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SysBioChalmers / RAVEN

The RAVEN Toolbox for genome scale model reconstruction, curation and analysis.
http://sysbiochalmers.github.io/RAVEN/
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bug: make binaries executable on Ubuntu #527

Closed edkerk closed 7 months ago

edkerk commented 7 months ago

Discussed in https://github.com/SysBioChalmers/RAVEN/discussions/526

Originally posted by **juferprada97** February 21, 2024 I have the following problem when installing Raven in matlab (Liinux64 - ubuntu) with the "make binaries executables". line 1: syntax error near unexpected token `(' /bin/bash: -c: line 1: `chmod +x "/home/jufer/Apps/Raven/RAVEN/software/blast+/blastp".(mexa64|mexglx|mexmaci64|mac|bat)' > In checkInstallation>makeBinaryExecutable (line 338) In checkInstallation (line 107) Warning: Failed to make /home/jufer/Apps/Raven/RAVEN/software/blast+/makeblastdb executable: /bin/bash: -c: line 1: syntax error near unexpected token `(' /bin/bash: -c: line 1: `chmod +x "/home/jufer/Apps/Raven/RAVEN/software/blast+/makeblastdb".(mexa64|mexglx|mexmaci64|mac|bat)' > In checkInstallation>makeBinaryExecutable (line 338) In checkInstallation (line 107) Warning: Failed to make /home/jufer/Apps/Raven/RAVEN/software/cd-hit/cd-hit executable: /bin/bash: -c: line 1: syntax error near unexpected token `(' /bin/bash: -c: line 1: `chmod +x "/home/jufer/Apps/Raven/RAVEN/software/cd-hit/cd-hit".(mexa64|mexglx|mexmaci64|mac|bat)' > In checkInstallation>makeBinaryExecutable (line 338) In checkInstallation (line 107) Warning: Failed to make /home/jufer/Apps/Raven/RAVEN/software/diamond/diamond executable: /bin/bash: -c: line 1: syntax error near unexpected token `(' /bin/bash: -c: line 1: `chmod +x "/home/jufer/Apps/Raven/RAVEN/software/diamond/diamond".(mexa64|mexglx|mexmaci64|mac|bat)' > In checkInstallation>makeBinaryExecutable (line 338) In checkInstallation (line 107) Warning: Failed to make /home/jufer/Apps/Raven/RAVEN/software/hmmer/hmmbuild executable: /bin/bash: -c: line 1: syntax error near unexpected token `(' /bin/bash: -c: line 1: `chmod +x "/home/jufer/Apps/Raven/RAVEN/software/hmmer/hmmbuild".(mexa64|mexglx|mexmaci64|mac|bat)' > In checkInstallation>makeBinaryExecutable (line 338) In checkInstallation (line 107) Warning: Failed to make /home/jufer/Apps/Raven/RAVEN/software/hmmer/hmmsearch executable: /bin/bash: -c: line 1: syntax error near unexpected token `(' /bin/bash: -c: line 1: `chmod +x "/home/jufer/Apps/Raven/RAVEN/software/hmmer/hmmsearch".(mexa64|mexglx|mexmaci64|mac|bat)' > In checkInstallation>makeBinaryExecutable (line 338) In checkInstallation (line 107) Warning: Failed to make /home/jufer/Apps/Raven/RAVEN/software/GLPKmex/glpkcc executable: /bin/bash: -c: line 1: syntax error near unexpected token `(' /bin/bash: -c: line 1: `chmod +x "/home/jufer/Apps/Raven/RAVEN/software/GLPKmex/glpkcc".(mexa64|mexglx|mexmaci64|mac|bat)' > In checkInstallation>makeBinaryExecutable (line 338) In checkInstallation (line 107) Warning: Failed to make /home/jufer/Apps/Raven/RAVEN/software/libSBML/TranslateSBML executable: /bin/bash: -c: line 1: syntax error near unexpected token `(' /bin/bash: -c: line 1: `chmod +x "/home/jufer/Apps/Raven/RAVEN/software/libSBML/TranslateSBML".(mexa64|mexglx|mexmaci64|mac|bat)' > In checkInstallation>makeBinaryExecutable (line 338) In checkInstallation (line 107) Warning: Failed to make /home/jufer/Apps/Raven/RAVEN/software/libSBML/OutputSBML executable: /bin/bash: -c: line 1: syntax error near unexpected token `(' /bin/bash: -c: line 1: `chmod +x "/home/jufer/Apps/Raven/RAVEN/software/libSBML/OutputSBML".(mexa64|mexglx|mexmaci64|mac|bat)' > In checkInstallation>makeBinaryExecutable (line 338) In checkInstallation (line 107) Warning: Failed to make /home/jufer/Apps/Raven/RAVEN/software/mafft/mafft-linux64/mafft executable: /bin/bash: -c: line 1: syntax error near unexpected token `(' /bin/bash: -c: line 1: `chmod +x "/home/jufer/Apps/Raven/RAVEN/software/mafft/mafft-linux64/mafft".(mexa64|mexglx|mexmaci64|mac|bat)' > In checkInstallation>makeBinaryExecutable (line 338) In checkInstallation (line 107) Warning: Failed to make /home/jufer/Apps/Raven/RAVEN/software/mafft/mafft-mac/mafft executable: /bin/bash: -c: line 1: syntax error near unexpected token `(' /bin/bash: -c: line 1: `chmod +x "/home/jufer/Apps/Raven/RAVEN/software/mafft/mafft-mac/mafft".(mexa64|mexglx|mexmaci64|mac|bat)' > In checkInstallation>makeBinaryExecutable (line 338) In checkInstallation (line 107) Fail