Some issues for installing PDL

[lijinw]

Hi, There is an error when I try to install the PDL modules. It's mostly due to the perl's issues, but I would appreciate if someone could provide some suggestions. I built an environment by Conda, and I install perl and PDL modules by Conda. However, when I install other modules using code: cpanm PDL::GSL::CDF, it jump to update PDL to version 2.059, and it failed as below. I'm not a root user, and I installed it in my cluster. Thanks!

cpanm (App::cpanminus) 1.7044 on perl 5.026002 built for x86_64-linux-thread-multi Work directory is /home/gmslijiw/.cpanm/work/1636358533.12635 You have make /usr/bin/make You have /usr/bin/wget You have /bin/tar: tar (GNU tar) 1.23 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. Written by John Gilmore and Jay Fenlason. You have /usr/bin/unzip Searching PDL () on cpanmetadb ... --> Working on PDL Fetching http://www.cpan.org/authors/id/E/ET/ETJ/PDL-2.059.tar.gz -> OK Unpacking PDL-2.059.tar.gz Entering PDL-2.059 Checking configure dependencies from META.json Checking if you have Carp 1.2 ... Yes (1.42) Checking if you have Devel::CheckLib 1.01 ... Yes (1.13) Checking if you have ExtUtils::Depends 0.402 ... Yes (0.8001) Checking if you have ExtUtils::MakeMaker 7.12 ... Yes (7.24) Checking if you have File::Path 0 ... Yes (2.12_01) Checking if you have ExtUtils::ParseXS 3.01 ... Yes (3.34) Configuring PDL-2.059 Running Makefile.PL Checking if your kit is complete... Looks good Devel::CheckLib with 'pthread' failed PDL will be built without POSIX thread support. ==> NOTE: PDL threads are unrelated to perl threads (usethreads=y)! ==> Enabling perl threads will not help! Warning (mostly harmless): No library found for -lm Types.pm.PL: using typedef long PDL_Indx Extracting Types.pm Warning (mostly harmless): No library found for -lm Warning (mostly harmless): No library found for -lm Warning (mostly harmless): No library found for -lm Warning (mostly harmless): No library found for -lm Warning (mostly harmless): No library found for -lm Warning (mostly harmless): No library found for -lm Will not build TriD graphics.

[wososa]

@lijinw ,

Sorry for my late reply. Your post disappeared earlier. If you are not a root user, you can try to use Docker:

docker pull docker.io/woodydon/psi_sigma_pipeline:3.4

Or, you can try Conda (I haven't tried):

conda create -n PSIsigma conda activate PSIsigma conda install -c conda-forge gcc conda install -c conda-forge gsl conda install -c bioconda perl-app-cpanminus cpanm PDL::LiteF cpanm PDL::GSL::CDF cpanm PDL::Stats cpanm Statistics::Multtest cpanm Statistics::R

Please let me know if these help. Feel free to send me an email to klin@cshl.edu.

Best, Woody

[lijinw]

Thanks a lot!

Best, Lijin

---

From: Woody Lin @.> Sent: Sunday, November 21, 2021 10:16:21 PM To: wososa/PSI-Sigma @.> Cc: lijinw @.>; Mention @.> Subject: Re: [wososa/PSI-Sigma] Some issues for installing PDL (Issue #30)

@lijinwhttps://github.com/lijinw ,

Sorry for my late reply. Your post disappeared earlier. If you are not a root user, you can try to use Docker:

docker pull docker.io/woodydon/psi_sigma_pipeline:3.4

Or, you can try Conda (I haven't tried):

conda create -n PSIsigma conda activate PSIsigma conda install -c conda-forge gcc conda install -c conda-forge gsl conda install -c bioconda perl-app-cpanminus cpanm PDL::LiteF cpanm PDL::GSL::CDF cpanm PDL::Stats cpanm Statistics::Multtest cpanm Statistics::R

Please let me know if these help. Feel free to send me an email to @.***

Best, Woody

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHubhttps://github.com/wososa/PSI-Sigma/issues/30#issuecomment-974825361, or unsubscribehttps://github.com/notifications/unsubscribe-auth/AKOZIY5KNIXDXUHUSE3NTKDUND5LLANCNFSM5HSAXZZQ. Triage notifications on the go with GitHub Mobile for iOShttps://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675 or Androidhttps://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub.

[wososa]

@lijinw

I added a section using Anaconda as an example. I added Python 3.9 to resolve some of the condo issues. Hope that this will make your installation easier:

conda create -n PSIsigma r-essentials r-base
conda activate PSIsigma
conda install python=3.9
conda install -c conda-forge gcc gsl
conda install -c bioconda perl-app-cpanminus
cpanm PDL::LiteF
cpanm PDL::GSL::CDF
cpanm PDL::Stats
cpanm Statistics::Multtest
cpanm Statistics::R

The easiest would be using Singularity. You only need to install singularity and do something like this:

singularity exec --bind /home:/home docker://woodydon/psi_sigma_pipeline:3.6 perl /usr/local/bin/PSI-Sigma-1.9r/dummyai.pl --gtf Homo_sapiens.GRCh38.100.sorted.gtf --nread 10 --name PSIsigma1d9r --type 1 --fmode 3

Best, Woody