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barakbri / dacomp

Non parametric differential abundance tests for microbiome data
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Error in package install on Linux #4

Open Ivy-ops opened 4 years ago

Ivy-ops commented 4 years ago

Hi developer, Thank for creating this package. I have successfully installed it on my mac. But I can not install it on Linux cluster. Would you mind to give me some suggestions? Here is the error message:

** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (vegan)
* installing *source* package ‘HHG’ ...
** package ‘HHG’ successfully unpacked and MD5 sums checked
checking whether the C++ compiler works... no
configure: error: in `/tmp/Rtmpfvw0Bp/R.INSTALL188a57b2d2c2d/HHG':
configure: error: C++ compiler cannot create executables
See `config.log' for more details
ERROR: configuration failed for package ‘HHG’
* removing ‘/R/HHG’
Error: Failed to install 'dacomp' from GitHub:
(converted from warning) installation of package ‘HHG’ had non-zero exit status
barakbri commented 4 years ago

Hi, The installation fails due to HHG failing to install from source (compiling C/C++ files).

  1. HHG happens to be another package maintained by me. Installation for HHG failed since it could not create executables. If you can provide the config.log file (as the error log suggests), we could perhaps look into it.

  2. HHG is installed from CRAN, and does not require compilation if your R is up-to-date. What version of R and Linux distro are you using? I would also try and install HHG manually from R, and see what error code you are receiving.

  3. If you cannot update R, or get permissions to compile software on the cluster, please let me know, and I will update DACOMP not to require HHG (change it to suggest perhaps?) (it is not mandatory for all package functions). Thanks, Barak

Ivy-ops commented 4 years ago

Hi @barakbri , May I please know where can I find the config.log file on linux? Thanks!!

barakbri commented 4 years ago

Hi @Ivy-ops ,

It seems getting the config.log is system-specific, as it is erased after compilation (even if failed).

I pushed a new version to the repository, 1.23, which takes the HHG package as a 'suggest' rather than dependency. The HHG package is used only in the "reference validation" function, which is not part of the mandatory pipeline for data analysis.

Can you let me know if now installation is OK? Thanks, Barak

Ivy-ops commented 4 years ago

@barakbri, Perfect! It can be installed successfully! I appreciate your help!