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WubingZhang / MAGeCKFlute

Integrative analysis pipeline for pooled CRISPR functional genetic screens
https://github.com/WubingZhang/MAGeCKFlute
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Installation error #3

Open WubingZhang opened 4 years ago

WubingZhang commented 4 years ago

Downloading GitHub repo WubingZhang/MAGeCKFlute@master sh: 1: /bin/gtar: not found sh: 1: /bin/gtar: not found Error: Failed to install 'MAGeCKFlute' from GitHub: error in running command In addition: Warning messages: 1: In system(cmd) : error in running command 2: In utils::untar(tarfile, ...) : ‘/bin/gtar -xf '/tmp/RtmpKmKPFX/file52ab788ff0fc.tar.gz' -C '/tmp/RtmpKmKPFX/remotes52ab4088f639'’ returned error code 127 Execution halted

WubingZhang commented 4 years ago

checking for xmlParseFile in -lxml2... yes You are trying to use a version 2.* edition of libxml but an incompatible library. The header files and library seem to be mismatched. If you have specified LIBXML_INCDIR, make certain to also specify an appropriate LIBXML_LIBDIR if the libxml2 library is not in the default directories. ERROR: configuration failed for package ‘XML’

WubingZhang commented 4 years ago

Downloading GitHub repo WubingZhang/MAGeCKFlute@master sh: 1: /bin/gtar: not found sh: 1: /bin/gtar: not found Error: Failed to install 'MAGeCKFlute' from GitHub: error in running command In addition: Warning messages: 1: In system(cmd) : error in running command 2: In utils::untar(tarfile, ...) : ‘/bin/gtar -xf '/tmp/RtmpKmKPFX/file52ab788ff0fc.tar.gz' -C '/tmp/RtmpKmKPFX/remotes52ab4088f639'’ returned error code 127 Execution halted

tar is not available, then you should install it first. conda install -c conda-forge tar

WubingZhang commented 4 years ago

checking for xmlParseFile in -lxml2... yes You are trying to use a version 2.* edition of libxml but an incompatible library. The header files and library seem to be mismatched. If you have specified LIBXML_INCDIR, make certain to also specify an appropriate LIBXML_LIBDIR if the libxml2 library is not in the default directories. ERROR: configuration failed for package ‘XML’

  • removing ‘/Users/travis/miniconda/lib/R/library/XML’
  • restoring previous ‘/Users/travis/miniconda/lib/R/library/XML’ Error: Failed to install 'MAGeCKFlute' from GitHub: (converted from warning) installation of package ‘XML’ had non-zero exit status Execution halted The command "Rscript -e 'devtools::install_github("WubingZhang/MAGeCKFlute")'" failed and exited with 1 during .

This error is triggered by the incompatible of libxml2 and r-xml. It could be resolved by reinstalling libxml2 and r-xml using conda.

$ conda install -c anaconda libxml2 $ conda install -c r r-xml