Installation Error - R/Conda

[desmodus1984]

Hi,

I tried installing methylkit in R but I got an error:
Error in install_github("al2na/methylKit", build_vignettes = FALSE, repos = BiocManager::repositories(), :
could not find function "install_github"

Then, I found that it is also available in conda, and I got an error:
conda install -c bioconda bioconductor-methylkit
Collecting package metadata (current_repodata.json): done
Solving environment: failed with initial frozen solve. Retrying with flexible solve.
Solving environment: failed with repodata from current_repodata.json, will retry with next repodata source.
Collecting package metadata (repodata.json): done
Solving environment: failed with initial frozen solve. Retrying with flexible solve.
Solving environment: \
Found conflicts! Looking for incompatible packages.
This can take several minutes. Press CTRL-C to abort.
failed
UnsatisfiableError: The following specifications were found to be incompatible with your system:

• feature:/linux-64::__glibc==2.17=0
• bioconductor-methylkit -> libgcc-ng[version='>=10.3.0'] -> __glibc[version='>=2.17']
  Your installed version is: 2.17

Could you help me tell what can I do to install it?
I work in a computer cluster with Linux installed.

Thanks;

---

Update:
I tried installing it again. I managed to install R in Linux, and this time I got different error:
hfile_libcurl.c:47:10: fatal error: curl/curl.h: No such file or directory
47 | #include <curl/curl.h>
| ^~~~~~~~~~~~~
compilation terminated.
make[1]: *** [Makefile.Rhtslib:135: hfile_libcurl.o] Error 1
make[1]: Leaving directory '/tmp/RtmpQQkXm3/R.INSTALL32d77c12749967/Rhtslib/src/htslib-1.15.1'
make: *** [Makevars.common:22: htslib] Error 2
ERROR: compilation failed for package ‘Rhtslib’

• removing ‘/home/veggers/R/x86_64-pc-linux-gnu-library/4.3/Rhtslib’
  ERROR: dependencies ‘XML’, ‘RCurl’ are not available for package ‘restfulr’
• removing ‘/home/veggers/R/x86_64-pc-linux-gnu-library/4.3/restfulr’
  ERROR: dependency ‘RCurl’ is not available for package ‘GenomeInfoDb’
• removing ‘/home/veggers/R/x86_64-pc-linux-gnu-library/4.3/GenomeInfoDb’
  ERROR: dependency ‘GenomeInfoDb’ is not available for package ‘Biostrings’
• removing ‘/home/veggers/R/x86_64-pc-linux-gnu-library/4.3/Biostrings’
  ERROR: dependency ‘GenomeInfoDb’ is not available for package ‘GenomicRanges’
• removing ‘/home/veggers/R/x86_64-pc-linux-gnu-library/4.3/GenomicRanges’
  ERROR: dependencies ‘GenomicRanges’, ‘GenomeInfoDb’ are not available for package ‘SummarizedExperiment’
• removing ‘/home/veggers/R/x86_64-pc-linux-gnu-library/4.3/SummarizedExperiment’
  ERROR: dependencies ‘GenomeInfoDb’, ‘GenomicRanges’, ‘Biostrings’, ‘Rhtslib’ are not available for package ‘Rsamtools’
• removing ‘/home/veggers/R/x86_64-pc-linux-gnu-library/4.3/Rsamtools’
  ERROR: dependency ‘GenomicRanges’ is not available for package ‘fastseg’
• removing ‘/home/veggers/R/x86_64-pc-linux-gnu-library/4.3/fastseg’
  ERROR: dependencies ‘GenomeInfoDb’, ‘GenomicRanges’, ‘SummarizedExperiment’, ‘Biostrings’, ‘Rsamtools’ are not available for package ‘GenomicAlignments’
• removing ‘/home/veggers/R/x86_64-pc-linux-gnu-library/4.3/GenomicAlignments’
  ERROR: dependencies ‘GenomicRanges’, ‘XML’, ‘GenomeInfoDb’, ‘Biostrings’, ‘RCurl’, ‘Rsamtools’, ‘GenomicAlignments’, ‘restfulr’ are not available for package ‘rtracklayer’
• removing ‘/home/veggers/R/x86_64-pc-linux-gnu-library/4.3/rtracklayer’
  ERROR: dependencies ‘GenomicRanges’, ‘GenomeInfoDb’, ‘Rsamtools’, ‘fastseg’, ‘rtracklayer’, ‘Rhtslib’ are not available for package ‘methylKit’
• removing ‘/home/veggers/R/x86_64-pc-linux-gnu-library/4.3/methylKit’
  The downloaded source packages are in
  ‘/tmp/RtmpJrWfoM/downloaded_packages’
  Installation paths not writeable, unable to update packages
  path: /usr/lib/R/library
  packages:
  boot, foreign, Matrix, nlme, spatial, survival
  There were 13 warnings (use warnings() to see them)

I followed the instructions as stated in the website.

Thanks;

[alexg9010]

Hi @desmodus1984,

The recommended way to install methylKit from within R would be via Bioconductor:

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

If you are installing methylKit via Conda and are facing conflicts, sometimes it helps to install into a fresh environment.

---

Concerning your update, it seems like you are missing curl headers to build rhtslib and a common solution seems to be installing libcurl-dev. This may require root privileges, so could be difficult to achieve on compute clusters.

Best
Alex