gt; From my ignorance I dare to say that there is a package that is
> generating
> > the conflict with R version 4.5.1.
> >
> > Best regards,
> >
> > El mar, 15 jul 2025 a las 1:02, roy ( <
> rollinfor...@gmail.com>) escribió:
> >
> >
> &g
Did you already try installing the latest available release of RStudio? In
general, R and RStudio should be upgraded together.
If you still have problems with the latest release of RStudio, you should
file a big report at https://github.com/rstudio/rstudio/issues.
On Mon, Jul 14, 2025, 6:54 PM Jo
Not to be pithy, but R includes version components in its user library
paths by default for a reason...
On Sat, May 31, 2025, 8:35 AM Jeff Newmiller via R-SIG-Mac <
r-sig-mac@r-project.org> wrote:
> Carl: "Doctor, it hurts when I don't upgrade properly..."
> Duncan: "... then don't do that."
> Ca
Hi Gavin,
If you want to use gettext from Homebrew, you need to make sure the
compiler include paths are set up correctly. As a reference, R
installations from Homebrew use (among other tweaks, but I think these
are the most relevant):
CPPFLAGS = -I/opt/homebrew/opt/gettext/include
-I/opt/hom
Issues of this sort typically occur if a package is updated or
reinstalled while it is already loaded. See also:
https://bugs.r-project.org/show_bug.cgi?id=16644
The simplest resolution is to restart R after installing a package.
Best,
Kevin
On Mon, Mar 25, 2024 at 3:57 PM Simon Urbanek
wrote:
Since I'm able to reproduce the issue as well...
$ system_profiler SPHardwareDataType | grep Model
Model Name: MacBook Pro
Model Identifier: MacBookPro18,1
Model Number: Z14V0016HLL/A
and
> sessionInfo()
R version 4.3.2 (2023-10-31)
Platform: aarch64-apple-darwin20 (64-bit)
Run
I'm seeing this as well. In case it's relevant, I saw something
similar, but the points do appear to get appropriately redrawn if I
resize the Quartz window. (The window is fairly jittery / jumpy when I
try to do so, though.)
On Fri, Feb 16, 2024 at 12:17 PM roy wrote:
>
> On the following cfg:
>
My suspicion is the code here:
https://github.com/wch/r-source/blob/068a6a0d9d60b1ce42abc879900038649f4a929c/src/main/platform.c#L3358-L3363
It seems that the call to 'realpath()' fails on the path reported via
.dli_fname here, which (for me) is:
/System/Library/Frameworks/Accelerate.framework/V
On my macOS machine, files with the .R extension are seen as "Rez" source files:
$ touch hello.R && mdls -name kMDItemContentType hello.R
kMDItemContentType = "com.apple.rez-source"
I believe this is because Xcode comes with an Info.plist file that
declares and registers this file type; e.g. it h
This may also make your life challenging:
/usr/local/include/sys/_types.h:33:10: fatal error: 'machine/_types.h' file
not found
#include
^~
1 error generated.
You have some headers installed in /usr/local/include that are
shadowing the default macOS toolchain's headers,
> sessionInfo()
R version 4.1.2 (2021-11-01)
Platform: x86_64-apple-darwin17.0 (64-bit)
Running under: macOS Big Sur 10.16
Best,
Kevin
On Sun, Nov 28, 2021 at 6:22 PM Simon Urbanek
wrote:
> Kevin,
>
> that is a different story, yes, Rosetta2 is incomplete - the advice on M1
>
I can reproduce something similar on my M1 macOS machine, when using the
x86_64 build of R. I see:
> x1 <- mpfr(-50, 200)
*** caught illegal operation ***
address 0x10c5f623b, cause 'illegal opcode'
This is with the binary of Rmpfr 0.8-7 as from CRAN, with R 4.1.2. Here's
what LLDB says:
* thre
This error:
Error: package or namespace load failed for ‘rlang’ in
get(Info[i, 1], envir = env): lazy-load database
'/Users/hwb/Library/R/4.0/library/rlang/R/rlang.rdb' is corrupt
In addition: Warning message:
In get(Info[i, 1], envir = env) : internal error -3 in R_decompress1
The main thing that stands out to me in that error:
Referenced from: /usr/local/lib/libquadmath.0.dylib
Expected in: /usr/local/lib/libgcc_s_x86_64.1.dylib
R bundles its own copies of libquadmath and libgcc:
kevinushey@Kevins-MBP:/Library/Frameworks/R.framework/Resources/lib
$ ls -la
total 1
Normally, you shouldn't need to set -isysroot or SDKROOT when using
Apple Clang -- it will automatically find and use system headers for
you.
Per Hervé's original point, I wonder if you have a different compiler
on the PATH? What is the output of:
which clang
My suspicion is that you might h
The following works for me on macOS 10.15.4 using Apple Clang + libomp
from LLVM 10 (via Homebrew).
Install libomp from Homebrew with:
brew install libomp
Then, put the following in ~/.R/Makevars
CPPFLAGS += -I/usr/local/opt/libomp/include -Xclang -fopenmp
LDFLAGS += -L/usr/local/op
Can you confirm that you see this even with:
R --vanilla -s -e "writeLines(.libPaths())"
If you don't see the issue there, the most likely culprit is something
in a .Rprofile that's causing the old library path to be used.
Kevin
On Sat, Apr 25, 2020 at 4:59 AM Bob Rudis wrote:
>
> Can you
For what it's worth, Homebrew and macports both have scripts for
installing GTK+ from sources, so presumedly those could be cribbed
into a standalone shell script for a build if desired:
https://github.com/Homebrew/homebrew-core/blob/master/Formula/gtk+.rb
https://github.com/macports/macports-port
Hi,
For what it's worth, it looks like it is still possible to use OpenMP
on macOS with the system toolchain. Using the example file here:
https://computing.llnl.gov/tutorials/openMP/samples/C/omp_hello.c
I can compile + link + run this on macOS 10.15.4 and with:
$ /usr/bin/clang -Xpreprocessor
Hi,
I'm seeing the following when I attempt to install R-patched, as from
http://mac.r-project.org/:
---
“R-3.6-branch-el-capitan-signed.pkg” can’t be opened because Apple
cannot check it for malicious software.
This software needs to be updated. Contact the developer for more information.
---
There is a package providing gfortran 6.1 on the page at
https://cran.r-project.org/bin/macosx/tools/, and that should be used
now with the El Capitan builds of R.
FWIW, I've had success using gfortran from Homebrew gcc; you just need
to ensure that the correct Fortran libraries are passed along d
r this, the most common of which has the use of
> Jenkins (or other build pipeline managers) to manage build pipelines for
> macOS and iOS apps. I did a quick "jenkins macos code sign" and they all
> still seem to be there (just looked at the list, didn't dig into the URLs
>
Hi,
It looks like the builds of R from http://mac.r-project.org/ are typically
not code-signed, and so one normally gets a Gatekeeper warning when trying
to install them. E.g. I see (on macOS 10.14.6):
“R-3.6-branch-el-capitan.pkg” can’t be opened because it is from an
unidentified developer.
Yo
Hi,
Some users have reported issues when attempting to load packages using
C++ code on El Capitan -- for example:
Error: package or namespace load failed for ‘readr’ in dyn.load(file,
DLLpath = DLLpath, ...):
unable to load shared object
'/Library/Frameworks/R.framework/Versions/3.6/Resources/lib
I also recall after updating to Xcode 10.2 on my Mojave machine that
the system headers normally installed at /usr/include had vanished,
and re-installing the headers with the aforementioned package at
/Library/Developer/CommandLineTools/Packages/macOS_SDK_headers_for_macOS_10.14.pkg
fixed things u
If I understand correctly, the problem is that the character your keyboard
is inserting is not a regular caret (^, \u0053); rather, it's a 'modifier
character circumflex accent' (ˆ, \u02c6).
How are you inserting the carat on your laptop? For what it's worth, I get
a 'regular' caret with Shift + 6
RcppParallel is indeed a package produced and maintained by the Rcpp
core team, but RcppParallel is now considered ORPHANED on CRAN:
https://cran.r-project.org/package=RcppParallel
This is in spite of my repeated attempts to submit updates of this
package to CRAN (as the package maintainer); subm
>From what I understand, the issue ultimately stems from the mixing of
different C++ standard library implementations: the system-provided
libc++, and the LLVM libc++ bundled with R.
A similar issue is described and investigated with the V8 package:
https://github.com/jeroen/V8/issues/37
Thi
ntPast]];
467
468 }
Hopefully this helps...
Best,
Kevin
---
R version 3.3.2 (2016-10-31) -- "Sincere Pumpkin Patch"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin13.4.0 (64-bit)
macOS Sierra -- Version 10.12.1
On Sat, Nov 5, 20
It might be worth trying to launch R with lldb attached. You can run
the following command from the terminal:
/usr/bin/lldb -w -n R
Then, try launching R (or R.app) -- 'lldb' should then detect that R
has been launched, and you can enter 'c' in the 'lldb' terminal window
to continue execution
Are you able to locate a version of libcurl using mdfind, e.g. what
does this print:
mdfind libcurl.4.dylib
You might also try installing homebrew curl (brew install curl) if you
haven't already.
Kevin
On Tue, Feb 23, 2016 at 1:39 PM, peter dalgaard wrote:
> In general, homebrewers get to
My understanding is that gfortran 4.2.3 was used with CRAN R built
with pre-Mavericks OSes (ie, before Apple made the move from gcc to
clang); nowadays gfortran 4.8.2 is used. Considering that you're on
Yosemite, you want to be installing gfortran 4.8.2.
Unfortunately, this information is not very
FWIW, with a recent-ish CRAN R installation (3.2.2 patched, r69059) on
El Capitan, I have the same and all is well:
kevin:~$ which Rscript
/usr/local/bin/Rscript
kevin:~$ which Rscript | xargs greadlink
/Library/Frameworks/R.framework/Resources/bin/Rscript
kevin:~$ which Rscr
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
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 migh
The page lists R-devel as r69167, but r69078 is instead delivered from
http://r.research.att.com/mavericks/R-devel/R-devel-mavericks-signed.pkg.
This seems to be the case for R-patched and friends as well.
Best,
Kevin
___
R-SIG-Mac mailing list
R-SIG-Ma
for package ‘RMacoqui’
> * removing
> ‘/Library/Frameworks/R.framework/Versions/3.2/Resources/library/RMacoqui’
> Warning in install.packages :
> installation of package ‘/Users/joseca_IMac/Desktop/RMacoqui_1.0.tar.gz’
> had non-zero exit status
>
> Many thanks again,
>
There error here is, as it says:
> make: gfortran-4.8: No such file or directory
In other words, `make` is attempting to call `gfortran-4.8` to compile
FORTRAN code in your package, but is unable to find it -- likely
because it's not installed.
Since 'gfortran' is no longer distributed as part o
For what it's worth, I can reproduce the issue with the binary
provided by CRAN; however, the package successfully loads for me when
installed from source.
install.packages("tkrplot", type = "source")
library(tkrplot) ## no segfault
The error seems to occur as a result of loading the `Rpl
Perhaps the latest R-patched should also be published at
http://cran.r-project.org/bin/macosx/, just to make it more
discoverable + encourage its use by more users? (In other words --
should users be encouraged to run R 3.2.0-patched instead of R-3.2.0?
If so, the 'patched' link should be advertise
;>
>> Copyright (C) 2013 Free Software Foundation, Inc.
>> License GPLv3+: GNU GPL version 3 or later <
>> http://gnu.org/licenses/gpl.html>
>> This is free software: you are free to change and redistribute it.
>> There is NO WARRANTY, to the extent permitted
is is
>> still fine to be discussed in this thread, if not, I can open a new
>> one).
>>
>> Thanks & cheers,
>> Marius
>>
>>
>>
>> On Sun, May 10, 2015 at 2:45 PM, Kevin Ushey wrote:
>> > Hi Marius,
>> >
>> >
Hi Marius,
I've had success compiling (the latest versions of) R from source
using Apple's command line tools (shipped with Xcode), alongside
gfortran 4.8.2 installed from here (as hosted by Simon Urbanek):
http://r.research.att.com/libs/gfortran-4.8.2-darwin13.tar.bz2
Alternatively, (and wh
I've noticed that the PATH is actually duplicated in e.g. R.app (when
launched from the dock).
> env <- Sys.getenv()
> as.list(env[names(env) == "PATH"])
$PATH
[1] "/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/bin"
$PATH
[1] "/usr/bin:/bin:/usr/sbin:/sbin"
It is the second of
And more bizarrely, if I launch RStudio from the terminal, there are
_two_ PATH variables set:
> Sys.getenv()[names(Sys.getenv()) == "PATH"]
PATH
"/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/bin:/opt/X11/bin:/usr/texbin"
Hi John,
Regarding your issue in RStudio and pdflatex -- this is a general
problem with any applications not launched from the terminal;
presumedly it would be seen in R.app as well when not launched from
the terminal (this is related to the forward-PATH-to-subprocesses
problem discussed earlier)
Hi Roger,
Did you see this StackOverflow post?
http://stackoverflow.com/questions/15489065/rcppeclipse-on-mac-os-x/17054405
It sounds like the poster describes the same problem as what you're seeing,
and various prescriptions are offered.
Cheers,
Kevin
On Fri, Jul 25, 2014 at 6:44 AM, Roger De
Hi Tobey,
I'm running R on Mac OS X, installed netcdf from Homebrew, and I run into
the same problem when installing ncdf from source. I see one obvious error
in the configure step (my guess is you are having a similar error, but
without your configure output we can't know):
netcdf.m4: about
Can you post the output / errors you receive upon trying to install a
package from source? More information is required before your problem
can be diagnosed.
On Wed, Oct 23, 2013 at 7:20 AM, Avi Feller wrote:
> Dear List,
>
> I foolishly upgraded to the new Mac OS and am having trouble building
>
With XCode 5.0, clang is now the default compiler toolchain supplied,
and llvm-gcc-4.2 is no longer available.
FWIW, I and many others have had a lot of success compiling packages
with the version of clang supplied with XCode. The only requirement
(at this point) is that you set your own ~/.R/Make
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