On 2014-12-28 at 01:13:21 +0100, Pablo marin-garcia wrote:
> Dear Zakariyya,
>
> Thanks for the distribution, I was just looking this week for pdl/perl
> distributions to work with dataframes I use both in R and Perl. I was
> looking for something in pdl or Perl for doing dataframe subselections and
> calculations. I can use pdl for numbers (in the matrix part of dataframes)
> and for strings that are all of the same size with PDL::Char but was
> complicated to subselect by alphanumeric factors without prior
> 'numerification' .
>
> I hope your modules would be a good option for this functionality but
> unfortunately I was unable to install ithem at the first go.
I haven't forgot about this bug! I am still looking into debugging it,
but from what I have seen so far, this stack smashing error only happens
while running under the test harness. I don't know why, but at least
that is the first step towards reproducing it.
I'm not sure about the issue with the shared object. I think that is
from how R gets loaded using R's RHOME, but I don't know how to
reproduce it. What do
R RHOME
R CMD config --cppflags
R CMD config --ldflags
ldd `R RHOME`/bin/exec/R
give as output?
I suspect that the warnings can be fixed by making sure that the library
is loaded ahead of time:
export
LD_PRELOAD='/storage/ethernus_miscellanea/scratch_local/ugdg_software/R/R-3.0.2/library/stats/libs/stats.so'
cpanm --verbose Statistics::NiceR
but that's not optimal.
The library should be fine to use otherwise. Please let me know if this
helps.
Regards,
- Zaki Mughal
>
> Here I report my installation errors just in case are of any help
>
> Installation error report:
> ------------------------------
>
> Note1: I am reporting this here just in case if of any help to you.
>
> Note2: R does not come from a package but instead is compiled by myself.
>
> There is a recurrent error in each of the module test but test is reported
> OK ??!!
>
> unable to load shared object
> '/storage/ethernus_miscellanea/scratch_local/ugdg_software/R/R-3.0.2/library/stats/libs/stats.so':
> libRlapack.so: cannot open shared object file: No such file or
> directory
> Package ‘stats’ in options("defaultPackages") was not found
> t/conversion.t .............. ok
>
>
> But stats.so exists:
>
> $ locate stats.so
> /storage/ethernus_miscellanea/scratch_local/ugdg_software/R/R-3.0.2/library/stats/libs/stats.so
> --------
> # intallation command
> $ cpanm Statistics::NiceR
>
> Building and testing Statistics-NiceR-0.03 ... *** stack smashing detected
> ***: /home/pmg/perl5/perlbrew/perls/perl-5.16.0/bin/perl terminated
>
> ======= Backtrace: =========
> /lib/x86_64-linux-gnu/libc.so.6(__fortify_fail+0x37)[0x2b222e805807]
> /lib/x86_64-linux-gnu/libc.so.6(__fortify_fail+0x0)[0x2b222e8057d0]
> /soft_bio/R/R-3.0.2/lib/libR.so(+0xef05e)[0x2b22306e805e]
> [0x40f3648]
> ======= Memory map: ========
> 00400000-00555000 r-xp 00000000 fc:00 793010
> /home/pmg/perl5/perlbrew/perls/perl-5.16.0/bin/perl
> 00755000-00756000 r--p 00155000 fc:00 793010
> /home/pmg/perl5/perlbrew/perls/perl-5.16.0/bin/perl
> 00756000-0075b000 rw-p 00156000 fc:00 793010
> /home/pmg/perl5/perlbrew/perls/perl-5.16.0/bin/perl
> 0075b000-0075c000 rw-p 00000000 00:00 0
> 01d17000-04c45000 rw-p 00000000 00:00 0
> [heap]
> 2b222dd9c000-2b222ddbe000 r-xp 00000000 fc:00 1186920
> /lib/x86_64-linux-gnu/ld-2.15.so
> 2b222ddbe000-2b222ddc0000 rw-p 00000000 00:00 0
> 2b222dfbe000-2b222dfbf000 r--p 00022000 fc:00 1186920
> /lib/x86_64-linux-gnu/ld-2.15.so
> 2b222dfbf000-2b222dfc1000 rw-p 00023000 fc:00 1186920
> /lib/x86_64-linux-gnu/ld-2.15.so
> 2b222dfc1000-2b222dfc3000 r-xp 00000000 fc:00 1186905
> /lib/x86_64-linux-gnu/libdl-2.15.so
> 2b222dfc3000-2b222e1c3000 ---p 00002000 fc:00 1186905
> /lib/x86_64-linux-gnu/libdl-2.15.so
> 2b222e1c3000-2b222e1c4000 r--p 00002000 fc:00 1186905
> /lib/x86_64-linux-gnu/libdl-2.15.so
> 2b222e1c4000-2b222e1c5000 rw-p 00003000 fc:00 1186905
> /lib/x86_64-linux-gnu/libdl-2.15.so
> 2b222e1c5000-2b222e2c0000 r-xp 00000000 fc:00 1186914
> /lib/x86_64-linux-gnu/libm-2.15.so
> 2b222e2c0000-2b222e4bf000 ---p 000fb000 fc:00 1186914
> /lib/x86_64-linux-gnu/libm-2.15.so
> 2b222e4bf000-2b222e4c0000 r--p 000fa000 fc:00 1186914
> /lib/x86_64-linux-gnu/libm-2.15.so
> 2b222e4c0000-2b222e4c1000 rw-p 000fb000 fc:00 1186914
> /lib/x86_64-linux-gnu/libm-2.15.so
> 2b222e4c1000-2b222e4c2000 rw-p 00000000 00:00 0
> 2b222e4c2000-2b222e4cb000 r-xp 00000000 fc:00 1186915
> /lib/x86_64-linux-gnu/libcrypt-2.15.so
> 2b222e4cb000-2b222e6cb000 ---p 00009000 fc:00 1186915
> /lib/x86_64-linux-gnu/libcrypt-2.15.so
> 2b222e6cb000-2b222e6cc000 r--p 00009000 fc:00 1186915
> /lib/x86_64-linux-gnu/libcrypt-2.15.so
> 2b222e6cc000-2b222e6cd000 rw-p 0000a000 fc:00 1186915
> /lib/x86_64-linux-gnu/libcrypt-2.15.so
> 2b222e6cd000-2b222e6fb000 rw-p 00000000 00:00 0
> 2b222e6fb000-2b222e8b0000 r-xp 00000000 fc:00 1186906
> /lib/x86_64-linux-gnu/libc-2.15.so
> 2b222e8b0000-2b222eaaf000 ---p 001b5000 fc:00 1186906
> /lib/x86_64-linux-gnu/libc-2.15.so
> 2b222eaaf000-2b222eab3000 r--p 001b4000 fc:00 1186906
> /lib/x86_64-linux-gnu/libc-2.15.so
> 2b222eab3000-2b222eab5000 rw-p 001b8000 fc:00 1186906
> /lib/x86_64-linux-gnu/libc-2.15.so
> 2b222eab5000-2b222eabc000 rw-p 00000000 00:00 0
> 2b222eabc000-2b222ed85000 r--p 00000000 fc:00 1311449
> /usr/lib/locale/locale-archive
> 2b222ed85000-2b222ed90000 r-xp 00000000 fc:00 822259
> /home/pmg/perl5/perlbrew/perls/perl-5.16.0/lib/site_perl/5.16.0/x86_64-linux/auto/List/Util/Util.so
> 2b222ed90000-2b222ef8f000 ---p 0000b000 fc:00 822259
> /home/pmg/perl5/perlbrew/perls/perl-5.16.0/lib/site_perl/5.16.0/x86_64-linux/auto/List/Util/Util.so
> 2b222ef8f000-2b222ef90000 r--p 0000a000 fc:00 822259
> /home/pmg/perl5/perlbrew/perls/perl-5.16.0/lib/site_perl/5.16.0/x86_64-linux/auto/List/Util/Util.so
> 2b222ef90000-2b222ef91000 rw-p 0000b000 fc:00 822259
> /home/pmg/perl5/perlbrew/perls/perl-5.16.0/lib/site_perl/5.16.0/x86_64-linux/auto/List/Util/Util.so
> 2b222ef91000-2b222ef92000 r--p 00000000 fc:00 267913
> /usr/share/locale-langpack/en_GB/LC_MESSAGES/libc.mo
> 2b222ef92000-2b222ef97000 r-xp 00000000 fc:00 1183229
>
> /home/pmg/perl5/perlbrew/perls/perl-5.16.0/lib/5.16.0/x86_64-linux/auto/Time/HiRes/HiRes.so
> 2b222ef97000-2b222f196000 ---p 00005000 fc:00 1183229
>
> /home/pmg/perl5/perlbrew/perls/perl-5.16.0/lib/5.16.0/x86_64-linux/auto/Time/HiRes/HiRes.so
> 2b222f196000-2b222f197000 r--p 00004000 fc:00 1183229
>
> /home/pmg/perl5/perlbrew/perls/perl-5.16.0/lib/5.16.0/x86_64-linux/auto/Time/HiRes/HiRes.so
> 2b222f197000-2b222f198000 rw-p 00005000 fc:00 1183229
>
> /home/pmg/perl5/perlbrew/perls/perl-5.16.0/lib/5.16.0/x86_64-linux/auto/Time/HiRes/HiRes.so
> 2b222f198000-2b222f19f000 r-xp 00000000 fc:00 1186910
> /lib/x86_64-linux-gnu/librt-2.15.so
> 2b222f19f000-2b222f39e000 ---p 00007000 fc:00 1186910
> /lib/x86_64-linux-gnu/librt-2.15.so
> 2b222f39e000-2b222f39f000 r--p 00006000 fc:00 1186910
> /lib/x86_64-linux-gnu/librt-2.15.so
> 2b222f39f000-2b222f3a0000 rw-p 00007000 fc:00 1186910
> /lib/x86_64-linux-gnu/librt-2.15.so
> 2b222f3a0000-2b222f3b8000 r-xp 00000000 fc:00 1186908
> /lib/x86_64-linux-gnu/libpthread-2.15.so
> 2b222f3b8000-2b222f5b7000 ---p 00018000 fc:00 1186908
> /lib/x86_64-linux-gnu/libpthread-2.15.so
> 2b222f5b7000-2b222f5b8000 r--p 00017000 fc:00 1186908
> /lib/x86_64-linux-gnu/libpthread-2.15.so
> 2b222f5b8000-2b222f5b9000 rw-p 00018000 fc:00 1186908
> /lib/x86_64-linux-gnu/libpthread-2.15.so
> 2b222f5b9000-2b222f5bd000 rw-p 00000000 00:00 0
> 2b222f5bd000-2b222f5c1000 r-xp 00000000 fc:00 1183155
>
> /home/pmg/perl5/perlbrew/perls/perl-5.16.0/lib/5.16.0/x86_64-linux/auto/mro/mro.so
> 2b222f5c1000-2b222f7c0000 ---p 00004000 fc:00 1183155
>
> /home/pmg/perl5/perlbrew/perls/perl-5.16.0/lib/5.16.0/x86_64-linux/auto/mro/mro.so
> 2b222f7c0000-2b222f7c1000 r--p 00003000 fc:00 1183155
>
> /home/pmg/perl5/perlbrew/perls/perl-5.16.0/lib/5.16.0/x86_64-linux/auto/mro/mro.so
>
>
> == The output of cpanm build.log
>
> [...]
>
> Building and testing Statistics-NiceR-0.03
>
> Error in dyn.load(file, DLLpath = DLLpath, ...) :
>
> unable to load shared object
> '/storage/ethernus_miscellanea/scratch_local/ugdg_software/R/R-3.0.2/library/stats/libs/stats.so':
>
> libRlapack.so: cannot open shared object file: No such file or directory
>
> During startup - Warning message:
>
> package ‘stats’ in options("defaultPackages") was not found
>
> Manifying 13 pod documents
>
> Error in dyn.load(file, DLLpath = DLLpath, ...) :
>
> unable to load shared object
> '/storage/ethernus_miscellanea/scratch_local/ugdg_software/R/R-3.0.2/library/stats/libs/stats.so':
>
> libRlapack.so: cannot open shared object file: No such file or directory
>
> During startup - Warning message:
>
> package ‘stats’ in options("defaultPackages") was not found
>
> PERL_DL_NONLAZY=1 "/home/pmg/perl5/perlbrew/perls/perl-5.16.0/bin/perl"
> "-MExtUtils::Command::MM" "-MTest::Harness" "-e" "undef
> *Test::Harness::Switches; test_harness(0, 'blib/lib', 'blib/arch')" t/*.t
>
> Error in dyn.load(file, DLLpath = DLLpath, ...) :
>
> unable to load shared object
> '/storage/ethernus_miscellanea/scratch_local/ugdg_software/R/R-3.0.2/library/stats/libs/stats.so':
>
> libRlapack.so: cannot open shared object file: No such file or directory
>
> During startup - Warning message:
>
> package ‘stats’ in options("defaultPackages") was not found
>
> t/conversion.t .............. ok
>
> Error in dyn.load(file, DLLpath = DLLpath, ...) :
>
> unable to load shared object
> '/storage/ethernus_miscellanea/scratch_local/ugdg_software/R/R-3.0.2/library/stats/libs/stats.so':
>
> libRlapack.so: cannot open shared object file: No such file or directory
>
> During startup - Warning message:
>
> package ‘stats’ in options("defaultPackages") was not found
>
> t/equality.t ................ ok
>
> [...]
>
> Error in dyn.load(file, DLLpath = DLLpath, ...) :
>
> unable to load shared object
> '/storage/ethernus_miscellanea/scratch_local/ugdg_software/R/R-3.0.2/library/stats/libs/stats.so':
>
> libRlapack.so: cannot open shared object file: No such file or directory
>
> During startup - Warning message:
>
> package ‘stats’ in options("defaultPackages") was not found
>
> Error: could not find function "DESTROY"
>
> In addition: Warning message:
>
> In mean.default(X[[5L]], ...) :
>
> argument is not numeric or logical: returning NA
>
> t/lapply.t .................. ok
>
> Error in dyn.load(file, DLLpath = DLLpath, ...) :
>
> unable to load shared object
> '/storage/ethernus_miscellanea/scratch_local/ugdg_software/R/R-3.0.2/library/stats/libs/stats.so':
>
> libRlapack.so: cannot open shared object file: No such file or directory
>
> During startup - Warning message:
>
> package ‘stats’ in options("defaultPackages") was not found
>
> Error: negative length vectors are not allowed
>
>
> *** caught segfault ***
>
> address (nil), cause 'memory not mapped'
>
>
> Possible actions:
>
> 1: abort (with core dump, if enabled)
>
> 2: normal R exit
>
> 3: exit R without saving workspace
>
> 4: exit R saving workspace
>
> make: *** [test_dynamic] Interrupt
>
> make: *** [test_dynamic] Interrupt
> =================================
>
> On Wed, Dec 24, 2014 at 6:01 AM, Zakariyya Mughal <[email protected]>
> wrote:
>
> > Hi everyone,
> >
> > I have uploaded modules for working with the R interpreter from Perl.
> > The CPAN links are below, but to get a taste of what the API
> > looks like, check out my blog post <
> > http://enetdown.org/dot-plan/posts/2014/12/24/a_fast_and_natural_interface_to_R_from_Perl/
> > >.
> >
> > - Statistics::NiceR <http://p3rl.org/Statistics::NiceR>
> > - Data::Frame <http://p3rl.org/Data::Frame>
> >
> > I'd love to have feedback on how to improve them.
> >
> > Regards and happy hacking,
> > - Zaki Mughal
> > _______________________________________________
> > Bioperl-l mailing list
> > [email protected]
> > http://mailman.open-bio.org/mailman/listinfo/bioperl-l
> >
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