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install Bioconductor package and its dependencies

Hi! I am trying to install package "motifbreakR" from Bioconductor, but it seems it has too many dependencies that are not available on my computer. Is there a way to install a Bioconductor package and all its dependencies at once? Thanks!

bioconductor r
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updated by karyowgene • karyowgene • written by alessandrotestori7 alessandrotestori7

How are you installing this package? Dependencies are installed automatically, normally.

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written by WouterDeCoster WouterDeCoster

I am installing this package from R:

biocLite("motifbreakR")

It seems there is a problem with "libcurl": "Package libcurl was not found in the pkg-config search path. Perhaps you should add the directory containing `libcurl.pc' to the PKG_CONFIG_PATH environment variable". Then configurations of all other packages fail.

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updated by WouterDeCoster WouterDeCoster • written by alessandrotestori7 alessandrotestori7

On trying to install motifbreakerR, I get the following errors and warnings :

*** Could not run GSL test program, checking why...
*** The test program failed to compile or link. See the file config.log for the
*** exact error that occured. This usually means GSL was incorrectly installed
*** or that you have moved GSL since it was installed. In the latter case, you
*** may want to edit the gsl-config script: /usr/bin/gsl-config
configure: error: Cannot find Gnu Scientific Library >=1.6
ERROR: configuration failed for package ‘MotIV’
* removing ‘/home/uday/R/x86_64-pc-linux-gnu-library/3.5/MotIV’
ERROR: dependency ‘MotIV’ is not available for package ‘motifStack’
* removing ‘/home/uday/R/x86_64-pc-linux-gnu-library/3.5/motifStack’
ERROR: dependency ‘motifStack’ is not available for package ‘motifbreakR’
* removing ‘/home/uday/R/x86_64-pc-linux-gnu-library/3.5/motifbreakR’

The downloaded source packages are in
    ‘/tmp/RtmpMtZoRJ/downloaded_packages’
Warning messages:
1: In install.packages(pkgs = doing, lib = lib, repos = repos, ...) :
  installation of package ‘MotIV’ had non-zero exit status
2: In install.packages(pkgs = doing, lib = lib, repos = repos, ...) :
  installation of package ‘motifStack’ had non-zero exit status
3: In install.packages(pkgs = doing, lib = lib, repos = repos, ...) :
  installation of package ‘motifbreakR’ had non-zero exit status

On installing gsl package, it exits as following : 

ERROR: configuration failed for package ‘gsl’
* removing ‘/home/uday/R/x86_64-pc-linux-gnu-library/3.5/gsl’
* restoring previous ‘/home/uday/R/x86_64-pc-linux-gnu-library/3.5/gsl’
Warning in install.packages :
  installation of package ‘gsl’ had non-zero exit status

Please help.

• 0 views • link
written by bioinfo456 bioinfo456

On doing so, there was slight progress and then it stopped at :

RandPSSMGen.cpp:32:10: fatal error: gsl/gsl_histogram.h: No such file or directory
 #include <gsl/gsl_histogram.h>
          ^~~~~~~~~~~~~~~~~~~~~
compilation terminated.
make: *** [/home/uday/anaconda3/envs/rstudio/lib/R/etc/Makeconf:167: RandPSSMGen.o] Error 1
ERROR: compilation failed for package ‘MotIV’
* removing ‘/home/uday/R/x86_64-pc-linux-gnu-library/3.5/MotIV’
ERROR: dependency ‘MotIV’ is not available for package ‘motifStack’
* removing ‘/home/uday/R/x86_64-pc-linux-gnu-library/3.5/motifStack’
ERROR: dependency ‘motifStack’ is not available for package ‘motifbreakR’
* removing ‘/home/uday/R/x86_64-pc-linux-gnu-library/3.5/motifbreakR’

This is also the case when I try to install the MotIV package explicitly.

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written by bioinfo456 bioinfo456

conda install bioconductor-motifbreakr

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written by Devon Ryan Devon Ryan

Still not working in R.

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written by bioinfo456 bioinfo456

Define "not working".

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written by Devon Ryan Devon Ryan 
RandPSSMGen.cpp:32:10: fatal error: gsl/gsl_histogram.h: No such file or directory
 #include <gsl/gsl_histogram.h>
          ^~~~~~~~~~~~~~~~~~~~~
compilation terminated.
make: *** [/home/uday/anaconda3/envs/rstudio/lib/R/etc/Makeconf:167: RandPSSMGen.o] Error 1
ERROR: compilation failed for package ‘MotIV’
* removing ‘/home/uday/R/x86_64-pc-linux-gnu-library/3.5/MotIV’
• 0 views • link
written by bioinfo456 bioinfo456

Which command did you use to get that?

• 0 views • link
written by WouterDeCoster WouterDeCoster

On running the following on R studio : 

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")
BiocManager::install("MotIV", version = "3.8")
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written by bioinfo456 bioinfo456

Stop trying to compile things, use conda for EVERYTHING.

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written by Devon Ryan Devon Ryan

I need it to work in R studio.

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written by bioinfo456 bioinfo456

You mean to say install r and r studio using conda commands and then trying the same?

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written by bioinfo456 bioinfo456

You can point rstudio to any R you want, so point it to the one from conda.

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written by Devon Ryan Devon Ryan

Done! Like you said, few of the dependencies such as rtracklayer, libiconv and gsl belonged to different versions or not present at all, for which I had to (re)install using conda and start a new R instance at the end of each installation, to check if it's properly installed or not. Thanks for your time.

• 0 views • link
written by bioinfo456 bioinfo456

2 answers

Maybe there is... for example, the github page has these instructions:

Getting prerequisite packages from Bioconductor

source("http://bioconductor.org/biocLite.R")
biocLite(c("BiocParallel", "motifStack", "BSgenome", "BiocGenerics",
           "Biostrings", "GenomeInfoDb", "GenomicRanges", "Gviz", "S4Vectors",
           "rtracklayer", "IRanges", "MotifDb", "BSgenome.Hsapiens.UCSC.hg19",
           "SNPlocs.Hsapiens.dbSNP.20120608", "SNPlocs.Hsapiens.dbSNP142.GRCh37",
           "VariantAnnotation", "matrixStats", "BiocStyle"))
install.packages(c("TFMPvalue", "knitr", "rmarkdown"))
• 1 views • link
written by h.mon h.mon

Here is how it works for me:

conda create -n your_env
conda activate your_env
conda config --add channels bioconda
conda install bioconductor-motifbreakr
• 0 views • link
written by karyowgene • karyowgene

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