: macOS Catalina 10.15.1 Both of the commands highlighted are accurate. Though, the order should be changed to: sudo xcode-select --reset sudo xcode-select --install The reset changes back to using the default command line tools path. This was needed for Mojave. Sincerely, JJB On 10/29/19, 4:01 PM, "R-SIG-Mac on behalf of Spencer Graves" wrote: Hello, All: "update.packages()" fails for me on packages DescTools, digest, jpeg, mgcv, openxlsx, rlang, and spam. It first says: There are binary versions available but the source versions are later: binary source needs_compilation DescTools 0.99.29 0.99.30 TRUE digest 0.6.21 0.6.22 TRUE jpeg0.1-8 0.1-8.1 TRUE mgcv 1.8-29 1.8-30 TRUE openxlsx 4.1.0.1 4.1.2 TRUE rlang 0.4.0 0.4.1 TRUE spam2.3-0 2.3-0.2 TRUE It then asks, "Do you want to install from sources the packages which need compilation? (Yes/no/cancel)". I reply "y" or "Yes". For each package, it says it was ... successfully unpacked and MD5 sums checked ** using staged installation ** libs xcrun: error: invalid active developer path (/Library/Developer/CommandLineTools), missing xcrun at: /Library/Developer/CommandLineTools/usr/bin/xcrun ERROR: compilation failed for package ‘DescTools’ * removing ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library/DescTools’ * restoring previous ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library/DescTools’ A web search for "xcrun: error: invalid active developer path" identified a couple of discussions on StackExchange that say that I need to have Xcode installed correctly. I think I have everything up to date: macOS 10.15.1 Catalina with Xcode downloaded and installed via the App store. RStudio 1.2.5001 with: sessionInfo() R version 3.6.1 (2019-07-05) Platform: x86_64-apple-darwin15.6.0 (64-bit) Running under: macOS Catalina 10.15.1 Matrix products: default BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib LAPACK: /Library/Frameworks/R.framework/Versions/3.6/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 [6] methods base loaded via a namespace (and not attached): [1] compiler_3.6.1 tools_3.6.1 "https://apple.stackexchange.com/questions/254380/why-am-i-getting-an-invalid-active-developer-path-when-attempting-to-use-git-a; recommends, "xcode-select --install", which to me seems like it should be equivalent to the install I just did via the App Store. This StackExchange discussion also said, "If the above alone doesn't do it, then also run: xcode-select --reset". However, before I do that, I thought I'd ask here if anyone else is having a problem like this. And if yes, and if they've fixed it, what did they do to fix it? Thanks, Spencer Graves ___ 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
[R-SIG-Mac] update.packages() cannot install from source
Hello, All: "update.packages()" fails for me on packages DescTools, digest, jpeg, mgcv, openxlsx, rlang, and spam. It first says: There are binary versions available but the source versions are later: binary source needs_compilation DescTools 0.99.29 0.99.30 TRUE digest 0.6.21 0.6.22 TRUE jpeg 0.1-8 0.1-8.1 TRUE mgcv 1.8-29 1.8-30 TRUE openxlsx 4.1.0.1 4.1.2 TRUE rlang 0.4.0 0.4.1 TRUE spam 2.3-0 2.3-0.2 TRUE It then asks, "Do you want to install from sources the packages which need compilation? (Yes/no/cancel)". I reply "y" or "Yes". For each package, it says it was ... successfully unpacked and MD5 sums checked ** using staged installation ** libs xcrun: error: invalid active developer path (/Library/Developer/CommandLineTools), missing xcrun at: /Library/Developer/CommandLineTools/usr/bin/xcrun ERROR: compilation failed for package ‘DescTools’ * removing ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library/DescTools’ * restoring previous ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library/DescTools’ A web search for "xcrun: error: invalid active developer path" identified a couple of discussions on StackExchange that say that I need to have Xcode installed correctly. I think I have everything up to date: macOS 10.15.1 Catalina with Xcode downloaded and installed via the App store. RStudio 1.2.5001 with: sessionInfo() R version 3.6.1 (2019-07-05) Platform: x86_64-apple-darwin15.6.0 (64-bit) Running under: macOS Catalina 10.15.1 Matrix products: default BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib LAPACK: /Library/Frameworks/R.framework/Versions/3.6/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 [6] methods base loaded via a namespace (and not attached): [1] compiler_3.6.1 tools_3.6.1 "https://apple.stackexchange.com/questions/254380/why-am-i-getting-an-invalid-active-developer-path-when-attempting-to-use-git-a; recommends, "xcode-select --install", which to me seems like it should be equivalent to the install I just did via the App Store. This StackExchange discussion also said, "If the above alone doesn't do it, then also run: xcode-select --reset". However, before I do that, I thought I'd ask here if anyone else is having a problem like this. And if yes, and if they've fixed it, what did they do to fix it? Thanks, Spencer Graves ___ R-SIG-Mac mailing list R-SIG-Mac@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-mac
Re: [R-SIG-Mac] Catalina and gfortran (also: My silliness)
Catalina advertised that it would no longer accept 32 bit applications. Isn't there a 64 bit version of gfortran to use with Catalina? Spencer Graves On 2019-10-10 10:36, Erich Subscriptions wrote: gfortran 6.1 from the tools directory (which I simply did not notice) did install. But it also seems to be 32bi and therefore does not work on Catalina. Sorry for bothering people here. ___ 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] Where is "sh" used by "R CMD check"?
Hi, Marc: Thanks. I got exactly the same two answers as you got. Now I need to get back with Bitdefender to figure out what to do with that information. Spencer On 2019-09-20 16:14, Marc Schwartz wrote: On Sep 20, 2019, at 5:02 PM, Spencer Graves wrote: Hello: How can I find "sh" that is used by "R CMD check" on my Mac? I ask, my "Bitdefender Antivirus for Mac" blocks "R CMD check" with a pop up saying, "Bitdefender Safe Files blocked a new process, sh, from accessing your protected files. What would you like to do?" I'm allowed to allow access "For 5 minutes" or "For this time only" -- or I can block it forever. I've been clicking "Allow access". If I knew where "sh" was on my hard drive, I might be able to add it to a "white list" maintained by the antivirus. Sadly, I don't know where it is. Thanks, Spencer Graves Hi Spencer, Typically via 'which' from a terminal: ~ which sh /bin/sh There is also 'whereis', but that will only check default system binary paths, whereas 'which' will also search your $PATH. In this case, they return the same information: ~ whereis sh /bin/sh It sounds like you have the "Safe Files" option in Bitdefender enabled, which is optional, which is why the messages. I use BF also. Regards, Marc Schwartz ___ R-SIG-Mac mailing list R-SIG-Mac@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-mac
[R-SIG-Mac] Where is "sh" used by "R CMD check"?
Hello: How can I find "sh" that is used by "R CMD check" on my Mac? I ask, my "Bitdefender Antivirus for Mac" blocks "R CMD check" with a pop up saying, "Bitdefender Safe Files blocked a new process, sh, from accessing your protected files. What would you like to do?" I'm allowed to allow access "For 5 minutes" or "For this time only" -- or I can block it forever. I've been clicking "Allow access". If I knew where "sh" was on my hard drive, I might be able to add it to a "white list" maintained by the antivirus. Sadly, I don't know where it is. Thanks, Spencer Graves ___ R-SIG-Mac mailing list R-SIG-Mac@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-mac
Re: [R-SIG-Mac] point size in svg
Hi, Peter et al.:
Thanks, Peter, for the information that it works for you.
What do you suggest I do to try to correct a font misconfiguration?
Sadly the problem did not disappear when I upgraded to 3.6.1; see
sessionInfo below.
Thanks,
Spencer
> sessionInfo()
R version 3.6.1 (2019-07-05)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: macOS Mojave 10.14.5
Matrix products: default
BLAS:
/System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
LAPACK:
/Library/Frameworks/R.framework/Versions/3.6/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
[7] base
loaded via a namespace (and not attached):
[1] compiler_3.6.1 tools_3.6.1
>
On 2019-06-24 04:10, peter dalgaard wrote:
Works fine for me on 10.14.5, both with CRAN-supplied 3.6.0 and locally
compiled 3.6.0 Patched (2019-06-23 r76734).
I suspect that you might have a font misconfiguration of sorts on your Mojave
machine.
-pd
On 24 Jun 2019, at 09:25 , Spencer Graves wrote:
�� Thanks to David Winsemius for his reply.� His attachment came
through and displayed consistent with the R documentation.� Thus, the
cex.axis and cex arguments work fine with R 3.5.1 (2018-07-02) and
"Feather Spray" on OS X 10.11.6, but they don't work properly with the
current version of R under the current version of macOS.
�� Spencer
On 2019-06-24 00:59, David Winsemius wrote:
On Jun 23, 2019, at 10:04 PM, Spencer Graves
wrote:
Hello, All:
I'm unable to control font size in plots created by "svg" in R 3.6.0 on
macOS Mojave 10.14.5. Consider the following:
svg('cex-svg.svg')
cex. <- 5
plot(1:2, cex.axis=cex.)
text(1:2, 1:2, c('as', 'DF'),
cex=cex.)
dev.off()
When I run this in R 3.5.2 under Windows 7, it works fine. In R 3.6.0 under macOS
10.14.5, I get tiny fonts. Changing "cex." has no impact on the result. A
question about this to R-Devel generated replies from Peter Langfelder and David
Winsemius, who noted that it worked fine under Ubuntu 18.04 (supposedly with R 3.15.2 --
probably R 3.5.2, but I'm not sure).
You should be sure.
I experimented with the width, height, pointsize and family arguments for
"svg", without solving this problem.
With R version 3.5.1 (2018-07-02) -- "Feather Spray" on OS X 10.11.6 I am
unable to reproduce. My Mac hardware is considered well past (Apple) end of life despite
its functionality, so I cannot upgrade my OS. I'm attaching the file that is the result
so Spencer can view it, although I suspect it will be scrubbed by the mail-server.
[[alternative HTML version deleted]]
___
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] point size in svg
� Thanks to David Winsemius for his reply.� His attachment came
through and displayed consistent with the R documentation.� Thus, the
cex.axis and cex arguments work fine with R 3.5.1 (2018-07-02) and
"Feather Spray" on OS X 10.11.6, but they don't work properly with the
current version of R under the current version of macOS.
� Spencer
On 2019-06-24 00:59, David Winsemius wrote:
>> On Jun 23, 2019, at 10:04 PM, Spencer Graves
>> wrote:
>>
>> Hello, All:
>>
>>
>>I'm unable to control font size in plots created by "svg" in R 3.6.0
>> on macOS Mojave 10.14.5. Consider the following:
>>
>>
>> svg('cex-svg.svg')
>> cex. <- 5
>> plot(1:2, cex.axis=cex.)
>> text(1:2, 1:2, c('as', 'DF'),
>>cex=cex.)
>> dev.off()
>>
>>
>>When I run this in R 3.5.2 under Windows 7, it works fine. In R
>> 3.6.0 under macOS 10.14.5, I get tiny fonts. Changing "cex." has no impact
>> on the result. A question about this to R-Devel generated replies from
>> Peter Langfelder and David Winsemius, who noted that it worked fine under
>> Ubuntu 18.04 (supposedly with R 3.15.2 -- probably R 3.5.2, but I'm not
>> sure).
> You should be sure.
>
>> I experimented with the width, height, pointsize and family arguments for
>> "svg", without solving this problem.
> With R version 3.5.1 (2018-07-02) -- "Feather Spray" on OS X 10.11.6 I am
> unable to reproduce. My Mac hardware is considered well past (Apple) end of
> life despite its functionality, so I cannot upgrade my OS. I'm attaching the
> file that is the result so Spencer can view it, although I suspect it will be
> scrubbed by the mail-server.
>
>
>
[[alternative HTML version deleted]]
___
R-SIG-Mac mailing list
R-SIG-Mac@r-project.org
https://stat.ethz.ch/mailman/listinfo/r-sig-mac
[R-SIG-Mac] point size in svg
Hello, All:
I'm unable to control font size in plots created by "svg" in R
3.6.0 on macOS Mojave 10.14.5. Consider the following:
svg('cex-svg.svg')
cex. <- 5
plot(1:2, cex.axis=cex.)
text(1:2, 1:2, c('as', 'DF'),
cex=cex.)
dev.off()
When I run this in R 3.5.2 under Windows 7, it works fine. In R
3.6.0 under macOS 10.14.5, I get tiny fonts. Changing "cex." has no
impact on the result. A question about this to R-Devel generated
replies from Peter Langfelder and David Winsemius, who noted that it
worked fine under Ubuntu 18.04 (supposedly with R 3.15.2 -- probably R
3.5.2, but I'm not sure). I experimented with the width, height,
pointsize and family arguments for "svg", without solving this problem.
I believe this problem is fairly recent: I just looked at svg
files I created with R on this same computer probably last fall, and the
font size looks reasonable -- better than what I get today. I'm not 100
percent sure, but I think I was able to control the font size with the
cex and cex.axis arguments with those earlier versions of R and macOS.
Suggestions?
Thanks,
Spencer Graves
# This script worked as expected on Windows:
sessionInfo()
R version 3.5.2 (2018-12-20)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 7 x64 (build 7601) Service Pack 1
Matrix products: default
locale:
[1] LC_COLLATE=English_United States.1252
[2] LC_CTYPE=English_United States.1252
[3] LC_MONETARY=English_United States.1252
[4] LC_NUMERIC=C
[5] LC_TIME=English_United States.1252
attached base packages:
[1] stats graphics grDevices utils datasets
[6] methods base
loaded via a namespace (and not attached):
[1] compiler_3.5.2 tools_3.5.2 yaml_2.2.0
# It failed on macOS:
sessionInfo()
R version 3.6.0 (2019-04-26)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: macOS Mojave 10.14.5
Matrix products: default
BLAS:
/System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
LAPACK:
/Library/Frameworks/R.framework/Versions/3.6/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
[6] methods base
other attached packages:
[1] Ecdat_0.3-2 Ecfun_0.2-1
__
r-de...@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-devel
__
r-de...@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-devel
___
R-SIG-Mac mailing list
R-SIG-Mac@r-project.org
https://stat.ethz.ch/mailman/listinfo/r-sig-mac
Re: [R-SIG-Mac] clang: error: unsupported option '-fopenmp'
Adding .Renviron as you described solved the problem. Thanks. Spencer
On 2019-05-07 11:18, Balamuta, James Joseph wrote:
Greetings and Salutations Spencer,
Modifying the path traditionally was done in `~/.R/Makevars` by setting the
implicit variables: `CXX`, `CXX11` , ...
I've found a better approach is to modify the `~/.Renviron` file. Since `.Renviron` is a
"dot file", macOS will hide it by default.
You can view the .Renviron file within Finder if you enable showing dot files
by using the keyboard shortcut: CMD + SHIFT + .
From terminal, the file must be created using:
touch ~/.Renviron
vi ~/.Renviron
Inside the file, add a line with:
PATH="/usr/local/clang7/bin:${PATH}"
Once done, leave `vi` by pressing the ESC key and, then, typing ":wq" in the
prompt.
Regarding the gfortran uninstall, this is because there were old artifacts
lying around on some users systems.
It was easier to clean the system and, then, install the toolchain relative to
R.
Sincerely,
JJB
On 5/7/19, 10:24 AM, "Spencer Graves" wrote:
Hi, JJB:
Thanks. Upon reading more carefully
"https://cran.r-project.org/bin/macosx/tools/;, I see that I need
clang7, not the clang8 that I previously installed. I downloaded and
installed it, but I'm confused about how to modify my path, and I'm
still getting the same error as before without that. I don't recall
ever modifying a path on a Mac before, and I don't find the
"~/.Renviron" file you mentioned.
Thanks,
Spencer Graves
p.s. I'm also a little spooked by your instructions to remove gfortran,
because it might be used by something else. I don't find
"/usr/local/gfortran" that you mention, but I do find files (not
folders) "/usr/local/bin/gfortran" and "/usr/local/bin/gfortran-4.8".
??? Thanks again.
On 2019-05-07 08:56, Balamuta, James Joseph wrote:
> Greetings and Salutations All,
>
> For R 3.6.x, you want:
>
> https://cran.r-project.org/bin/macosx/tools/clang-7.0.0.pkg
>
> To let R know about the complier, we need to modify the ~/.Renviron. You
may need to create the file by running in Terminal (Applications -> Utilities):
>
> touch ~/.Renviron
>
> Then, inside of ~/.Renviron add:
>
> PATH="/usr/local/clang7/bin:${PATH}"
>
> More details can be found here (disclaimer: I wrote it):
>
>
http://thecoatlessprofessor.com/programming/r-compiler-tools-for-rcpp-on-macos/
>
> I'm working on updating a bash-script installer to autodetect and
install the appropriate toolchain based on the installed version of R here:
>
> https://github.com/rmacoslib/r-macos-rtools
>
> I'll update the list-serv when I've released a new version for R 3.6.x.
>
> Sincerely,
>
> JJB
>
>
>
> On 5/7/19, 8:34 AM, "R-SIG-Mac on behalf of Spencer Graves"
wrote:
>
> Hi, Bryon et al.:
>
>
> Thanks. I did that and got virtually the same response
ending
> with "clang: error: unsupported option '-fopenmp'".
>
>
> Specifically, I started by looking for a "clang" subdirectory
> under "/usr/local/", which is where clang-8.0.0.pkg from
> "https://cran.r-project.org/bin/macosx/tools/; installed. I did not
> find one. I then downloaded and installed Clang8, and it appeared
in
> directory "/usr/local/clang8". I then rebooted and tried "R CMD
build
> bssm" as before with the following results:
>
>
> > R CMD build bssm
> * checking for file ‘bssm/DESCRIPTION’ ... OK
> * preparing ‘bssm’:
> * checking DESCRIPTION meta-information ... OK
> * cleaning src
> * installing the package to build vignettes
> ---
> * installing *source* package ‘bssm’ ...
> ** using staged installation
> ** libs
> clang++ -std=gnu++11
> -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG
>
-I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/BH/include"
>
-I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include"
>
-I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppArmadillo/include"
>
-I"/Library/Frameworks/R.framework/Versions/3.6/Reso
Re: [R-SIG-Mac] clang: error: unsupported option '-fopenmp'
Hi, JJB:
Thanks. Upon reading more carefully
"https://cran.r-project.org/bin/macosx/tools/;, I see that I need
clang7, not the clang8 that I previously installed. I downloaded and
installed it, but I'm confused about how to modify my path, and I'm
still getting the same error as before without that. I don't recall
ever modifying a path on a Mac before, and I don't find the
"~/.Renviron" file you mentioned.
Thanks,
Spencer Graves
p.s. I'm also a little spooked by your instructions to remove gfortran,
because it might be used by something else. I don't find
"/usr/local/gfortran" that you mention, but I do find files (not
folders) "/usr/local/bin/gfortran" and "/usr/local/bin/gfortran-4.8".
??? Thanks again.
On 2019-05-07 08:56, Balamuta, James Joseph wrote:
Greetings and Salutations All,
For R 3.6.x, you want:
https://cran.r-project.org/bin/macosx/tools/clang-7.0.0.pkg
To let R know about the complier, we need to modify the ~/.Renviron. You may need
to create the file by running in Terminal (Applications -> Utilities):
touch ~/.Renviron
Then, inside of ~/.Renviron add:
PATH="/usr/local/clang7/bin:${PATH}"
More details can be found here (disclaimer: I wrote it):
http://thecoatlessprofessor.com/programming/r-compiler-tools-for-rcpp-on-macos/
I'm working on updating a bash-script installer to autodetect and install the
appropriate toolchain based on the installed version of R here:
https://github.com/rmacoslib/r-macos-rtools
I'll update the list-serv when I've released a new version for R 3.6.x.
Sincerely,
JJB
On 5/7/19, 8:34 AM, "R-SIG-Mac on behalf of Spencer Graves"
wrote:
Hi, Bryon et al.:
Thanks. I did that and got virtually the same response ending
with "clang: error: unsupported option '-fopenmp'".
Specifically, I started by looking for a "clang" subdirectory
under "/usr/local/", which is where clang-8.0.0.pkg from
"https://cran.r-project.org/bin/macosx/tools/; installed. I did not
find one. I then downloaded and installed Clang8, and it appeared in
directory "/usr/local/clang8". I then rebooted and tried "R CMD build
bssm" as before with the following results:
> R CMD build bssm
* checking for file ‘bssm/DESCRIPTION’ ... OK
* preparing ‘bssm’:
* checking DESCRIPTION meta-information ... OK
* cleaning src
* installing the package to build vignettes
---
* installing *source* package ‘bssm’ ...
** using staged installation
** libs
clang++ -std=gnu++11
-I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG
-I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/BH/include"
-I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include"
-I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppArmadillo/include"
-I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/ramcmc/include"
-I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/sitmo/include"
-isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk
-I/usr/local/include -fopenmp -fPIC -Wall -g -O2 -c R_approx.cpp -o
R_approx.o
clang: error: unsupported option '-fopenmp'
make: *** [R_approx.o] Error 1
ERROR: compilation failed for package ‘bssm’
* removing
‘/private/var/folders/mh/mrm_14nx19g13lsnj9zmvwjrgn/T/Rtmp7TLdXk/Rinst6842b1d5fb3/bssm’
---
ERROR: package installation failed
Suggestions?
Thanks,
Spencer
On 2019-05-06 18:19, Byron Ellis wrote:
> Hi Spencer,
>
> You'll want to get the compiler tools from
> https://cran.r-project.org/bin/macosx/tools/ to build properly.
>
> Best,
> B
>
>
>
> On Mon, May 6, 2019 at 4:17 PM Spencer Graves
> mailto:spencer.gra...@prodsyse.com>> wrote:
>
> Hello, All:
>
>
>I'm getting "clang: error: unsupported option '-fopenmp'" when
> trying to build "https://github.com/helske/bssm; under macOS 10.14.14
> with R 3.6.0; see below.
>
>
>What do you suggest?
>
>
>Thanks,
>Spencer Graves
>
>
> p.s. Helske told me he thought my compiler was out of date. However,
> I've so far been unable to find instructions that are sufficiently
> current to convince me I might not do more ha
Re: [R-SIG-Mac] clang: error: unsupported option '-fopenmp'
Hi, Bryon et al.: Thanks. I did that and got virtually the same response ending with "clang: error: unsupported option '-fopenmp'". Specifically, I started by looking for a "clang" subdirectory under "/usr/local/", which is where clang-8.0.0.pkg from "https://cran.r-project.org/bin/macosx/tools/; installed. I did not find one. I then downloaded and installed Clang8, and it appeared in directory "/usr/local/clang8". I then rebooted and tried "R CMD build bssm" as before with the following results: > R CMD build bssm * checking for file ‘bssm/DESCRIPTION’ ... OK * preparing ‘bssm’: * checking DESCRIPTION meta-information ... OK * cleaning src * installing the package to build vignettes --- * installing *source* package ‘bssm’ ... ** using staged installation ** libs clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/BH/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppArmadillo/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/ramcmc/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/sitmo/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fopenmp -fPIC -Wall -g -O2 -c R_approx.cpp -o R_approx.o clang: error: unsupported option '-fopenmp' make: *** [R_approx.o] Error 1 ERROR: compilation failed for package ‘bssm’ * removing ‘/private/var/folders/mh/mrm_14nx19g13lsnj9zmvwjrgn/T/Rtmp7TLdXk/Rinst6842b1d5fb3/bssm’ --- ERROR: package installation failed Suggestions? Thanks, Spencer On 2019-05-06 18:19, Byron Ellis wrote: > Hi Spencer, > > You'll want to get the compiler tools from > https://cran.r-project.org/bin/macosx/tools/ to build properly. > > Best, > B > > > > On Mon, May 6, 2019 at 4:17 PM Spencer Graves > mailto:spencer.gra...@prodsyse.com>> wrote: > > Hello, All: > > > I'm getting "clang: error: unsupported option '-fopenmp'" when > trying to build "https://github.com/helske/bssm; under macOS 10.14.14 > with R 3.6.0; see below. > > > What do you suggest? > > > Thanks, > Spencer Graves > > > p.s. Helske told me he thought my compiler was out of date. However, > I've so far been unable to find instructions that are sufficiently > current to convince me I might not do more harm than good > following them. > > > > R CMD build bssm > * checking for file ‘bssm/DESCRIPTION’ ... OK > * preparing ‘bssm’: > * checking DESCRIPTION meta-information ... OK > * cleaning src > * installing the package to build vignettes > --- > * installing *source* package ‘bssm’ ... > ** using staged installation > ** libs > clang++ -std=gnu++11 > -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG > > -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/BH/include" > > > -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" > > > -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppArmadillo/include" > > > -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/ramcmc/include" > > > -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/sitmo/include" > > -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk > -I/usr/local/include -fopenmp -fPIC -Wall -g -O2 -c R_approx.cpp -o > R_approx.o > clang: error: unsupported option '-fopenmp' > make: *** [R_approx.o] Error 1 > ERROR: compilation failed for package ‘bssm’ > * removing > > ‘/private/var/folders/mh/mrm_14nx19g13lsnj9zmvwjrgn/T/RtmppA2gBg/Rinst24427c5cbfeb/bssm’ > --- > ERROR: package installation failed > > ___ > R-SIG-Mac mailing list > R-SIG-Mac@r-project.org <mailto:R-SIG-Mac@r-project.org> > https://stat.ethz.ch/mailman/listinfo/r-sig-mac > > > > -- > Byron Ellis (byron.el...@gmail.com <mailto:byron.el...@gmail.com>) > "Oook" -- The Librarian [[alternative HTML version deleted]] ___ R-SIG-Mac mailing list R-SIG-Mac@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-mac
[R-SIG-Mac] clang: error: unsupported option '-fopenmp'
Hello, All: I'm getting "clang: error: unsupported option '-fopenmp'" when trying to build "https://github.com/helske/bssm; under macOS 10.14.14 with R 3.6.0; see below. What do you suggest? Thanks, Spencer Graves p.s. Helske told me he thought my compiler was out of date. However, I've so far been unable to find instructions that are sufficiently current to convince me I might not do more harm than good following them. R CMD build bssm * checking for file ‘bssm/DESCRIPTION’ ... OK * preparing ‘bssm’: * checking DESCRIPTION meta-information ... OK * cleaning src * installing the package to build vignettes --- * installing *source* package ‘bssm’ ... ** using staged installation ** libs clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/BH/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppArmadillo/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/ramcmc/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/sitmo/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fopenmp -fPIC -Wall -g -O2 -c R_approx.cpp -o R_approx.o clang: error: unsupported option '-fopenmp' make: *** [R_approx.o] Error 1 ERROR: compilation failed for package ‘bssm’ * removing ‘/private/var/folders/mh/mrm_14nx19g13lsnj9zmvwjrgn/T/RtmppA2gBg/Rinst24427c5cbfeb/bssm’ --- ERROR: package installation failed ___ R-SIG-Mac mailing list R-SIG-Mac@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-mac
[R-SIG-Mac] How can I find the "sh" application used by "R CMD check" on a Mac?
How can I find the "sh" application used by "R CMD check" on a Mac? I need to know to be able to add it to the "Application Access" list maintained by the "Anti-Ransomware" feature of my Bitdefender Antivirus for Mac. With that feature on, "R CMD check Ecfun" stopped with the following: checking whether package ‘Ecfun’ can be installed ...sh: ... Permission denied When I saw that, I also got a popup from Bitdefender that would only allow me to allow this once but not permanently. To allow it permanently, I need to know where it is on my hard drive. Thanks, Spencer Graves ___ R-SIG-Mac mailing list R-SIG-Mac@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-mac
[R-SIG-Mac] how to install RODBC on macOS Sierra 10.12.4?
Hello:
I recently upgraded to R 3.4.0, and I've so far been unable to
"install.packages('RODBC')" or "R CMD INSTALL RODBC_1.3-15.tar.gz". Both
end with the following:
configure: error: "ODBC headers sql.h and sqlext.h not found"
ERROR: configuration failed for package ‘RODBC’
I had RODBC installed in R 3.3, but that was before I upgraded to
macOS Sierra 10.12.4. I've tried to RTFM, but I don't know which FMTR,
and I can't decrypt the documentation I've found that seem relevant. I
couldn't find the answer in Ripley's "ODBC Connectivity" vignette.
"iodbc-42.5/iodbc/README.MACOSX" says, "You first need to install
the latest Mac OS X Developer Packages, which can be found at
"http://developer.apple.com/tools;. I think I've done that, but I don't
know how to check it.
"iodbc-42.5/iodbc/README.MACOSX" continues, "Then, you can open
the Xcode Project Builder files under mac/iODBCinst, mac/iODBC,
mac/iODBCtest and mac/iODBCtestw,". I don't know how find any of
these. It further continues, "or execute the following commands from a
terminal session to build all the frameworks and demo applications:
$ cd mac
$ make"
I just did "$ cd mac" and got, "-bash: cd: mac: No such file or
directory". Evidently, I need to substitute something for "mac" here,
but I don't know what.
Suggestions? Thanks,
Spencer Graves
___
R-SIG-Mac mailing list
R-SIG-Mac@r-project.org
https://stat.ethz.ch/mailman/listinfo/r-sig-mac
Re: [R-SIG-Mac] svn update > "xcrun: error: invalid active developer path" after uipgrade to 10.11 El Capitan
On 10/16/2015 3:15 AM, Prof Brian Ripley wrote:
On 16/10/2015 09:06, Spencer Graves wrote:
Hello:
I'm having a problem with "svn update" (with R-Forge) that may be
due to a recent upgrade to OS X 10.11 El Capitan. I'm getting the
following:
$ svn update
xcrun: error: invalid active developer path
(/Library/Developer/CommandLineTools), missing xcrun at:
/Library/Developer/CommandLineTools/usr/bin/xcrun
Google sent me to
"http://stackoverflow.com/questions/28706428/invalid-active-developer-path-on-mac-os-x-after-installing-ruby;
and "https://github.com/Homebrew/homebrew/issues/23500; for ruby and
git. Stackoverflow seems to suggest that "sudo xcode-select --install"
may fix the problem. However, I know so little about this, I felt a
need to ask here.
What do you think?
I think you should read the R manual,
https://cran.r-project.org/doc/manuals/r-patched/R-admin.html#OS-X
which tells you
1) To reinstall the CLT after an OS update.
2) To use xcode-select --install to do so. (sudo may or may not be
needed.)
And after all these years, please do read and follow the posting
guide: it is expected that you check in the manuals before posting.
Thanks very much for the reply -- and for all the work you've invested
in producing the fine manual. You're correct, of course, that I should
have checked that manual.
Thanks again,
Spencer Graves
___
R-SIG-Mac mailing list
R-SIG-Mac@r-project.org
https://stat.ethz.ch/mailman/listinfo/r-sig-mac
[R-SIG-Mac] svn update > "xcrun: error: invalid active developer path" after uipgrade to 10.11 El Capitan
Hello: I'm having a problem with "svn update" (with R-Forge) that may be due to a recent upgrade to OS X 10.11 El Capitan. I'm getting the following: $ svn update xcrun: error: invalid active developer path (/Library/Developer/CommandLineTools), missing xcrun at: /Library/Developer/CommandLineTools/usr/bin/xcrun Google sent me to "http://stackoverflow.com/questions/28706428/invalid-active-developer-path-on-mac-os-x-after-installing-ruby; and "https://github.com/Homebrew/homebrew/issues/23500; for ruby and git. Stackoverflow seems to suggest that "sudo xcode-select --install" may fix the problem. However, I know so little about this, I felt a need to ask here. What do you think? Thanks, Spencer ___ R-SIG-Mac mailing list R-SIG-Mac@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-mac
Re: [R-SIG-Mac] Experiences with El Capitan
On 10/12/2015 10:21 PM, Roy Mendelssohn - NOAA Federal wrote: CLT = command line tools. Otherwise you only have the compilers from the Xcode interface. in order to have tex2dvi, you need a tex distribution installed. I do remember if Simon has one on his R mac site, nut you can do an install from say (as the RStudio help says): To build manuals and vignettes you'll also need to install the MacTeX LaTeX distribution (or another version of LaTeX for the Mac). You can download MacTeX from here:http://www.tug.org/mactex/downloading.html. HTH, Yes, it didn't just help, it fixed the problem. Thanks. (My Father once said, "That not only hit the spot, it erased it.") Best Wishes, Spencer Roy On Oct 12, 2015, at 7:58 PM, Spencer Graves<spencer.gra...@prodsyse.com> wrote: On 10/12/2015 8:51 PM, Kevin Ushey wrote: The simplest way to fix your issue is to symlink R to /usr/local/bin, e.g. ln -s /Library/Frameworks/R.framework/Resources/bin/R /usr/local/bin/R This worked. Thanks. Spencer ... but not completely: "R CMD build" worked. "R CMD check" ended with: Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet, : pdflatex is not available Or, as Professor Ripley said in his initial post, R installers from 3.2.2 on El Capitan will now install a symlink at /usr/local/bin/R, so you might want to just re-install or update R. Updating the CLT is normally just a matter of downloading the latest What's CLT? Central Limit Theorem? Charlotte Douglas International Airport? version of Xcode from the App Store, if I understand correctly. (You I requested "Xcode" at the App Store. It asked for my Apple password then went away. I rebooted and still got "pdflatex is not available". may need to read + confirm a license agreement on your next run of the clang compiler -- try running 'clang' after installing Xcode to see if you're prompted) $ clang xcrun: error: invalid active developer path (/Library/Developer/CommandLineTools), missing xcrun at: /Library/Developer/CommandLineTools/usr/bin/xcrun Thanks again for your prompt reply. Other suggestions? (All this worked before I upgraded to OS X 10.11.) Spencer Kevin On Mon, Oct 12, 2015 at 6:33 PM, Spencer Graves <spencer.gra...@prodsyse.com> wrote: On 10/5/2015 2:46 PM, Simon Urbanek wrote: On Oct 5, 2015, at 3:34 AM, Rainer M Krug<rai...@krugs.de> wrote: peter dalgaard<pda...@gmail.com> writes: Agreed. I just would like to dd that in the case of using homebrew, which installs everything under /usr/local/... which did not cause any problems at all. I moved the contents of /usr/local to an other location before upgrade because the upgrade to Yosemite took because of a large /usr/local several hours instead of about half an hour, moved it back afterwards and everything worked fins without problems. One question concerning mixed usage of homebrew and the Official R installers: do the Official R installers fail if an R binary already exist, or do they raise a warning? To make this easier, would it be possible, to install the binaries under /usr/local/bin/R.X.Y.Z and then just create links in /usr/local/bin ? Tghis would make the whole process more transparent and easier to switch between different versions and means of installation. R installer never installs any R binaries outside of the framework/app. The only thing we provide on 10.10 is a softlink for R and Rscript in /usr/local/bin into the framework (removing anything else in that name if it exists). In earlier OS X versions this applies to /usr/bin instead. Cheers, Simon Thanks for the clarifications, Rainer -pd On 04 Oct 2015, at 18:53 , Prof Brian Ripley<rip...@stats.ox.ac.uk> wrote: The machine which provides the 'r-devel-osx-x86_64-clang' checks on the CRAN check farm has been upgraded from Yosemite to El Capitan and a complete round of checks has been run. 1) There is a lot of misinformation around about 'System Integrity Protection' aka 'rootless'. Upgrading to El Capitan moves files which are not allowed under /usr to /Library/SystemMigration/usr, so you will be able to see what was lost. This includes /usr/bin/R, /usr/bin/Rscript (but the installer installs these under /usr/local/bin on El Capitan as from R 3.2.2), /usr/X11R6, /usr/texbin . Contrary to reports from betas, the link /usr/X11 is preserved. If an installer tries to create a disallowed file such as /usr/bin/R, this is silently ignored (at least in the cases we tested). So you can install e.g. R 3.1.3 but the executables will not appear in the default Terminal path (more details in the current manual). 2) After updating you need to re-install the Command Line Tools and R (to get the links in /usr/local). I did not need to re-install Java nor XQuartz. How do you suggest I "re-install the Comma
Re: [R-SIG-Mac] Experiences with El Capitan
On 10/12/2015 8:51 PM, Kevin Ushey wrote: The simplest way to fix your issue is to symlink R to /usr/local/bin, e.g. ln -s /Library/Frameworks/R.framework/Resources/bin/R /usr/local/bin/R This worked. Thanks. Spencer ... but not completely: "R CMD build" worked. "R CMD check" ended with: Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet, : pdflatex is not available Or, as Professor Ripley said in his initial post, R installers from 3.2.2 on El Capitan will now install a symlink at /usr/local/bin/R, so you might want to just re-install or update R. Updating the CLT is normally just a matter of downloading the latest What's CLT? Central Limit Theorem? Charlotte Douglas International Airport? version of Xcode from the App Store, if I understand correctly. (You I requested "Xcode" at the App Store. It asked for my Apple password then went away. I rebooted and still got "pdflatex is not available". may need to read + confirm a license agreement on your next run of the clang compiler -- try running 'clang' after installing Xcode to see if you're prompted) $ clang xcrun: error: invalid active developer path (/Library/Developer/CommandLineTools), missing xcrun at: /Library/Developer/CommandLineTools/usr/bin/xcrun Thanks again for your prompt reply. Other suggestions? (All this worked before I upgraded to OS X 10.11.) Spencer Kevin On Mon, Oct 12, 2015 at 6:33 PM, Spencer Graves <spencer.gra...@prodsyse.com> wrote: On 10/5/2015 2:46 PM, Simon Urbanek wrote: On Oct 5, 2015, at 3:34 AM, Rainer M Krug <rai...@krugs.de> wrote: peter dalgaard <pda...@gmail.com> writes: Agreed. I just would like to dd that in the case of using homebrew, which installs everything under /usr/local/... which did not cause any problems at all. I moved the contents of /usr/local to an other location before upgrade because the upgrade to Yosemite took because of a large /usr/local several hours instead of about half an hour, moved it back afterwards and everything worked fins without problems. One question concerning mixed usage of homebrew and the Official R installers: do the Official R installers fail if an R binary already exist, or do they raise a warning? To make this easier, would it be possible, to install the binaries under /usr/local/bin/R.X.Y.Z and then just create links in /usr/local/bin ? Tghis would make the whole process more transparent and easier to switch between different versions and means of installation. R installer never installs any R binaries outside of the framework/app. The only thing we provide on 10.10 is a softlink for R and Rscript in /usr/local/bin into the framework (removing anything else in that name if it exists). In earlier OS X versions this applies to /usr/bin instead. Cheers, Simon Thanks for the clarifications, Rainer -pd On 04 Oct 2015, at 18:53 , Prof Brian Ripley <rip...@stats.ox.ac.uk> wrote: The machine which provides the 'r-devel-osx-x86_64-clang' checks on the CRAN check farm has been upgraded from Yosemite to El Capitan and a complete round of checks has been run. 1) There is a lot of misinformation around about 'System Integrity Protection' aka 'rootless'. Upgrading to El Capitan moves files which are not allowed under /usr to /Library/SystemMigration/usr, so you will be able to see what was lost. This includes /usr/bin/R, /usr/bin/Rscript (but the installer installs these under /usr/local/bin on El Capitan as from R 3.2.2), /usr/X11R6, /usr/texbin . Contrary to reports from betas, the link /usr/X11 is preserved. If an installer tries to create a disallowed file such as /usr/bin/R, this is silently ignored (at least in the cases we tested). So you can install e.g. R 3.1.3 but the executables will not appear in the default Terminal path (more details in the current manual). 2) After updating you need to re-install the Command Line Tools and R (to get the links in /usr/local). I did not need to re-install Java nor XQuartz. How do you suggest I "re-install the Command Line Tools and R"? I upgraded to 10.11 days ago but only now tried "R CMD build" and got, "-bash: R: command not found". How can I get past this? Thanks, Spencer p.s. Thanks very much for all your work, including the comments on this thread. 3) All the 'Mavericks' binary packages tested worked. The source packages of rJava and rgl (only) cannot be installed and the maintainers have patched versions available. There is updated information in the latest 'R Installation and Administration' manual in R-patched and R-devel (in the sources, or the online versions at https://cran.r-project.org/manuals.html will update in a day or two). -- Brian D. Ripley, rip...@stats.ox.ac.uk Emeritus Professor of Applied Statistics, University of Oxford 1 South Par
[R-SIG-Mac] R 3.2.2 install problems under OS X 10.10.3
Hello: After upgrading from R 3.2.1 to 3.2.2 under OS X 10.10.3, attempts to start the default R GUI fail with, Problem Report for R: R cannot be opened because of a problem. Problem Details and System Configuration are copied below. (R 3.2.2 seems to work fine within RStudio 0.98.1103.) What do you suggest I do to fix this problem? Thanks, Spencer Graves Problem Details and System Configuration Process: R [569] Path: /Applications/R.app/Contents/MacOS/R Identifier:org.R-project.R Version: ??? Code Type: X86-64 (Native) Parent Process:??? [1] Responsible: R [569] User ID: 501 Date/Time: 2015-08-17 19:46:47.942 -0500 OS Version:Mac OS X 10.10.3 (14D136) Report Version:11 Anonymous UUID:6621BCEA-EA0C-3D7A-AE0A-BFCE63A9A8B4 Sleep/Wake UUID: 9C8F92EE-E940-4B17-A64C-C0F470DFE449 Time Awake Since Boot: 2600 seconds Time Since Wake: 700 seconds Crashed Thread:0 Exception Type:EXC_BREAKPOINT (SIGTRAP) Exception Codes: 0x0002, 0x Application Specific Information: dyld: launch, loading dependent libraries Dyld Error Message: Library not loaded: /Library/Frameworks/R.framework/Versions/3.1/Resources/lib/libR.dylib Referenced from: /Applications/R.app/Contents/MacOS/R Reason: image not found Binary Images: 0x7fff6b9f - 0x7fff6ba26837 dyld (353.2.1) 65DCCB06-339C-3E25-9702-600A28291D0E /usr/lib/dyld Model: MacBookPro11,3, BootROM MBP112.0138.B14, 4 processors, Intel Core i7, 2.8 GHz, 16 GB, SMC 2.19f12 Graphics: Intel Iris Pro, Intel Iris Pro, Built-In Graphics: NVIDIA GeForce GT 750M, NVIDIA GeForce GT 750M, PCIe, 2048 MB Memory Module: BANK 0/DIMM0, 8 GB, DDR3, 1600 MHz, 0x80AD, 0x484D54343147533641465238412D50422020 Memory Module: BANK 1/DIMM0, 8 GB, DDR3, 1600 MHz, 0x80AD, 0x484D54343147533641465238412D50422020 AirPort: spairport_wireless_card_type_airport_extreme (0x14E4, 0x134), Broadcom BCM43xx 1.0 (7.15.166.24.3) Bluetooth: Version 4.3.4f4 15601, 3 services, 27 devices, 1 incoming serial ports Network Service: Wi-Fi, AirPort, en0 Serial ATA Device: APPLE SSD SM1024F, 1 TB USB Device: Internal Memory Card Reader USB Device: BRCM20702 Hub USB Device: Bluetooth USB Host Controller USB Device: Apple Internal Keyboard / Trackpad Thunderbolt Bus: MacBook Pro, Apple Inc., 17.1 ___ R-SIG-Mac mailing list R-SIG-Mac@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-mac
[R-SIG-Mac] “pdflatex is not available” from “R CMD check”
Hello: What should I do to diagnose and fix “pdflatex is not available” from “R CMD check” on a Mac running OS X 10.10.1 (see below for more details including sessionInfo.)? A blog on Building R packages: missing path to pdflatex” (http://www.r-bloggers.com/building-r-packages-missing-path-to-pdflatex/ http://www.r-bloggers.com/building-r-packages-missing-path-to-pdflatex/) suggested the following: Sys.which(pdflatex”) # Sys.getenv(PATH) # [1] /usr/bin:/bin:/usr/sbin:/sbin:/usr/local/bin” However, the suggested fix did not work for me. 1. How can I determine if pdflatex is installed? 2. If it is, how can I find it? If it’s not, what i the recommended install procedure? Thanks Spencer Graves ## R CMD check … ... * checking PDF version of manual ... WARNING LaTeX errors when creating PDF version. This typically indicates Rd problems. * checking PDF version of manual without hyperrefs or index ... ERROR Re-running with no redirection of stdout/stderr. Hmm ... looks like a package Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet, : pdflatex is not available Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet, : pdflatex is not available Error in running tools::texi2pdf() You may want to clean up by 'rm -rf /var/folders/mh/mrm_14nx19g13lsnj9zmvwjrgn/T//RtmpjOTCtB/Rd2pdf1651fa89c1’ # sessionInfo() R version 3.1.2 (2014-10-31) Platform: x86_64-apple-darwin13.4.0 (64-bit) 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 [7] base loaded via a namespace (and not attached): [1] tools_3.1.2 [[alternative HTML version deleted]] ___ R-SIG-Mac mailing list R-SIG-Mac@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-mac
