Installation broken

[visze]

The way how it is described on the README does not work. When running

install_github("kircherlab/BCalm")

I get the error:

ERROR: dependencies ‘BiocGenerics’, ‘SummarizedExperiment’, ‘limma’, ‘mpra’, ‘S4Vectors’, ‘GenomeInfoDb’, ‘IRanges’, ‘GenomicRanges’, ‘Biobase’, ‘DelayedArray’ are not available for package ‘BCalm’
* removing ‘/data/cephfs-1/scratch/groups/kircher/users/schubacm_c/tmp/RtmphWrrzx/Rinst9089d42e89346/BCalm’
      -----------------------------------
ERROR: package installation failed
STDOUT:
* checking for file ‘/data/cephfs-1/scratch/groups/kircher/users/schubacm_c/tmp/Rtmp67rGxf/remotes8594a699c940d/kircherlab-BCalm-74ee9dc/DESCRIPTION’ ... OK
* preparing ‘BCalm’:
* checking DESCRIPTION meta-information ... OK
* installing the package to process help pages
      -----------------------------------
ERROR: dependencies ‘BiocGenerics’, ‘SummarizedExperiment’, ‘limma’, ‘mpra’, ‘S4Vectors’, ‘GenomeInfoDb’, ‘IRanges’, ‘GenomicRanges’, ‘Biobase’, ‘DelayedArray’ are not available for package ‘BCalm’
* removing ‘/data/cephfs-1/scratch/groups/kircher/users/schubacm_c/tmp/RtmphWrrzx/Rinst9089d42e89346/BCalm’
      -----------------------------------
ERROR: package installation failed
STDERR:

Error: Failed to install 'BCalm' from GitHub:
  Failed to `R CMD build` package, try `build = FALSE`.
In addition: Warning message:
packages ‘DelayedArray’, ‘Biobase’, ‘GenomicRanges’, ‘IRanges’, ‘GenomeInfoDb’, ‘S4Vectors’, ‘mpra’, ‘limma’, ‘SummarizedExperiment’, ‘BiocGenerics’ are not available for this version of R

Versions of these packages for your version of R might be available elsewhere,
see the ideas at
https://cran.r-project.org/doc/manuals/r-patched/R-admin.html#Installing-packages

I tried several other ways (getting all dependencies from Bioconda, using Bioconductor, etc.). Was not successful at all.

[visze]

There were two issues on my side:

1. Packages are downloaded via curl. My file .curlrc in the work folder contained a wrong path to the certificates, so downloads were always failing.

2. Thanks to @pi-zz-a, I solved the installation via Bioconda. Here, the problem is the package bioconductor-genomeinfodbdata.

   You have to run conda install -c bioconda/label/gcc7 to get it working. In short:

   conda install -c bioconda/label/gcc7 -c conda-forge bioconductor-mpra r-devtools r-tidyr r-ggplot2 r-argparse

   (r-argparse was just in my case because my script needs it)

3. I still am not able to install BCalm as it is described in the README.

[visze]

@pi-zz-a See PR #11 for an improved documentation (alternative dependency installation way)