Re: [R] Compilation problems with R4.4.0

2024-05-09 Thread Ivan Krylov via R-help
Glad you got R working!

В Thu, 9 May 2024 12:19:49 +
Simon Andrews  пишет:

> Does this need reporting upstream as a bug in R or lapack?

Maybe in AlmaLinux (and I think RHEL9 too, but that's up to Miguel
Esteva). Best case scenario, they somehow built the reference BLAS and
LAPACK packages with the wrong Fortran compiler version or flags, which
is why gfortran-11 gets a zero instead of the return value from DOUBLE
COMPLEX zdotu(...) and crashes when calling dgesv(...) from
lapack-3.9.0-10.el9.x86_64. Worst case scenario, the zdotu() problem
and the crash have two completely different causes elsewhere.

-- 
Best regards,
Ivan

__
R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.


Re: [R] Compilation problems with R4.4.0

2024-05-09 Thread Simon Andrews via R-help
Thank you!

Installing openblas and then using ./configure --without-lapack --with-blas 
--enable-R-shlib

..got everything working.  Does this need reporting upstream as a bug in R or 
lapack?  I'm good now,  but it might help others to get this fixed.

Simon.

-Original Message-
From: Ivan Krylov  
Sent: 08 May 2024 20:05
To: Simon Andrews 
Cc: Simon Andrews via R-help ; Miguel Esteva 

Subject: Re: [R] Compilation problems with R4.4.0

В Wed, 8 May 2024 16:59:25 +
Simon Andrews  пишет:

> The lapack libraries are:
> 
> $ rpm -qa | grep lapack
> lapack-3.9.0-10.el9.x86_64
> lapack64_-3.9.0-10.el9.x86_64
> lapack64-3.9.0-10.el9.x86_64
> lapack-devel-3.9.0-10.el9.x86_64

Thanks for this information! I figured out I needed to enable the 
"PowerTools/CRB" repo, installed lapack-devel from there, and now I get the 
same configure output and the same crash: by linking with R's built-in Rblas 
but and system-provided LAPACK-3.9.0.

If I configure --without-lapack, i.e. use both Rblas and R-provided functions 
from LAPACK up to 3.12.0, the build doesn't crash.

If I try to enable --with-blas=-lblas, here's what happens:

configure:47862: checking whether double complex BLAS can be used
configure:47946: result: no

The test compares the result of the BLAS function zdotu with the manually 
computed vector norm for a complex vector [*]. In this case, the Fortran 
program thinks that the BLAS returns a zero instead of the correct answer, thus 
failing the test and refusing to compile with system BLAS.

I think that you somehow stumbled upon a Fortran ABI incompatibility regarding 
passing complex numbers between the Fortran code compiled during R build and 
the BLAS and LAPACK provided in the PowerTools/CRB repo. I don't know what 
exactly is the problem, but at least --without-lapack is an easy workaround 
without any cost in performance.

In fact, if you install openblas-devel and configure --with-blas (to replace 
Rblas with OpenBLAS), the double complex BLAS test will pass, the build won't 
crash, and you will get even better performance.

--
Best regards,
Ivan

[*] https://stat.ethz.ch/pipermail/r-devel/2024-March/083302.html


This email has been scanned for spam & viruses. If you believe this email 
should have been stopped by our filters, click the following link to report it 
(https://portal-uk.mailanyone.net/index.html#/outer/reportspam?token=dXNlcj1zaW1vbi5hbmRyZXdzQGJhYnJhaGFtLmFjLnVrO3RzPTE3MTUxOTUxMjQ7dXVpZD02NjNCQ0NGMzA1RDJGMzA3RDhDMjIxQTZCRUE3MEQ3MDt0b2tlbj0yZTdkOWY0ZjNjZmQ2NGQyZGFlMmYwZjQ2MTk5NjdmODk2ZDM3YjQyOw%3D%3D).

__
R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.


Re: [R] Compilation problems with R4.4.0

2024-05-08 Thread Ivan Krylov via R-help
В Wed, 8 May 2024 16:59:25 +
Simon Andrews  пишет:

> The lapack libraries are:
> 
> $ rpm -qa | grep lapack
> lapack-3.9.0-10.el9.x86_64
> lapack64_-3.9.0-10.el9.x86_64
> lapack64-3.9.0-10.el9.x86_64
> lapack-devel-3.9.0-10.el9.x86_64

Thanks for this information! I figured out I needed to enable the
"PowerTools/CRB" repo, installed lapack-devel from there, and now I get
the same configure output and the same crash: by linking with R's
built-in Rblas but and system-provided LAPACK-3.9.0.

If I configure --without-lapack, i.e. use both Rblas and R-provided
functions from LAPACK up to 3.12.0, the build doesn't crash.

If I try to enable --with-blas=-lblas, here's what happens:

configure:47862: checking whether double complex BLAS can be used
configure:47946: result: no

The test compares the result of the BLAS function zdotu with the
manually computed vector norm for a complex vector [*]. In this case,
the Fortran program thinks that the BLAS returns a zero instead of the
correct answer, thus failing the test and refusing to compile with
system BLAS.

I think that you somehow stumbled upon a Fortran ABI incompatibility
regarding passing complex numbers between the Fortran code compiled
during R build and the BLAS and LAPACK provided in the PowerTools/CRB
repo. I don't know what exactly is the problem, but at least
--without-lapack is an easy workaround without any cost in performance.

In fact, if you install openblas-devel and configure --with-blas (to
replace Rblas with OpenBLAS), the double complex BLAS test will pass,
the build won't crash, and you will get even better performance.

-- 
Best regards,
Ivan

[*] https://stat.ethz.ch/pipermail/r-devel/2024-March/083302.html

__
R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.


Re: [R] Compilation problems with R4.4.0

2024-05-08 Thread Simon Andrews via R-help
Also just did a full errata update and retried the compilation.  It failed 
exactly as before.

-Original Message-
From: Ivan Krylov  
Sent: 08 May 2024 16:09
To: Simon Andrews 
Cc: Simon Andrews via R-help ; Miguel Esteva 

Subject: Re: [R] Compilation problems with R4.4.0

В Wed, 8 May 2024 14:25:08 +
Simon Andrews  пишет:

> #8  0x73f87c0b in dgesv (
>  n=12884901891, nrhs=4294967299,
>  a=,  
> lda=12884901891, ipiv=...,  b= optimized out>,  ldb=12884901891, info=0
> ) at /usr/src/debug/lapack-3.9.0-10.el9.x86_64/SRC/dgesv.f:167
> #9 0x750b2a17 in La_solve (
>  tolin=, Bin=, A=0x18f2f68
> ) at Lapack.c:1246
> #10 mod_do_lapack (
>  call=, op=, args=,  
> env=
> ) at Lapack.c:1483

It looks like this R build is linked to a LAPACK. I now also notice
LAPACK(generic) in the list of external libraries in your ./configure output. 
I've tried to link R to AlmaLinux's builds of reference BLAS and LAPACK using 
--with-blas='-l:libblas.so.3'
--with-lapack='-l:liblapack.so.3' (where do I get libblas.so on AlmaLinux?), 
but that doesn't crash either.

What does the config.log currently say about your BLAS and LAPACK situation? 
It's a number of lines between

configure:47012: checking whether 'struct tm' includes tm_gmtoff

and

configure:48858: checking for iconv.h.

If you'd like to link your R to custom BLAS and LAPACK, try specifying the 
necessary linker flags explicitly with --with-blas=-lwhatever, 
--with-lapack=-lwhatever. If you're fine with reference BLAS & LAPACK that come 
with R, try ./configure --without-blas --without-lapack.
Normally, R's ./configure tries to prevent linking to an external LAPACK 
without linking to an external BLAS; I'm not sure how it got you
LAPACK(generic) without BLAS(generic).

--
Best regards,
Ivan


This email has been scanned for spam & viruses. If you believe this email 
should have been stopped by our filters, click the following link to report it 
(https://portal-uk.mailanyone.net/index.html#/outer/reportspam?token=dXNlcj1zaW1vbi5hbmRyZXdzQGJhYnJhaGFtLmFjLnVrO3RzPTE3MTUxODA5NjA7dXVpZD02NjNCOTVBMDY0RkEzNzNCMDM5QTkwQkZCQzJDRUJERjt0b2tlbj0yOTE5M2Q0NjFkZjQzYzhlMzk0ZDgxMTRkNjgyYTUwZjU3OWZlODgxOw%3D%3D).

__
R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.


Re: [R] Compilation problems with R4.4.0

2024-05-08 Thread Simon Andrews via R-help
The lapack parts of the configure are:

checking whether 'struct tm' includes tm_zone... yes
checking whether 'struct tm' includes tm_gmtoff... yes
checking for dgemm_ in -llapack... no
checking for ATLAS routines in liblapack... no
checking for dpstrf_ in -llapack... yes
checking for liblapack dependency with both BLAS and LAPACK routines... no
checking if LAPACK version >= 3.9.0... 3.9.0, so yes
checking for iconv.h... yes
checking for iconv... yes

The lapack libraries are:

$ rpm -qa | grep lapack
lapack-3.9.0-10.el9.x86_64
lapack64_-3.9.0-10.el9.x86_64
lapack64-3.9.0-10.el9.x86_64
lapack-devel-3.9.0-10.el9.x86_64

-Original Message-
From: Ivan Krylov  
Sent: 08 May 2024 16:09
To: Simon Andrews 
Cc: Simon Andrews via R-help ; Miguel Esteva 

Subject: Re: [R] Compilation problems with R4.4.0

В Wed, 8 May 2024 14:25:08 +
Simon Andrews  пишет:

> #8  0x73f87c0b in dgesv (
>  n=12884901891, nrhs=4294967299,
>  a=,  
> lda=12884901891, ipiv=...,  b= optimized out>,  ldb=12884901891, info=0
> ) at /usr/src/debug/lapack-3.9.0-10.el9.x86_64/SRC/dgesv.f:167
> #9 0x750b2a17 in La_solve (
>  tolin=, Bin=, A=0x18f2f68
> ) at Lapack.c:1246
> #10 mod_do_lapack (
>  call=, op=, args=,  
> env=
> ) at Lapack.c:1483

It looks like this R build is linked to a LAPACK. I now also notice
LAPACK(generic) in the list of external libraries in your ./configure output. 
I've tried to link R to AlmaLinux's builds of reference BLAS and LAPACK using 
--with-blas='-l:libblas.so.3'
--with-lapack='-l:liblapack.so.3' (where do I get libblas.so on AlmaLinux?), 
but that doesn't crash either.

What does the config.log currently say about your BLAS and LAPACK situation? 
It's a number of lines between

configure:47012: checking whether 'struct tm' includes tm_gmtoff

and

configure:48858: checking for iconv.h.

If you'd like to link your R to custom BLAS and LAPACK, try specifying the 
necessary linker flags explicitly with --with-blas=-lwhatever, 
--with-lapack=-lwhatever. If you're fine with reference BLAS & LAPACK that come 
with R, try ./configure --without-blas --without-lapack.
Normally, R's ./configure tries to prevent linking to an external LAPACK 
without linking to an external BLAS; I'm not sure how it got you
LAPACK(generic) without BLAS(generic).

--
Best regards,
Ivan


This email has been scanned for spam & viruses. If you believe this email 
should have been stopped by our filters, click the following link to report it 
(https://portal-uk.mailanyone.net/index.html#/outer/reportspam?token=dXNlcj1zaW1vbi5hbmRyZXdzQGJhYnJhaGFtLmFjLnVrO3RzPTE3MTUxODA5NjA7dXVpZD02NjNCOTVBMDY0RkEzNzNCMDM5QTkwQkZCQzJDRUJERjt0b2tlbj0yOTE5M2Q0NjFkZjQzYzhlMzk0ZDgxMTRkNjgyYTUwZjU3OWZlODgxOw%3D%3D).

__
R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.


Re: [R] Compilation problems with R4.4.0

2024-05-08 Thread Ivan Krylov via R-help
В Wed, 8 May 2024 14:25:08 +
Simon Andrews  пишет:

> #8  0x73f87c0b in dgesv (
>  n=12884901891, nrhs=4294967299,
>  a=,
>  lda=12884901891, ipiv=...,
>  b=,
>  ldb=12884901891, info=0
> ) at /usr/src/debug/lapack-3.9.0-10.el9.x86_64/SRC/dgesv.f:167
> #9 0x750b2a17 in La_solve (
>  tolin=, Bin=, A=0x18f2f68
> ) at Lapack.c:1246
> #10 mod_do_lapack (
>  call=, op=, args=,
>  env=
> ) at Lapack.c:1483

It looks like this R build is linked to a LAPACK. I now also notice
LAPACK(generic) in the list of external libraries in your ./configure
output. I've tried to link R to AlmaLinux's builds of reference BLAS
and LAPACK using --with-blas='-l:libblas.so.3'
--with-lapack='-l:liblapack.so.3' (where do I get libblas.so on
AlmaLinux?), but that doesn't crash either.

What does the config.log currently say about your BLAS and LAPACK
situation? It's a number of lines between

configure:47012: checking whether 'struct tm' includes tm_gmtoff

and

configure:48858: checking for iconv.h.

If you'd like to link your R to custom BLAS and LAPACK, try specifying
the necessary linker flags explicitly with --with-blas=-lwhatever,
--with-lapack=-lwhatever. If you're fine with reference BLAS & LAPACK
that come with R, try ./configure --without-blas --without-lapack.
Normally, R's ./configure tries to prevent linking to an external
LAPACK without linking to an external BLAS; I'm not sure how it got you
LAPACK(generic) without BLAS(generic).

-- 
Best regards,
Ivan

__
R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.


Re: [R] Compilation problems with R4.4.0

2024-05-08 Thread Simon Andrews via R-help
1
#62 0x77cb13ac in Rf_applyClosure (unpromise=TRUE, 
suppliedvars=, rho=0x8eb288, arglist=, 
op=0x7e0b70, call=0x78a960)
at eval.c:2333
#63 Rf_eval (e=0x78a960, rho=rho@entry=0x8eb288) at eval.c:1285
#64 0x77cb6322 in do_set (call=0x78a8b8, op=0x421338, args=0x78a8f0, 
rho=0x8eb288) at ../../src/include/Rinlinedfuns.h:90
#65 0x77cb16b6 in Rf_eval (e=0x78a8b8, rho=rho@entry=0x8eb288) at 
eval.c:1237
#66 0x77cb4e68 in do_begin (call=0x78a880, op=0x42c4a0, args=0x78a848, 
rho=0x8eb288) at ../../src/include/Rinlinedfuns.h:90
#67 0x77cb16b6 in Rf_eval (e=e@entry=0x78a880, rho=rho@entry=0x8eb288) 
at eval.c:1237
#68 0x77cb92ac in do_for (call=, op=, 
args=, rho=) at eval.c:2892
#69 0x77cb16b6 in Rf_eval (e=0x78a068, rho=rho@entry=0x8eb288) at 
eval.c:1237
#70 0x77cb4e68 in do_begin (call=0x78a030, op=0x42c4a0, args=0x789ff8, 
rho=0x8eb288) at ../../src/include/Rinlinedfuns.h:90
#71 0x77cb16b6 in Rf_eval (e=e@entry=0x78a030, rho=rho@entry=0x8eb288) 
at eval.c:1237
#72 0x77cb330f in R_execClosure (call=call@entry=0x8eb330, 
newrho=newrho@entry=0x8eb288, sysparent=, rho=rho@entry=0x45a518,
arglist=arglist@entry=0x423210, op=op@entry=0x789e38) at eval.c:2398
#73 0x77cb40f7 in applyClosure_core (call=call@entry=0x8eb330, 
op=op@entry=0x789e38, arglist=0x423210, rho=rho@entry=0x45a518,
--Type  for more, q to quit, c to continue without paging--
suppliedvars=, unpromise=unpromise@entry=TRUE) at eval.c:2311
#74 0x77cb13ac in Rf_applyClosure (unpromise=TRUE, 
suppliedvars=, rho=0x45a518, arglist=, 
op=0x789e38, call=0x8eb330)
at eval.c:2333
#75 Rf_eval (e=0x8eb330, rho=0x45a518) at eval.c:1285
#76 0x77ce5a57 in setup_Rmainloop () at main.c:1166
#77 0x77ce6ae9 in Rf_mainloop () at main.c:1222
#78 0x0040106b in main (ac=, av=) at 
Rmain.c:29



-Original Message-----
From: Ivan Krylov  
Sent: 08 May 2024 15:12
To: Simon Andrews via R-help 
Cc: Simon Andrews ; Miguel Esteva 

Subject: Re: [R] Compilation problems with R4.4.0

Dear Simon,

В Wed, 8 May 2024 10:17:41 +
Simon Andrews via R-help  пишет:

> I'm having a strange problem compiling R4.4.0 on an AlmaLinux9 box.

> make[4]: Entering directory '/bi/apps/R/R-4.4.0/src/library/grDevices'
> byte-compiling package 'grDevices'
> 
> *** caught segfault ***
> address 0x18017a8110, cause 'memory not mapped'
> 
> Traceback:
> 1: solve.default(rgb)

Miguel Esteva has recently complained about the same problem on RHEL9, but 
didn't provide enough details, nor was I able to reproduce it
myself: https://stat.ethz.ch/pipermail/r-help/2024-May/479288.html

Thanks for letting us know it's reproducible on AlmaLinux and telling us your 
compiler version!

Unfortunately, I wasn't able to reproduce the crash, neither with 
gcc-toolset-13, nor with the ordinary gcc & gfortran 11.4.1 20231218 (Red Hat 
11.4.1-3) from the repository. I see that your compiler version is slightly 
different (11.4.1-2). I'm running `podman run -it --rm almalinux:9`. Would an 
upgrade help?

Can you run R under the debugger and obtain a backtrace? Something like the 
following, in the src/library/grDevices subdirectory:

_R_COMPILE_PKGS_=1 R_COMPILER_SUPPRESS_ALL=1 \  R_DEFAULT_PACKAGES=NULL 
LC_ALL=C \ ../../../bin/R -d gdb --vanilla --no-echo -e \  
'tools:::makeLazyLoading("grDevices")'

--
Best regards,
Ivan


This email has been scanned for spam & viruses. If you believe this email 
should have been stopped by our filters, click the following link to report it 
(https://portal-uk.mailanyone.net/index.html#/outer/reportspam?token=dXNlcj1zaW1vbi5hbmRyZXdzQGJhYnJhaGFtLmFjLnVrO3RzPTE3MTUxNzc1NTg7dXVpZD02NjNCODg1NTEyNjcyMzlDMjY5RkMwQTY5MUE2RDg5Njt0b2tlbj0zZjFiOWNmMGM5NTY3NjU3YjM0YmZhY2QwMTEzM2E3YmRlMDUxY2IwOw%3D%3D).

__
R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.


Re: [R] Compilation problems with R4.4.0

2024-05-08 Thread Ivan Krylov via R-help
Dear Simon,

В Wed, 8 May 2024 10:17:41 +
Simon Andrews via R-help  пишет:

> I'm having a strange problem compiling R4.4.0 on an AlmaLinux9 box.

> make[4]: Entering directory '/bi/apps/R/R-4.4.0/src/library/grDevices'
> byte-compiling package 'grDevices'
> 
> *** caught segfault ***
> address 0x18017a8110, cause 'memory not mapped'
> 
> Traceback:
> 1: solve.default(rgb)

Miguel Esteva has recently complained about the same problem on RHEL9,
but didn't provide enough details, nor was I able to reproduce it
myself: https://stat.ethz.ch/pipermail/r-help/2024-May/479288.html

Thanks for letting us know it's reproducible on AlmaLinux and telling
us your compiler version!

Unfortunately, I wasn't able to reproduce the crash, neither with
gcc-toolset-13, nor with the ordinary gcc & gfortran 11.4.1 20231218
(Red Hat 11.4.1-3) from the repository. I see that your compiler version
is slightly different (11.4.1-2). I'm running `podman run -it --rm
almalinux:9`. Would an upgrade help?

Can you run R under the debugger and obtain a backtrace? Something like
the following, in the src/library/grDevices subdirectory:

_R_COMPILE_PKGS_=1 R_COMPILER_SUPPRESS_ALL=1 \
 R_DEFAULT_PACKAGES=NULL LC_ALL=C \
../../../bin/R -d gdb --vanilla --no-echo -e \
 'tools:::makeLazyLoading("grDevices")'

-- 
Best regards,
Ivan

__
R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.


[R] Compilation problems with R4.4.0

2024-05-08 Thread Simon Andrews via R-help
I'm having a strange problem compiling R4.4.0 on an AlmaLinux9 box.  I've 
compiled previous versions OK on the same hardware/software (last was R4.3.2) 
but 4.4.0 is repeatedly failing.

Configuration works OK.

./configure --prefix=/bi/apps/R/4.4.0 --enable-R-shlib

R is now configured for x86_64-pc-linux-gnu

  Source directory:.
  Installation directory:  /bi/apps/R/4.4.0

  C compiler:  gcc  -g -O2
  Fortran fixed-form compiler: gfortran  -g -O2

  Default C++ compiler:g++ -std=gnu++17  -g -O2
  C++11 compiler:  g++ -std=gnu++11  -g -O2
  C++14 compiler:  g++ -std=gnu++14  -g -O2
  C++17 compiler:  g++ -std=gnu++17  -g -O2
  C++20 compiler:  g++ -std=gnu++20  -g -O2
  C++23 compiler:  g++ -std=gnu++23  -g -O2
  Fortran free-form compiler:  gfortran  -g -O2
  Obj-C compiler:

  Interfaces supported:X11
  External libraries:  pcre2, readline, LAPACK(generic), curl
  Additional capabilities: PNG, JPEG, TIFF, NLS, cairo, ICU
  Options enabled: shared R library, shared BLAS, R profiling

  Capabilities skipped:
  Options not enabled: memory profiling

  Recommended packages:yes

configure: WARNING: neither inconsolata.sty nor zi4.sty found: PDF vignettes 
and package manuals will not be rendered optimally
configure: WARNING: I could not determine a browser
configure: WARNING: I could not determine a PDF viewer

..but after running make it gets though most of it then dies with:

make[4]: Entering directory '/bi/apps/R/R-4.4.0/src/library/grDevices'
byte-compiling package 'grDevices'

*** caught segfault ***
address 0x18017a8110, cause 'memory not mapped'

Traceback:
1: solve.default(rgb)
2: solve(rgb)
3: drop(whitexyz %*% solve(rgb))
4: make.rgb(red = c(0.625, 0.34), green = c(0.28, 0.595), blue = c(0.155, 
0.07), gamma = 1.8, white = "D65", name = "Apple RGB")
5: eval(exprs[i], envir)
6: eval(exprs[i], envir)
7: sys.source(codeFile, env, keep.source = keep.source, keep.parse.data = 
keep.parse.data)
8: doTryCatch(return(expr), name, parentenv, handler)
9: tryCatchOne(expr, names, parentenv, handlers[[1L]])
10: tryCatchList(expr, classes, parentenv, handlers)
11: tryCatch(expr, error = function(e) {call <- conditionCall(e)if 
(!is.null(call)) {if (identical(call[[1L]], quote(doTryCatch))) 
call <- sys.call(-4L)dcall <- deparse(call, nlines = 1L)
prefix <- paste("Error in", dcall, ": ")LONG <- 75Lsm <- 
strsplit(conditionMessage(e), "\n")[[1L]]w <- 14L + nchar(dcall, type = 
"w") + nchar(sm[1L], type = "w")if (is.na(w)) w <- 14L + 
nchar(dcall, type = "b") + nchar(sm[1L], type = "b")if 
(w > LONG) prefix <- paste0(prefix, "\n  ")}else prefix <- 
"Error : "msg <- paste0(prefix, conditionMessage(e), "\n")
.Internal(seterrmessage(msg[1L]))if (!silent && 
isTRUE(getOption("show.error.messages"))) {cat(msg, file = outFile) 
   .Internal(printDeferredWarnings())}invisible(structure(msg, class = 
"try-error", condition = e))})
12: try(sys.source(codeFile, env, keep.source = keep.source, keep.parse.data = 
keep.parse.data))
13: loadNamespace(package = package, lib.loc = lib.loc, keep.source = 
keep.source, keep.parse.data = keep.parse.data, partial = TRUE)
14: withCallingHandlers(expr, packageStartupMessage = function(c) 
tryInvokeRestart("muffleMessage"))
15: suppressPackageStartupMessages(loadNamespace(package = package, lib.loc 
= lib.loc, keep.source = keep.source, keep.parse.data = keep.parse.data, 
partial = TRUE))
16: code2LazyLoadDB(package, lib.loc = lib.loc, keep.source = keep.source, 
keep.parse.data = keep.parse.data, compress = compress, set.install.dir = 
set.install.dir)
17: tools:::makeLazyLoading("grDevices")
An irrecoverable exception occurred. R is aborting now ...
make[4]: *** [../../../share/make/lazycomp.mk:9: 
../../../library/grDevices/R/grDevices.rdb] Error 139

I can reproduce the error directly by running make in 
/bi/apps/R/R-4.4.0/src/library/grDevices.  Nothing strange is in my 
environment, I'm using the stock version of make and gcc

$ which make
/usr/bin/make
$ which gcc
/usr/bin/gcc

$ make --version
GNU Make 4.3
Built for x86_64-redhat-linux-gnu

$ gcc --version
gcc (GCC) 11.4.1 20230605 (Red Hat 11.4.1-2)


I can't find any other instances of others hitting the same problem.

Any suggestions for what this could be?

Thanks

Simon.




[[alternative HTML version deleted]]

__
R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.