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hemberg-lab / scmap

A tool for unsupervised projection of single cell RNA-seq data
http://bioconductor.org/packages/scmap
GNU General Public License v3.0
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trouble installing scmap #2

Closed dat4git closed 7 years ago

dat4git commented 7 years ago

I want to run scmap on some single cell datasets but ran into the following problems when installing the package. Any help would be much appreciated. Thx!

  1. Installing from Bioconductor (OS X El Capitan 10.11.6 )

    source("https://bioconductor.org/biocLite.R") Bioconductor version 3.5 (BiocInstaller 1.26.1), ?biocLite for help biocLite("scmap") BioC_mirror: https://bioconductor.org Using Bioconductor 3.5 (BiocInstaller 1.26.1), R 3.4.2 (2017-09-28). Installing package(s) ‘scmap’ Warning message: package ‘scmap’ is not available (for R version 3.4.2)

  2. Installing from github (OS X El Capitan 10.11.6 )

    devtools::install_github("hemberg-lab/scmap") ** testing if installed package can be loaded Creating a generic function for ‘toJSON’ from package ‘jsonlite’ in package ‘googleVis’ Error: package or namespace load failed for ‘scmap’ in dyn.load(file, DLLpath = DLLpath, ...): unable to load shared object '/Users/dat4git/Library/R/3.4/library/scmap/libs/scmap.so': dlopen(/Users/dat4git/Library/R/3.4/library/scmap/libs/scmap.so, 6): Library not loaded: /Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libRlapack.dylib Referenced from: /Users/dat4git/Library/R/3.4/library/scmap/libs/scmap.so Reason: Incompatible library version: scmap.so requires version 3.5.0 or later, but libRlapack.dylib provides version 3.4.0 Error: loading failed Execution halted

Note: Looks like the libRlapack.dylib version is causing the problem. Is there a simple way to fix this on a Mac?

sessionInfo() R version 3.4.2 (2017-09-28) Platform: x86_64-apple-darwin15.6.0 (64-bit) Running under: OS X El Capitan 10.11.6 BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib LAPACK: /Library/Frameworks/R.framework/Versions/3.4/Resources/lib/libRlapack.dylib ...

  1. Also tried installing on Linux ..

devtools::install_github("hemberg-lab/scmap") Downloading GitHub repo hemberg-lab/scmap@master from URL https://api.github.com/repos/hemberg-lab/scmap/zipball/master Installing scmap '/broad/software/free/Linux/redhat_6_x86_64/pkgs/r_3.4.0/lib64/R/bin/R' \ --no-site-file --no-environ --no-save --no-restore --quiet CMD INSTALL \ '/tmp/15148918.1.interactive/Rtmp7l66Tu/devtools718c38bee8c4/hemberg-lab-scmap-b9cdf52' \ --library='/home/unix/dat4git/R/x86_64-pc-linux-gnu-library/3.4' \ --install-tests

sessionInfo() R version 3.4.0 (2017-04-21) Platform: x86_64-pc-linux-gnu (64-bit) Running under: Red Hat Enterprise Linux Server release 6.9 (Santiago)

Matrix products: default BLAS: /broad/software/free/Linux/redhat_6_x86_64/pkgs/r_3.4.0/lib64/R/lib/libRblas.so LAPACK: /broad/software/free/Linux/redhat_6_x86_64/pkgs/r_3.4.0/lib64/R/lib/libRlapack.so ...

wikiselev commented 7 years ago

Hi, thanks for reporting this! Can you try devtools::install_github("hemberg-lab/scmap") again, please? And let me know what it says?

dat4git commented 7 years ago

Thanks! Successfully installed on OS X El Capitan 10.11.6.

wikiselev commented 7 years ago

Great, thanks for letting me know! I forgot to remove dynamically generated files from the src folder. And when you use devtools::install_github I suppose it will not recompile those files if you already have them. Since I have a devel version of R (3.5) you had an R version conflict on your system. Now I have removed the dynamic files from the src folder. Thanks again!