Hi, My workstation is running Debian 10 with the default version 3.5.1 of R. I need to use the Bioconductor package "GoSeq" to perform functional enrichment tests as described in “Running GOSeq” pipeline (https://github.com/trinityrnaseq/trinityrnaseq/wiki/Running-GOSeq). I got a trouble with it. The package "GoSeq" exists only for “R version "3.6" in Bioconductor Release 3.10 which works with R version 3.6.0. After updating the R to the latest version 3.6.2 (https://community.hetzner.com/tutorials/how-to-install-r-on-debian-10) Bioconductor can’t install GoSeq with errors (below). Should I downgrade R to 3.6.0 version? If yes, how to do it in Debian?

sudo R if (!requireNamespace("BiocManager", quietly = TRUE)) install.packages("BiocManager") BiocManager::install("goseq") install.packages('goseq')

ERROR: dependencies ‘GenomeInfoDb’, ‘GenomicRanges’, ‘SummarizedExperiment’, ‘Rsamtools’ are not available for package ‘GenomicAlignments’ * removing ‘/usr/local/lib/R/site-library/GenomicAlignments’ ERROR: dependencies ‘RSQLite’, ‘curl’, ‘httr’ are not available for package ‘BiocFileCache’ * removing ‘/usr/local/lib/R/site-library/BiocFileCache’ ERROR: dependencies ‘GenomicRanges’, ‘GenomeInfoDb’, ‘RCurl’, ‘Rsamtools’, ‘GenomicAlignments’ are not available for package ‘rtracklayer’ * removing ‘/usr/local/lib/R/site-library/rtracklayer’ ERROR: dependencies ‘AnnotationDbi’, ‘httr’, ‘openssl’, ‘BiocFileCache’ are not available for package ‘biomaRt’ * removing ‘/usr/local/lib/R/site-library/biomaRt’ ERROR: dependencies ‘GenomeInfoDb’, ‘GenomicRanges’, ‘AnnotationDbi’, ‘RSQLite’, ‘RCurl’, ‘rtracklayer’, ‘biomaRt’ are not available for package ‘GenomicFeatures’ * removing ‘/usr/local/lib/R/site-library/GenomicFeatures’ ERROR: dependencies ‘rtracklayer’, ‘GenomicFeatures’ are not available for package ‘geneLenDataBase’ * removing ‘/usr/local/lib/R/site-library/geneLenDataBase’ ERROR: dependencies ‘geneLenDataBase’, ‘AnnotationDbi’, ‘GO.db’ are not available for package ‘goseq’ * removing ‘/usr/local/lib/R/site-library/goseq’ The downloaded source packages are in ‘/tmp/RtmpUkhEuR/downloaded_packages’ There were 20 warnings (use warnings() to see them)

sessionInfo() R version 3.6.2 (2019-12-12) Platform: x8664-pc-linux-gnu (64-bit) Running under: Debian GNU/Linux 10 (buster) Matrix products: default BLAS: /usr/lib/x8664-linux-gnu/blas/libblas.so.3.8.0 LAPACK: /usr/lib/x8664-linux-gnu/lapack/liblapack.so.3.8.0 locale: [1] LCCTYPE=enUS.UTF-8 LCNUMERIC=C
[3] LCTIME=ruRU.UTF-8 LCCOLLATE=enUS.UTF-8
[5] LCMONETARY=ruRU.UTF-8 LCMESSAGES=enUS.UTF-8
[7] LCPAPER=ruRU.UTF-8 LCNAME=C
[9] LCADDRESS=C LCTELEPHONE=C
[11] LCMEASUREMENT=ruRU.UTF-8 LCIDENTIFICATION=C
attached base packages: [1] stats graphics grDevices utils datasets methods base
loaded via a namespace (and not attached): [1] BiocManager1.30.10 compiler3.6.2 tools_3.6.2

Thank you for your reply, Martin. After installing libcurl4-openssl-dev with Sinaptic PM the story became a little better, but as a result, it still failed. The selected error report is below.

    > if (!requireNamespace("BiocManager", quietly = TRUE))
    +     install.packages("BiocManager")
    > 
    > BiocManager::install("goseq")
    Bioconductor version 3.10 (BiocManager 1.30.10), R 3.6.2 (2019-12-12)
    Installing package(s) 'goseq'
    also installing the dependencies ‘curl’, ‘Rhtslib’, ‘SummarizedExperiment’, ‘httr’, ‘openssl’, ‘BiocFileCache’, ‘GenomicRanges’, ‘GenomeInfoDb’, ‘RCurl’, ‘Rsamtools’, ‘GenomicAlignments’, ‘biomaRt’, ‘blob’, ‘rtracklayer’, ‘GenomicFeatures’, ‘RSQLite’, ‘geneLenDataBase’, ‘AnnotationDbi’, ‘GO.db’

 ...
 Error: .onLoad failed in loadNamespace() for 'vctrs', details:
  call: loadNamespace(name)
  error: there is no package called ‘backports’
Execution halted
ERROR: lazy loading failed for package ‘blob’
* removing ‘/usr/local/lib/R/site-library/blob’
ERROR: dependency ‘openssl’ is not available for package ‘httr’
* removing ‘/usr/local/lib/R/site-library/httr’
...
ERROR: dependency ‘blob’ is not available for package ‘RSQLite’
* removing ‘/usr/local/lib/R/site-library/RSQLite’
ERROR: dependencies ‘RSQLite’, ‘httr’ are not available for package ‘BiocFileCache’
* removing ‘/usr/local/lib/R/site-library/BiocFileCache’
...
ERROR: dependency ‘RSQLite’ is not available for package ‘AnnotationDbi’
* removing ‘/usr/local/lib/R/site-library/AnnotationDbi’
...
ERROR: dependencies ‘AnnotationDbi’, ‘httr’, ‘openssl’, ‘BiocFileCache’ are not available for package ‘biomaRt’
* removing ‘/usr/local/lib/R/site-library/biomaRt’
ERROR: dependency ‘AnnotationDbi’ is not available for package ‘GO.db’
* removing ‘/usr/local/lib/R/site-library/GO.db’
...
ERROR: dependencies ‘AnnotationDbi’, ‘RSQLite’, ‘biomaRt’ are not available for package ‘GenomicFeatures’
* removing ‘/usr/local/lib/R/site-library/GenomicFeatures’
ERROR: dependency ‘GenomicFeatures’ is not available for package ‘geneLenDataBase’
* removing ‘/usr/local/lib/R/site-library/geneLenDataBase’
ERROR: dependencies ‘geneLenDataBase’, ‘AnnotationDbi’, ‘GO.db’ are not available for package ‘goseq’
* removing ‘/usr/local/lib/R/site-library/goseq’
...
The downloaded source packages are in
    ‘/tmp/RtmpbnqmVF/downloaded_packages’
There were 11 warnings (use warnings() to see them)

> warnings()
Warning messages:
1: In install.packages(...) :
  installation of package ‘openssl’ had non-zero exit status
2: In install.packages(...) :
  installation of package ‘blob’ had non-zero exit status
3: In install.packages(...) :
  installation of package ‘httr’ had non-zero exit status
4: In install.packages(...) :
  installation of package ‘RSQLite’ had non-zero exit status
5: In install.packages(...) :
  installation of package ‘BiocFileCache’ had non-zero exit status
6: In install.packages(...) :
  installation of package ‘AnnotationDbi’ had non-zero exit status
7: In install.packages(...) :
  installation of package ‘biomaRt’ had non-zero exit status
8: In install.packages(...) :
  installation of package ‘GO.db’ had non-zero exit status
9: In install.packages(...) :
  installation of package ‘GenomicFeatures’ had non-zero exit status
10: In install.packages(...) :
  installation of package ‘geneLenDataBase’ had non-zero exit status
11: In install.packages(...) :
  installation of package ‘goseq’ had non-zero exit status

Review the error report and troubleshoot the first package that fails to install.

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