“guix pack -RR r“ fails?

“guix pack -RR r“ fails?

[zimoun]

Dear,

Using Guix fd0ef0e, I run:

--8<---------------cut here---------------start------------->8---
rsync -av --progress                            \
      $(guix pack -RR --save-provenance         \
                  -S /bin=bin                   \
                  -S /etc=etc                   \
                  -S /include=include           \
                  -S /lib=lib                   \
                  -S /share=share               \
                  -S /site-library=site-library \
                  r)                            \
      cluster:/path/to/my/stuff
--8<---------------cut here---------------end--------------->8---

then log via SSH to cluster and untar the pack.

--8<---------------cut here---------------start------------->8---
$ ls -ahl
total 422M
drwxrwxr-x   3 sitour sitour 3.8K Nov  4 19:05 .
drwxrwxrwx. 15 root   root   3.8K Nov  4 19:02 ..
-r--r--r--   1 sitour sitour 421M Jan  1  1970 5n55mgjcj33s700g91x0zzf3ngflnba7-tarball-pack.tar.gz
lrwxrwxrwx   1 sitour sitour   54 Nov  4 19:05 bin -> gnu/store/fvvn6mc4s7p52frdlsfj502k4zbqb9j7-profile/bin
lrwxrwxrwx   1 sitour sitour   54 Nov  4 19:05 etc -> gnu/store/fvvn6mc4s7p52frdlsfj502k4zbqb9j7-profile/etc
drwxrwxr-x   3 sitour sitour 3.8K Nov  4 19:03 gnu
lrwxrwxrwx   1 sitour sitour   58 Nov  4 19:05 include -> gnu/store/fvvn6mc4s7p52frdlsfj502k4zbqb9j7-profile/include
lrwxrwxrwx   1 sitour sitour   54 Nov  4 19:05 lib -> gnu/store/fvvn6mc4s7p52frdlsfj502k4zbqb9j7-profile/lib
lrwxrwxrwx   1 sitour sitour   56 Nov  4 19:05 share -> gnu/store/fvvn6mc4s7p52frdlsfj502k4zbqb9j7-profile/share
lrwxrwxrwx   1 sitour sitour   63 Nov  4 19:05 site-library -> gnu/store/fvvn6mc4s7p52frdlsfj502k4zbqb9j7-profile/site-library
--8<---------------cut here---------------end--------------->8---

The usual ‘./bin/R’ fails with:

--8<---------------cut here---------------start------------->8---
$ ./bin/R
: unsupported Guix execution engine; ignoring
./bin/R
R version 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out"

[...]

 *** caught segfault ***
address 0x7f44f4b11008, cause 'memory not mapped'
--8<---------------cut here---------------end--------------->8---

and then has to be killed.  Last,

--8<---------------cut here---------------start------------->8---
$ gdb ./bin/R
GNU gdb (GDB) Red Hat Enterprise Linux (7.2-92.el6)
Copyright (C) 2010 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 by law.  Type "show copying"
and "show warranty" for details.
This GDB was configured as "x86_64-redhat-linux-gnu".
For bug reporting instructions, please see:
<http://www.gnu.org/software/gdb/bugs/>...
Reading symbols from /data2/tmp/foo/gnu/store/yz0zww6i4pafvwh6ysmqxr5pm72ks7lv-r-minimal-4.0.3R/bin/R...(no debugging symbols found)...done.
(gdb) run
Starting program: /data2/tmp/foo/gnu/store/yz0zww6i4pafvwh6ysmqxr5pm72ks7lv-r-minimal-4.0.3R/bin/R 
: unsupported Guix execution engine; ignoring
/data2/tmp/foo/gnu/store/yz0zww6i4pafvwh6ysmqxr5pm72ks7lv-r-minimal-4.0.3R/bin/Rprocess 36927 is executing new program: /data2/tmp/foo/gnu/store/jwdvnklncaqw15376vbbr1vgpfr17j18-proot-static-5.1.0/bin/proot
Detaching after fork from child process 36930.

R version 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out"
Copyright (C) 2020 The R Foundation for Statistical Computing
Platform: x86_64-unknown-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

Error: package or namespace load failed for 'grDevices' in dyn.load(file, DLLpath = DLLpath, ...):
 unable to load shared object '/gnu/store/nqqhaz59gdr5q6mb6mw9dd8jk133rna2-r-minimal-4.0.3/lib/R/library/grDevices/libs/grDevices.so':
  /gnu/store/nqqhaz59gdr5q6mb6mw9dd8jk133rna2-r-minimal-4.0.3/lib/R/library/grDevices/libs/grDevices.so: cannot open shared object file: Bad address
Error: package or namespace load failed for 'graphics' in dyn.load(file, DLLpath = DLLpath, ...):
 unable to load shared object '/gnu/store/nqqhaz59gdr5q6mb6mw9dd8jk133rna2-r-minimal-4.0.3/lib/R/library/grDevices/libs/grDevices.so':
  /gnu/store/nqqhaz59gdr5q6mb6mw9dd8jk133rna2-r-minimal-4.0.3/lib/R/library/grDevices/libs/grDevices.so: cannot open shared object file: Bad address
Error: package or namespace load failed for 'stats' in dyn.load(file, DLLpath = DLLpath, ...):
 unable to load shared object '/gnu/store/nqqhaz59gdr5q6mb6mw9dd8jk133rna2-r-minimal-4.0.3/lib/R/library/grDevices/libs/grDevices.so':
  /gnu/store/nqqhaz59gdr5q6mb6mw9dd8jk133rna2-r-minimal-4.0.3/lib/R/library/grDevices/libs/grDevices.so: cannot open shared object file: Bad address
During startup - Warning messages:
1: package 'grDevices' in options("defaultPackages") was not found 
2: package 'graphics' in options("defaultPackages") was not found 
3: package 'stats' in options("defaultPackages") was not found 
4: Setting LC_CTYPE failed, using "C" 
5: Setting LC_COLLATE failed, using "C" 
6: Setting LC_TIME failed, using "C" 
7: Setting LC_MESSAGES failed, using "C" 
8: Setting LC_MONETARY failed, using "C" 
9: Setting LC_PAPER failed, using "C" 
10: Setting LC_MEASUREMENT failed, using "C" 
>
--8<---------------cut here---------------end--------------->8---


The cluster machine is an old kernel:

--8<---------------cut here---------------start------------->8---
HEAD$ uname -a
Linux HEAD 2.6.32-573.8.1.el6.x86_64 #1 SMP Tue Nov 10 18:01:38 UTC 2015 x86_64 x86_64 x86_64 GNU/Linux
--8<---------------cut here---------------end--------------->8---


What do I miss?


All the best,
simon

Re: “guix pack -RR r“ fails?

[Roel Janssen]

Hi Simon,

On Wed, 2020-11-04 at 19:13 +0100, zimoun wrote:
> Dear,
> 
> Using Guix fd0ef0e, I run:
> 
> --8<---------------cut here---------------start------------->8---
> rsync -av --progress                            \
>       $(guix pack -RR --save-provenance         \
>                   -S /bin=bin                   \
>                   -S /etc=etc                   \
>                   -S /include=include           \
>                   -S /lib=lib                   \
>                   -S /share=share               \
>                   -S /site-library=site-library \
>                   r)                            \
>       cluster:/path/to/my/stuff
> --8<---------------cut here---------------end--------------->8---
> 
> then log via SSH to cluster and untar the pack.
> 
> --8<---------------cut here---------------start------------->8---
> $ ls -ahl
> total 422M
> drwxrwxr-x   3 sitour sitour 3.8K Nov  4 19:05 .
> drwxrwxrwx. 15 root   root   3.8K Nov  4 19:02 ..
> -r--r--r--   1 sitour sitour 421M Jan  1  1970
> 5n55mgjcj33s700g91x0zzf3ngflnba7-tarball-pack.tar.gz
> lrwxrwxrwx   1 sitour sitour   54 Nov  4 19:05 bin ->
> gnu/store/fvvn6mc4s7p52frdlsfj502k4zbqb9j7-profile/bin
> lrwxrwxrwx   1 sitour sitour   54 Nov  4 19:05 etc ->
> gnu/store/fvvn6mc4s7p52frdlsfj502k4zbqb9j7-profile/etc
> drwxrwxr-x   3 sitour sitour 3.8K Nov  4 19:03 gnu
> lrwxrwxrwx   1 sitour sitour   58 Nov  4 19:05 include ->
> gnu/store/fvvn6mc4s7p52frdlsfj502k4zbqb9j7-profile/include
> lrwxrwxrwx   1 sitour sitour   54 Nov  4 19:05 lib ->
> gnu/store/fvvn6mc4s7p52frdlsfj502k4zbqb9j7-profile/lib
> lrwxrwxrwx   1 sitour sitour   56 Nov  4 19:05 share ->
> gnu/store/fvvn6mc4s7p52frdlsfj502k4zbqb9j7-profile/share
> lrwxrwxrwx   1 sitour sitour   63 Nov  4 19:05 site-library ->
> gnu/store/fvvn6mc4s7p52frdlsfj502k4zbqb9j7-profile/site-library
> --8<---------------cut here---------------end--------------->8---
> 
> The usual ‘./bin/R’ fails with:
> 
> --8<---------------cut here---------------start------------->8---
> $ ./bin/R
> : unsupported Guix execution engine; ignoring
> ./bin/R
> R version 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out"
> 
> [...]
> 
>  *** caught segfault ***
> address 0x7f44f4b11008, cause 'memory not mapped'
> --8<---------------cut here---------------end--------------->8---
> 
> and then has to be killed.  Last,
> 
> --8<---------------cut here---------------start------------->8---
> $ gdb ./bin/R
> GNU gdb (GDB) Red Hat Enterprise Linux (7.2-92.el6)
> Copyright (C) 2010 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 by law.  Type "show
> copying"
> and "show warranty" for details.
> This GDB was configured as "x86_64-redhat-linux-gnu".
> For bug reporting instructions, please see:
> <http://www.gnu.org/software/gdb/bugs/>...
> Reading symbols from
> /data2/tmp/foo/gnu/store/yz0zww6i4pafvwh6ysmqxr5pm72ks7lv-r-minimal-
> 4.0.3R/bin/R...(no debugging symbols found)...done.
> (gdb) run
> Starting program:
> /data2/tmp/foo/gnu/store/yz0zww6i4pafvwh6ysmqxr5pm72ks7lv-r-minimal-
> 4.0.3R/bin/R 
> : unsupported Guix execution engine; ignoring
> /data2/tmp/foo/gnu/store/yz0zww6i4pafvwh6ysmqxr5pm72ks7lv-r-minimal-
> 4.0.3R/bin/Rprocess 36927 is executing new program:
> /data2/tmp/foo/gnu/store/jwdvnklncaqw15376vbbr1vgpfr17j18-proot-
> static-5.1.0/bin/proot
> Detaching after fork from child process 36930.
> 
> R version 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out"
> Copyright (C) 2020 The R Foundation for Statistical Computing
> Platform: x86_64-unknown-linux-gnu (64-bit)
> 
> R is free software and comes with ABSOLUTELY NO WARRANTY.
> You are welcome to redistribute it under certain conditions.
> Type 'license()' or 'licence()' for distribution details.
> 
> R is a collaborative project with many contributors.
> Type 'contributors()' for more information and
> 'citation()' on how to cite R or R packages in publications.
> 
> Type 'demo()' for some demos, 'help()' for on-line help, or
> 'help.start()' for an HTML browser interface to help.
> Type 'q()' to quit R.
> 
> Error: package or namespace load failed for 'grDevices' in
> dyn.load(file, DLLpath = DLLpath, ...):
>  unable to load shared object
> '/gnu/store/nqqhaz59gdr5q6mb6mw9dd8jk133rna2-r-minimal-
> 4.0.3/lib/R/library/grDevices/libs/grDevices.so':
>   /gnu/store/nqqhaz59gdr5q6mb6mw9dd8jk133rna2-r-minimal-
> 4.0.3/lib/R/library/grDevices/libs/grDevices.so: cannot open shared
> object file: Bad address
> Error: package or namespace load failed for 'graphics' in
> dyn.load(file, DLLpath = DLLpath, ...):
>  unable to load shared object
> '/gnu/store/nqqhaz59gdr5q6mb6mw9dd8jk133rna2-r-minimal-
> 4.0.3/lib/R/library/grDevices/libs/grDevices.so':
>   /gnu/store/nqqhaz59gdr5q6mb6mw9dd8jk133rna2-r-minimal-
> 4.0.3/lib/R/library/grDevices/libs/grDevices.so: cannot open shared
> object file: Bad address
> Error: package or namespace load failed for 'stats' in dyn.load(file,
> DLLpath = DLLpath, ...):
>  unable to load shared object
> '/gnu/store/nqqhaz59gdr5q6mb6mw9dd8jk133rna2-r-minimal-
> 4.0.3/lib/R/library/grDevices/libs/grDevices.so':
>   /gnu/store/nqqhaz59gdr5q6mb6mw9dd8jk133rna2-r-minimal-
> 4.0.3/lib/R/library/grDevices/libs/grDevices.so: cannot open shared
> object file: Bad address
> During startup - Warning messages:
> 1: package 'grDevices' in options("defaultPackages") was not found 
> 2: package 'graphics' in options("defaultPackages") was not found 
> 3: package 'stats' in options("defaultPackages") was not found 
> 4: Setting LC_CTYPE failed, using "C" 
> 5: Setting LC_COLLATE failed, using "C" 
> 6: Setting LC_TIME failed, using "C" 
> 7: Setting LC_MESSAGES failed, using "C" 
> 8: Setting LC_MONETARY failed, using "C" 
> 9: Setting LC_PAPER failed, using "C" 
> 10: Setting LC_MEASUREMENT failed, using "C" 
> > 
> --8<---------------cut here---------------end--------------->8---
> 
> 
> The cluster machine is an old kernel:
> 
> --8<---------------cut here---------------start------------->8---
> HEAD$ uname -a
> Linux HEAD 2.6.32-573.8.1.el6.x86_64 #1 SMP Tue Nov 10 18:01:38 UTC
> 2015 x86_64 x86_64 x86_64 GNU/Linux
> --8<---------------cut here---------------end--------------->8---
> 
> 
> What do I miss?

Perhaps completely misguided, but is this inside an SGE or SLURM job?
I've seen similar errors when starting R on a cluster node with too
little memory allocated to the compute job. In my experience you need
at least 2G of memory available.

Kind regards,
Roel Janssen

Re: “guix pack -RR r“ fails?

[Ludovic Courtès]

Hi,

zimoun <zimon.toutoune@gmail.com> skribis:

> The usual ‘./bin/R’ fails with:
>
> $ ./bin/R
> : unsupported Guix execution engine; ignoring

‘GUIX_EXECUTION_ENGINE’ is set to the empty string.

> ./bin/R
> R version 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out"
>
> [...]
>
>  *** caught segfault ***
> address 0x7f44f4b11008, cause 'memory not mapped'

[...]

> Error: package or namespace load failed for 'grDevices' in dyn.load(file, DLLpath = DLLpath, ...):
>  unable to load shared object '/gnu/store/nqqhaz59gdr5q6mb6mw9dd8jk133rna2-r-minimal-4.0.3/lib/R/library/grDevices/libs/grDevices.so':
>   /gnu/store/nqqhaz59gdr5q6mb6mw9dd8jk133rna2-r-minimal-4.0.3/lib/R/library/grDevices/libs/grDevices.so: cannot open shared object file: Bad address
> Error: package or namespace load failed for 'graphics' in dyn.load(file, DLLpath = DLLpath, ...):
>  unable to load shared object '/gnu/store/nqqhaz59gdr5q6mb6mw9dd8jk133rna2-r-minimal-4.0.3/lib/R/library/grDevices/libs/grDevices.so':
>   /gnu/store/nqqhaz59gdr5q6mb6mw9dd8jk133rna2-r-minimal-4.0.3/lib/R/library/grDevices/libs/grDevices.so: cannot open shared object file: Bad address
> Error: package or namespace load failed for 'stats' in dyn.load(file, DLLpath = DLLpath, ...):
>  unable to load shared object '/gnu/store/nqqhaz59gdr5q6mb6mw9dd8jk133rna2-r-minimal-4.0.3/lib/R/library/grDevices/libs/grDevices.so':

Can you try ‘strace -f -s 500 -o log ./bin/R’ and send the tail of the
‘log’ file?

> The cluster machine is an old kernel:
>
> HEAD$ uname -a
> Linux HEAD 2.6.32-573.8.1.el6.x86_64 #1 SMP Tue Nov 10 18:01:38 UTC 2015 x86_64 x86_64 x86_64 GNU/Linux

Our libc is built with ‘--enable-kernel=3.2.0’ so it’s not clear whether
this can work at all (this ‘2.6’ kernel certainly contains stuff
backported from 3.x though, who knows.)

HTH,
Ludo’.

Re: “guix pack -RR r“ fails?

[zimoun]

Hi,

Thank you for the help.


On Fri, 06 Nov 2020 at 11:05, Ludovic Courtès <ludo@gnu.org> wrote:

>> $ ./bin/R
>> : unsupported Guix execution engine; ignoring
>
> ‘GUIX_EXECUTION_ENGINE’ is set to the empty string.

Yes, sorry.  I have tried another one than the default and have been
lazy to open the manual and check which one is the default.

The result is the same with the default.


> Can you try ‘strace -f -s 500 -o log ./bin/R’ and send the tail of the
> ‘log’ file?

--8<---------------cut here---------------start------------->8---
$ strace -f -s 500 -o log ./bin/R
proot error: ptrace(TRACEME): Operation not permitted
proot error: execve("/gnu/store/nqqhaz59gdr5q6mb6mw9dd8jk133rna2-r-minimal-4.0.3/bin/R"): Operation not permitted
proot info: possible causes:
  * the program is a script but its interpreter (eg. /bin/sh) was not found;
  * the program is an ELF but its interpreter (eg. ld-linux.so) was not found;
  * the program is a foreign binary but qemu was not specified;
  * qemu does not work correctly (if specified);
  * the loader was not found or doesn't work.
fatal error: see `proot --help`.
proot error: can't chmod '/tmp/proot-12809-PB78qJ': No such file or directory
--8<---------------cut here---------------end--------------->8---

and then the tail of ’log’:

--8<---------------cut here---------------start------------->8---
[..]
12809 wait4(-1, [{WIFEXITED(s) && WEXITSTATUS(s) == 1}], __WALL, NULL) = 12810
12809 ptrace(PTRACE_SYSCALL, 12810, 0, SIG_0) = -1 ESRCH (No such process)
12809 wait4(-1, 0x7ffe63a965cc, __WALL, NULL) = -1 ECHILD (No child processes)
12809 stat(".", {st_mode=S_IFDIR|0775, st_size=3864, ...}) = 0
12809 stat("/data2/tmp/foo", {st_mode=S_IFDIR|0775, st_size=3864, ...}) = 0
12809 chmod("/tmp/proot-12809-PB78qJ", 0700) = -1 ENOENT (No such file or directory)
12809 write(2, "proot error: ", 13)     = 13
12809 write(2, "can't chmod '/tmp/proot-12809-PB78qJ'", 37) = 37
12809 write(2, ": ", 2)                 = 2
12809 write(2, "No such file or directory\n", 26) = 26
12809 chdir("/data2/tmp/foo")           = 0
12809 exit_group(1)                     = ?
--8<---------------cut here---------------end--------------->8---




>> The cluster machine is an old kernel:
>>
>> HEAD$ uname -a
>> Linux HEAD 2.6.32-573.8.1.el6.x86_64 #1 SMP Tue Nov 10 18:01:38 UTC 2015 x86_64 x86_64 x86_64 GNU/Linux
>
> Our libc is built with ‘--enable-kernel=3.2.0’ so it’s not clear whether
> this can work at all (this ‘2.6’ kernel certainly contains stuff
> backported from 3.x though, who knows.)

Ok.  I will be annoyed if it does not work…


All the best,
simon

Re: “guix pack -RR r“ fails?

[zimoun]

Hi Roel,

On Thu, 05 Nov 2020 at 13:38, Roel Janssen <roel@gnu.org> wrote:

>> What do I miss?
>
> Perhaps completely misguided, but is this inside an SGE or SLURM job?
> I've seen similar errors when starting R on a cluster node with too
> little memory allocated to the compute job. In my experience you need
> at least 2G of memory available.

Thank you for sharing.  I am on the master node and launched as a
regular user (not tried as root).

If I understand correctly, my issue should come from the kernel which is
too old and/or not compiled with the correct options.


All the best,
simon

Re: “guix pack -RR r“ fails?

[Ludovic Courtès]

Hi,

zimoun <zimon.toutoune@gmail.com> skribis:

> $ strace -f -s 500 -o log ./bin/R
> proot error: ptrace(TRACEME): Operation not permitted
> proot error: execve("/gnu/store/nqqhaz59gdr5q6mb6mw9dd8jk133rna2-r-minimal-4.0.3/bin/R"): Operation not permitted
> proot info: possible causes:
>   * the program is a script but its interpreter (eg. /bin/sh) was not found;
>   * the program is an ELF but its interpreter (eg. ld-linux.so) was not found;
>   * the program is a foreign binary but qemu was not specified;
>   * qemu does not work correctly (if specified);
>   * the loader was not found or doesn't work.
> fatal error: see `proot --help`.
> proot error: can't chmod '/tmp/proot-12809-PB78qJ': No such file or directory

Oh right, you’d need to pick a different execution engine, most likely
‘fakechroot’ is the only one that works on this machine:

  export GUIX_EXECUTION_ENGINE=fakechroot
  strace -f -s 500 -o log ./bin/R

HTH,
Ludo’.

Re: “guix pack -RR r“ fails?

[zimoun]

Hi,

On Sun, 8 Nov 2020 at 18:34, Ludovic Courtès <ludo@gnu.org> wrote:

> Oh right, you’d need to pick a different execution engine, most likely
> ‘fakechroot’ is the only one that works on this machine:
>
>   export GUIX_EXECUTION_ENGINE=fakechroot
>   strace -f -s 500 -o log ./bin/R

Hum?  I do not know if I am doing correctly.  The packages
fakechroot-2.9-24.5.el6_1.1.x86_64.rpm and
fakechroot-libs-2.9-24.5.el6_1.1.x86_64.rpm are installed.  And I get
as regular user:

--8<---------------cut here---------------start------------->8---
$ export GUIX_EXECUTION_ENGINE=fakechroot
$ strace -f -s 500 -o logg ./bin/R
fakechroot: unsupported Guix execution engine; ignoring
./bin/Rproot error: ptrace(TRACEME): Operation not permitted
proot error: execve("/gnu/store/nqqhaz59gdr5q6mb6mw9dd8jk133rna2-r-minimal-4.0.3/bin/R"):
Operation not permitted
proot info: possible causes:
  * the program is a script but its interpreter (eg. /bin/sh) was not found;
  * the program is an ELF but its interpreter (eg. ld-linux.so) was not found;
  * the program is a foreign binary but qemu was not specified;
  * qemu does not work correctly (if specified);
  * the loader was not found or doesn't work.
fatal error: see `proot --help`.
proot error: can't chmod '/tmp/proot-41950-9kDMBf': No such file or directory
--8<---------------cut here---------------end--------------->8---
However, as root, simply running ./bin/R returns:

--8<---------------cut here---------------start------------->8---
# ./bin/R
R: run.c:245: disallow_setgroups: Unexpected error: No such file or directory.
Abandon
[root@HEAD foo]#
R version 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out"
Copyright (C) 2020 The R Foundation for Statistical Computing
Platform: x86_64-unknown-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

During startup - Warning messages:
1: Setting LC_CTYPE failed, using "C"
2: Setting LC_COLLATE failed, using "C"
3: Setting LC_TIME failed, using "C"
4: Setting LC_MESSAGES failed, using "C"
5: Setting LC_MONETARY failed, using "C"
6: Setting LC_PAPER failed, using "C"
7: Setting LC_MEASUREMENT failed, using "C"
>
--8<---------------cut here---------------end--------------->8---


All the best,
simon

Re: “guix pack -RR r“ fails?

[Ludovic Courtès]

Hi,

zimoun <zimon.toutoune@gmail.com> skribis:

> On Sun, 8 Nov 2020 at 18:34, Ludovic Courtès <ludo@gnu.org> wrote:
>
>> Oh right, you’d need to pick a different execution engine, most likely
>> ‘fakechroot’ is the only one that works on this machine:
>>
>>   export GUIX_EXECUTION_ENGINE=fakechroot
>>   strace -f -s 500 -o log ./bin/R
>
> Hum?  I do not know if I am doing correctly.  The packages
> fakechroot-2.9-24.5.el6_1.1.x86_64.rpm and
> fakechroot-libs-2.9-24.5.el6_1.1.x86_64.rpm are installed.  And I get
> as regular user:

You do not need these packages: the tarball includes a copy of
libfakechroot.so (see
<https://hpc.guix.info/blog/2020/05/faster-relocatable-packs-with-fakechroot/>).

> $ export GUIX_EXECUTION_ENGINE=fakechroot
> $ strace -f -s 500 -o logg ./bin/R
> fakechroot: unsupported Guix execution engine; ignoring

You would need to use ‘guix pack -RR’ instead of ‘guix pack -R’ to get
the ‘fakechroot’ execution engine.

> However, as root, simply running ./bin/R returns:
>
> # ./bin/R
> R: run.c:245: disallow_setgroups: Unexpected error: No such file or directory.
> Abandon

That indicates that user namespaces are not supported.

But wait, if you’re root, you can just as well upgrade to a kernel that
supports unprivileged user namespaces… or even install Guix?  :-)

HTH,
Ludo’.

Re: “guix pack -RR r“ fails?

[zimoun]

Hi,

On Thu, 12 Nov 2020 at 21:41, Ludovic Courtès <ludo@gnu.org> wrote:

>> Hum?  I do not know if I am doing correctly.  The packages
>> fakechroot-2.9-24.5.el6_1.1.x86_64.rpm and
>> fakechroot-libs-2.9-24.5.el6_1.1.x86_64.rpm are installed.  And I get
>> as regular user:
>
> You do not need these packages: the tarball includes a copy of
> libfakechroot.so (see
> <https://hpc.guix.info/blog/2020/05/faster-relocatable-packs-with-fakechroot/>).
>
>> $ export GUIX_EXECUTION_ENGINE=fakechroot
>> $ strace -f -s 500 -o logg ./bin/R
>> fakechroot: unsupported Guix execution engine; ignoring
>
> You would need to use ‘guix pack -RR’ instead of ‘guix pack -R’ to get
> the ‘fakechroot’ execution engine.
>
>> However, as root, simply running ./bin/R returns:
>>
>> # ./bin/R
>> R: run.c:245: disallow_setgroups: Unexpected error: No such file or directory.
>> Abandon
>
> That indicates that user namespaces are not supported.

I have used ’-RR’ but because it is not working, then I tried to install
extra stuff in case.  But if the kernel is not supporting the namespace,
that’s a end.  Period.


> But wait, if you’re root, you can just as well upgrade to a kernel that
> supports unprivileged user namespaces… or even install Guix?  :-)

That’s not so simple.  It is an old RHEL and I am not sure that the
upgrading path is smooth…  So I am applying the well-known rule: do not
fix it if it is not broken. ;-) Well, I do not want to spend hours to
figure out what is wrong with the new configuration (hardware).

Installing Guix (the package manager) cannot work because the same
problem: kernel.

I am configuring another machine (Dell T620) to smooth the switch.  But
I hit the very same problem: spending hours to figure out what’s wrong
because I am missing obscure hardware configurations.


Thank you for your help.

Cheers,
simon