Question: problem installing rtracklayer
0
gravatar for pegah.taklifi
7 weeks ago by
pegah.taklifi0 wrote:

I'm pretty new to Rstudio on ubuntu .so I'm trying to install "rtracklayer" package from BiocManager I used this code:

if (!requireNamespace("BiocManager", quietly = TRUE))
install.packages("BiocManager")

BiocManager::install("rtracklayer")

and I see everything goes well and packages download completely but in the end I get these errors:

ERROR: configuration failed for package ‘RCurl’

removing ‘/home/ubuntu/R/x86_64-pc-linux-gnu-library/4.0/RCurl’
ERROR: dependency ‘RCurl’ is not available for package ‘GenomeInfoDb’
removing ‘/home/ubuntu/R/x86_64-pc-linux-gnu-library/4.0/GenomeInfoDb’
ERROR: dependency ‘GenomeInfoDb’ is not available for package ‘GenomicRanges’
removing ‘/home/ubuntu/R/x86_64-pc-linux-gnu-library/4.0/GenomicRanges’
ERROR: dependencies ‘GenomicRanges’, ‘GenomeInfoDb’ are not available for package ‘SummarizedExperiment’
removing ‘/home/ubuntu/R/x86_64-pc-linux-gnu-library/4.0/SummarizedExperiment’
ERROR: dependencies ‘GenomeInfoDb’, ‘GenomicRanges’, ‘Rhtslib’ are not available for package ‘Rsamtools’
removing ‘/home/ubuntu/R/x86_64-pc-linux-gnu-library/4.0/Rsamtools’
ERROR: dependencies ‘GenomeInfoDb’, ‘GenomicRanges’, ‘SummarizedExperiment’, ‘Rsamtools’ are not available for package ‘GenomicAlignments’
removing ‘/home/ubuntu/R/x86_64-pc-linux-gnu-library/4.0/GenomicAlignments’
ERROR: dependencies ‘GenomicRanges’, ‘XML’, ‘GenomeInfoDb’, ‘RCurl’, ‘Rsamtools’, ‘GenomicAlignments’ are not available for package ‘rtracklayer’
removing ‘/home/ubuntu/R/x86_64-pc-linux-gnu-library/4.0/rtracklayer’
The downloaded source packages are in
‘/tmp/RtmpjzWMQf/downloaded_packages’
Installation path not writeable, unable to update packages: foreign, nlme, spatial, survival

and a bunch of warning messages:

1: In install.packages(...) :
installation of package ‘Rhtslib’ had non-zero exit status
2: In install.packages(...) :
installation of package ‘XML’ had non-zero exit status
3: In install.packages(...) :
installation of package ‘RCurl’ had non-zero exit status
4: In install.packages(...) :
installation of package ‘GenomeInfoDb’ had non-zero exit status
5: In install.packages(...) :
installation of package ‘GenomicRanges’ had non-zero exit status
6: In install.packages(...) :
installation of package ‘SummarizedExperiment’ had non-zero exit status
7: In install.packages(...) :
installation of package ‘Rsamtools’ had non-zero exit status
8: In install.packages(...) :
installation of package ‘GenomicAlignments’ had non-zero exit status
9: In install.packages(...) :
installation of package ‘rtracklayer’ had non-zero exit status

can anyone help me what i need to do??

R software error • 203 views
ADD COMMENTlink modified 7 weeks ago by h.mon31k • written 7 weeks ago by pegah.taklifi0
1

What happens when you try install.packages("RCurl")?

ADD REPLYlink written 7 weeks ago by RamRS30k
1
gravatar for h.mon
7 weeks ago by
h.mon31k
Brazil
h.mon31k wrote:

One alternative is to use the conda package manager to install R and its packages, conda will handle all dependencies needed.

If you really want to troubleshoot why BiocManager::install("rtracklayer") failed, you will need to run (or scroll the terminal up) BiocManager::install("RCurl"), then read the error message carefully to identify why RCurl install is failing, fix RCurl install, then try to install rtracklayer again.

I suspect you are missing curl headers, you will have to install them, and you will need administrative permissions to do so. It will be something like (see here):

apt-get install libcurl4-gnutls-dev
ADD COMMENTlink written 7 weeks ago by h.mon31k
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