Question

Can't install 'pqsfinder'

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aabarnes2 • 0

@aabarnes2-20026

Last seen 5.2 years ago

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 • 1.2k views

ADD COMMENT • link 5.2 years ago aabarnes2 • 0

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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 REPLY • link 5.2 years ago shepherl 3.9k

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> 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 REPLY • link updated 5.2 years ago by James W. MacDonald 65k • written 5.2 years ago by aabarnes2 • 0

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> 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 REPLY • link updated 5.2 years ago by James W. MacDonald 65k • written 5.2 years ago by aabarnes2 • 0

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

ADD REPLY • link 5.2 years ago shepherl 3.9k

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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 REPLY • link 5.2 years ago jiri.hon ▴ 10

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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 REPLY • link 5.2 years ago Martin Morgan 25k

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No, and have tested multiple environments

ADD REPLY • link 5.2 years ago aabarnes2 • 0

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

ADD REPLY • link 5.2 years ago jiri.hon ▴ 10