install Bioconductor package and its dependencies

Question

[alessandrotestori7]

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!

[WouterDeCoster]

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

[alessandrotestori7]

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.

[Bastien Hervé]

If you have "devtools" package in your dependencies, there are some issues linked to libcurl and "devtools"

https://stackoverflow.com/questions/20923209/problems-installing-the-devtools-package

https://stackoverflow.com/questions/44228055/r-rstudio-install-devtools-fails

Maybe try :

sudo apt-get install libcurl4-openssl-dev libssl-dev

[alessandrotestori7]

Thanks a lot! This solved my problem!

[bioinfo456]

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.

[WouterDeCoster]

Have you tried installation using bioconda?

[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.

[Devon Ryan]

conda install bioconductor-motifbreakr

[bioinfo456]

Still not working in R.

[Devon Ryan]

Define "not working".

[bioinfo456]

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’

[Devon Ryan]

Stop trying to compile things, use conda for EVERYTHING.

[bioinfo456]

I need it to work in R studio.

[WouterDeCoster]

Then use conda.

[bioinfo456]

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

[Devon Ryan]

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

[bioinfo456]

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.

[WouterDeCoster]

Which command did you use to get that?

[bioinfo456]

On running the following on R studio :

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

Answer 1

[h.mon]

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"))

Answer 2

[karyowgene]

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