I'm trying to install the bioconductor package "Rqc" in a project within my workspace (https://rstudio.cloud/project/348360). It depends on VariantAnnotation, biovizBase, and ensembledb. I use the command "BiocManager::install("Rqc")" to try to do this. (I've also tried to install both the package and the prereqs with devtools with no luck). Can you please help?
BiocManager::install downloads the package and prerequisites normally, tries to compile them, and starts throwing errors here:
installing to /home/rstudio-user/R/x86_64-pc-linux-gnu-library/3.6/00LOCK-VariantAnnotation/00new/VariantAnnotation/libs
** R
** inst
** byte-compile and prepare package for lazy loading
Killed
ERROR: lazy loading failed for package āVariantAnnotationā
* removing ā/home/rstudio-user/R/x86_64-pc-linux-gnu-library/3.6/VariantAnnotationā
* installing *source* package āensembldbā ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
Killed
ERROR: lazy loading failed for package āensembldbā
* removing ā/home/rstudio-user/R/x86_64-pc-linux-gnu-library/3.6/ensembldbā
ERROR: dependencies āVariantAnnotationā, āensembldbā are not available for package ābiovizBaseā
* removing ā/home/rstudio-user/R/x86_64-pc-linux-gnu-library/3.6/biovizBaseā
ERROR: dependency āVariantAnnotationā is not available for package āGenomicFilesā
* removing ā/home/rstudio-user/R/x86_64-pc-linux-gnu-library/3.6/GenomicFilesā
ERROR: dependencies ābiovizBaseā, āGenomicFilesā are not available for package āRqcā
* removing ā/home/rstudio-user/R/x86_64-pc-linux-gnu-library/3.6/Rqcā
The downloaded source packages are in
ā/tmp/RtmpMtQLHG/downloaded_packagesā
installation path not writeable, unable to update packages: cluster,
nlme
Update old packages: 'AnnotationDbi', 'Biobase', 'BiocGenerics',
'BiocParallel', 'BiocStyle', 'biomaRt', 'Biostrings', 'bookdown',
'BSgenome', 'DelayedArray', 'GenomeInfoDb', 'GenomeInfoDbData',
'GenomicAlignments', 'GenomicFeatures', 'GenomicRanges', 'IRanges',
'pillar', 'ProtGenerics', 'rtracklayer', 'S4Vectors', 'ShortRead',
'SummarizedExperiment', 'XVector', 'zlibbioc'
Update all/some/none? [a/s/n]:
n
Warning messages:
1: In install.packages(pkgs = doing, lib = lib, repos = repos, ...) :
installation of package āVariantAnnotationā had non-zero exit status
2: In install.packages(pkgs = doing, lib = lib, repos = repos, ...) :
installation of package āensembldbā had non-zero exit status
3: In install.packages(pkgs = doing, lib = lib, repos = repos, ...) :
installation of package ābiovizBaseā had non-zero exit status
4: In install.packages(pkgs = doing, lib = lib, repos = repos, ...) :
installation of package āGenomicFilesā had non-zero exit status
5: In install.packages(pkgs = doing, lib = lib, repos = repos, ...) :
installation of package āRqcā had non-zero exit status