Question: Can't install 'pqsfinder'
0
gravatar for aabarnes2
5 months ago by
aabarnes20
aabarnes20 wrote:

When attempting to install I get the following error:

In install.packages(pkgs = doing, lib = lib, ...) : installation of package ‘pqsfinder’ had non-zero exit status

this is due to icpc: command line error: option '-openmp' is not supported. Please use the replacement option '-qopenmp'

Any workarounds?

pqsfinder • 204 views
ADD COMMENTlink written 5 months ago by aabarnes20

Could you please show the complete output from running BiocManager::install("pqsfinder") and also your sesssionInfo() - The sessionInfo will also provide your os and R version information.

ADD REPLYlink written 5 months ago by shepherl ♦♦ 1.4k
> BiocManager::install("pqsfinder")
Bioconductor version 3.8 (BiocManager 1.30.4), R 3.5.2 (2018-12-20)
Installing package(s) 'pqsfinder'
trying URL 'https://bioconductor.org/packages/3.8/bioc/src/contrib/pqsfinder_1.10.0.tar.gz'
Content type 'application/x-gzip' length 4249497 bytes (4.1 MB)
==================================================
downloaded 4.1 MB

* installing *source* package ‘pqsfinder’ ...
** libs
icpc -std=gnu++11 -I"/opt/packages/R/3.5.2-mkl/lib64/R/include" -DNDEBUG  -I"/opt/packages/R/3.5.2-mkl/lib64/R/library/Rcpp/include" -I"/opt/packages/R/3.5.2-mkl/lib64/R/library/BH/include" -I/usr/local/include   -fpic  -O3 -ipo -openmp -xHost -c RcppExports.cpp -o RcppExports.o
icpc: command line error: option '-openmp' is not supported. Please use the replacement option '-qopenmp'
make: *** [RcppExports.o] Error 1
ERROR: compilation failed for package ‘pqsfinder’
* removing ‘/home/alexab/R/x86_64-pc-linux-gnu-library/3.5/pqsfinder’

The downloaded source packages are in
    ‘/tmp/RtmpFkntK2/downloaded_packages’
installation path not writeable, unable to update packages: aod, BH,
  BiocParallel, checkmate, clipr, colorspace, curl, data.table, dplyr,
  evaluate, GenomeInfoDb, git2r, Hmisc, htmlTable, later, mgcv, openssl, purrr,
  R6, RcppArmadillo, rlang, Rsamtools, rstudioapi, stringi, stringr, tibble,
  VGAM, xfun, XML
Warning message:
In install.packages(pkgs = doing, lib = lib, repos = repos, ...) :
  installation of package ‘pqsfinder’ had non-zero exit status
ADD REPLYlink written 5 months ago by aabarnes20
> sessionInfo()
R version 3.5.2 (2018-12-20)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: CentOS Linux 7 (Core)

Matrix products: default
BLAS/LAPACK: /opt/intel/compilers_and_libraries_2017.4.196/linux/mkl/lib/intel64_lin/libmkl_intel_lp64.so

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
 [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8    
 [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8   
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

loaded via a namespace (and not attached):
[1] BiocManager_1.30.4 compiler_3.5.2     tools_3.5.2   
ADD REPLYlink written 5 months ago by aabarnes20
1

Thank you - this does seem to be an issue with the pqsfinder package itself - I will reach out to the maintainer.

ADD REPLYlink written 5 months ago by shepherl ♦♦ 1.4k

Hi, pqsfinder does not use openmp. I’m not sure from where the flag comes from, maybe Rcpp? I also thought gcc is the default on linux and no icpc. Do you have custom Makevars for your R environment?

ADD REPLYlink written 5 months ago by jiri.hon0

Just a comment that on Linux-like operating systems we would really like to support as many compilers as 'reasonable', even if most users (and the build system) have gcc or clang.

ADD REPLYlink written 5 months ago by Martin Morgan ♦♦ 23k

No, and have tested multiple environments

ADD REPLYlink written 5 months ago by aabarnes20

What do you mean by "tested multiple environments"? Did you try to use GCC?

ADD REPLYlink written 5 months ago by jiri.hon0
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 220 users visited in the last hour