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ncbi / EvoGeneX

This repository contains the source code of the R package for EvoGeneX, a software to infer the mode of evolution from the gene expression data.
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Failed to install 'EvoGeneX' from GitHub #4

Open basai1234 opened 1 year ago

basai1234 commented 1 year ago

Hello,

I would like to use 'EvoGeneX' however I couldn't install it.

I asked couple other colleagues to install it with:

"devtools::install_github("ncbi/EvoGeneX", subdir="Rpackage", build_vignettes=TRUE)"

And it sounds that we encountered the same issue (both MacOS and Linux):

Error: Failed to install 'EvoGeneX' from GitHub:
  ! System command 'R' failed
7c7a8/00LOCK-EvoGeneX/00new/EvoGeneX/libs/EvoGeneX.so':

I first got this warning something like a dozen of time:

#pragma clang diagnostic pop
                                ^
   In file included from RcppExports.cpp:4:
   In file included from /Library/Frameworks/R.framework/Versions/4.1/Resources/library/RcppEigen/include/RcppEigen.h:25:
   In file included from /Library/Frameworks/R.framework/Versions/4.1/Resources/library/RcppEigen/include/RcppEigenForward.h:30:
   In file included from /Library/Frameworks/R.framework/Versions/4.1/Resources/library/RcppEigen/include/Eigen/Dense:2:
   In file included from /Library/Frameworks/R.framework/Versions/4.1/Resources/library/RcppEigen/include/Eigen/LU:47:
   /Library/Frameworks/R.framework/Versions/4.1/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
       #pragma clang diagnostic pop
                                ^

And finally this one before it halt:

** testing if installed package can be loaded from temporary location
   Error: package or namespace load failed for ‘EvoGeneX’ in dyn.load(file, DLLpath = DLLpath, ...):, no matching push [-Wunknown-pragmas]
    unable to load shared object '/private/var/folders/pn/107n583j0_911v5jl1jwl8rc0000gn/T/RtmpLK4PWY/Rinst5832357c7a8/00LOCK-EvoGeneX/00new/EvoGeneX/libs/EvoGeneX.so':
     dlopen(/private/var/folders/pn/107n583j0_911v5jl1jwl8rc0000gn/T/RtmpLK4PWY/Rinst5832357c7a8/00LOCK-EvoGeneX/00new/EvoGeneX/libs/EvoGeneX.so, 6): Symbol not found: __Z12evogenex_fitiiiRKN4Rcpp6VectorILi14ENS_15PreserveStorageEEES4_S4_S4_RKNS_6MatrixILi14ES1_EEdd
     Referenced from: /private/var/folders/pn/107n583j0_911v5jl1jwl8rc0000gn/T/RtmpLK4PWY/Rinst5832357c7a8/00LOCK-EvoGeneX/00new/EvoGeneX/libs/EvoGeneX.so
     Expected in: flat namespace
    in /private/var/folders/pn/107n583j0_911v5jl1jwl8rc0000gn/T/RtmpLK4PWY/Rinst5832357c7a8/00LOCK-EvoGeneX/00new/EvoGeneX/libs/EvoGeneX.so
   Error: loading failed
   Execution halted
   ERROR: loading failed
─  removing ‘/private/var/folders/pn/107n583j0_911v5jl1jwl8rc0000gn/T/RtmpLK4PWY/Rinst5832357c7a8/EvoGeneX’
         -----------------------------------
   ERROR: package installation failed

If you could help install it, it would be great !

Thanks a lot!

soumitrakp commented 1 year ago

Hi Basai,

Thank you for your interest in EvoGeneX.

I am also facing the same problem. I am not sure if this is some issue with GitHub install function.

However, the following workaround worked for me.

Let me know if that works for you.

soumitrakp commented 1 year ago

Hi Basai,

Thank you for your interest in EvoGeneX.

I am also facing the same problem. I am not sure if this is some issue with GitHub install function.

However, the following workaround worked for me.

  1. Clone the GitHub repository on your local computer.
  2. On a shell terminal, CD to Rpackage directory within EvoGeneX repository.
  3. Then execute "Rscript build_install.R"

Let me know if that works for you.

Soumitra

From: basai1234 @.> Sent: Thursday, July 13, 2023 9:44 AM To: ncbi/EvoGeneX @.> Cc: Subscribed @.***> Subject: [EXTERNAL] [ncbi/EvoGeneX] Failed to install 'EvoGeneX' from GitHub (Issue #4)

Hello,

I would like to use 'EvoGeneX' however I couldn't install it.

I asked couple other colleagues to install it with:

"devtools::install_github("ncbi/EvoGeneX", subdir="Rpackage", build_vignettes=TRUE)"

And it sounds that we encountered the same issue (both MacOS and Linux):

Error: Failed to install 'EvoGeneX' from GitHub: ! System command 'R' failed 7c7a8/00LOCK-EvoGeneX/00new/EvoGeneX/libs/EvoGeneX.so':

I first got this warning something like a dozen of time:

pragma clang diagnostic pop

                            ^

In file included from RcppExports.cpp:4: In file included from /Library/Frameworks/R.framework/Versions/4.1/Resources/library/RcppEigen/include/RcppEigen.h:25: In file included from /Library/Frameworks/R.framework/Versions/4.1/Resources/library/RcppEigen/include/RcppEigenForward.h:30: In file included from /Library/Frameworks/R.framework/Versions/4.1/Resources/library/RcppEigen/include/Eigen/Dense:2: In file included from /Library/Frameworks/R.framework/Versions/4.1/Resources/library/RcppEigen/include/Eigen/LU:47: /Library/Frameworks/R.framework/Versions/4.1/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]

pragma clang diagnostic pop

                            ^

And finally this one before it halt:

** testing if installed package can be loaded from temporary location Error: package or namespace load failed for ‘EvoGeneX’ in dyn.load(file, DLLpath = DLLpath, ...):, no matching push [-Wunknown-pragmas] unable to load shared object '/private/var/folders/pn/107n583j0_911v5jl1jwl8rc0000gn/T/RtmpLK4PWY/Rinst5832357c7a8/00LOCK-EvoGeneX/00new/EvoGeneX/libs/EvoGeneX.so': dlopen(/private/var/folders/pn/107n583j0_911v5jl1jwl8rc0000gn/T/RtmpLK4PWY/Rinst5832357c7a8/00LOCK-EvoGeneX/00new/EvoGeneX/libs/EvoGeneX.so, 6): Symbol not found: __Z12evogenex_fitiiiRKN4Rcpp6VectorILi14ENS_15PreserveStorageEEES4_S4_S4_RKNS_6MatrixILi14ES1_EEdd Referenced from: /private/var/folders/pn/107n583j0_911v5jl1jwl8rc0000gn/T/RtmpLK4PWY/Rinst5832357c7a8/00LOCK-EvoGeneX/00new/EvoGeneX/libs/EvoGeneX.so Expected in: flat namespace in /private/var/folders/pn/107n583j0_911v5jl1jwl8rc0000gn/T/RtmpLK4PWY/Rinst5832357c7a8/00LOCK-EvoGeneX/00new/EvoGeneX/libs/EvoGeneX.so Error: loading failed Execution halted ERROR: loading failed ─ removing ‘/private/var/folders/pn/107n583j0_911v5jl1jwl8rc0000gn/T/RtmpLK4PWY/Rinst5832357c7a8/EvoGeneX’

ERROR: package installation failed

If you could help install it, it would be great !

Thanks a lot!

— Reply to this email directly, view it on GitHubhttps://github.com/ncbi/EvoGeneX/issues/4, or unsubscribehttps://github.com/notifications/unsubscribe-auth/AB7HEZGSHR4TY5VAZ7PCBU3XP73RPANCNFSM6AAAAAA2I7BY4Q. You are receiving this because you are subscribed to this thread.Message ID: @.***>

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basai1234 commented 1 year ago

Sounds like it worked!

I am now able to load the library !

Thanks a lot for this quick answer,

Have a good one,

B

Le jeu. 13 juil. 2023 à 16:06, Soumitra Pal @.***> a écrit :

Hi Basai,

Thank you for your interest in EvoGeneX.

I am also facing the same problem. I am not sure if this is some issue with GitHub install function.

However, the following workaround worked for me.

  • Clone the GitHub repository on your local computer.
  • On a shell terminal, CD to Rpackage directory within EvoGeneX repository.
  • Then execute "Rscript build_install.R"

Let me know if that works for you.

— Reply to this email directly, view it on GitHub https://github.com/ncbi/EvoGeneX/issues/4#issuecomment-1634309850, or unsubscribe https://github.com/notifications/unsubscribe-auth/AWE6AFSMZE5GUCG6MOTZCO3XP76FTANCNFSM6AAAAAA2I7BY4Q . You are receiving this because you authored the thread.Message ID: @.***>

soumitrakp commented 1 year ago

Glad to know. Thanks.