Question: install Bioconductor package and its dependencies
1
gravatar for alessandrotestori7
9 months ago by
alessandrotestori7330 wrote:

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 • 666 views
ADD COMMENTlink modified 9 months ago by h.mon22k • written 9 months ago by alessandrotestori7330

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

ADD REPLYlink written 9 months ago by WouterDeCoster35k

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.

ADD REPLYlink modified 9 months ago by WouterDeCoster35k • written 9 months ago by alessandrotestori7330
1

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
ADD REPLYlink modified 9 months ago • written 9 months ago by Bastien Hervé2.8k

Thanks a lot! This solved my problem!

ADD REPLYlink written 9 months ago by alessandrotestori7330

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.

ADD REPLYlink written 6 days ago by Uday Rangaswamy90

Have you tried installation using bioconda?

ADD REPLYlink written 6 days ago by WouterDeCoster35k

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.

ADD REPLYlink modified 6 days ago • written 6 days ago by Uday Rangaswamy90
2

conda install bioconductor-motifbreakr

ADD REPLYlink written 6 days ago by Devon Ryan87k

Still not working in R.

ADD REPLYlink written 6 days ago by Uday Rangaswamy90

Define "not working".

ADD REPLYlink written 6 days ago by Devon Ryan87k
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’
ADD REPLYlink written 6 days ago by Uday Rangaswamy90
1

Stop trying to compile things, use conda for EVERYTHING.

ADD REPLYlink written 6 days ago by Devon Ryan87k

I need it to work in R studio.

ADD REPLYlink written 6 days ago by Uday Rangaswamy90

Then use conda.

ADD REPLYlink written 6 days ago by WouterDeCoster35k

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

ADD REPLYlink written 6 days ago by Uday Rangaswamy90
1

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

ADD REPLYlink written 6 days ago by Devon Ryan87k

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.

ADD REPLYlink modified 5 days ago • written 5 days ago by Uday Rangaswamy90

Which command did you use to get that?

ADD REPLYlink written 6 days ago by WouterDeCoster35k

On running the following on R studio :

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")
BiocManager::install("MotIV", version = "3.8")
ADD REPLYlink written 6 days ago by Uday Rangaswamy90
1
gravatar for h.mon
9 months ago by
h.mon22k
Brazil
h.mon22k wrote:

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"))
ADD COMMENTlink written 9 months ago by h.mon22k
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 2.3.0
Traffic: 1213 users visited in the last hour