Dear all,
I am trying to install a list of R packages to be used on a notebook with an R kernel.
I cannot install this package from gtihub:
devtools::install_github( “Danko-Lab/BayesPrism/BayesPrism”)
Among the warning and errors, it seems that the first popping up is ‘Matrix (>= 1.5.0)’ not available, which then seems to generate error in multiple libraries.
My reading on the topic regarding this error is that R has to be updated, but I might be wrong. The package has a lot of dependencies and the error gets triggered at some point.
Would you have any advice on how to approach the problem ? Here is the full output that I am getting when I try to install the packages:
Downloading GitHub repo Danko-Lab/BayesPrism@HEAD
formatR (NA → 1.12 ) [CRAN]
futile.op… (NA → 1.0.1 ) [CRAN]
lambda.r (NA → 1.2.4 ) [CRAN]
snow (NA → 0.4-4 ) [CRAN]
futile.lo… (NA → 1.4.3 ) [CRAN]
RcppHNSW (NA → 0.3.0 ) [CRAN]
BiocNeigh… (NA → 1.16.0 ) [CRAN]
BiocParallel (NA → 1.32.6 ) [CRAN]
beachmat (NA → 2.14.2 ) [CRAN]
rsvd (NA → 1.0.5 ) [CRAN]
ScaledMatrix (NA → 1.6.0 ) [CRAN]
sparseMat… (NA → 1.10.0 ) [CRAN]
locfit (NA → 1.5-9.5 ) [CRAN]
DelayedMa… (NA → 1.20.0 ) [CRAN]
registry (NA → 0.5-1 ) [CRAN]
metapod (NA → 1.6.0 ) [CRAN]
bluster (NA → 1.8.0 ) [CRAN]
BiocSingular (NA → 1.14.0 ) [CRAN]
statmod (NA → 1.4.36 ) [CRAN]
edgeR (NA → 3.40.2 ) [CRAN]
scuttle (NA → 1.8.4 ) [CRAN]
gridBase (NA → 0.4-7 ) [CRAN]
rngtools (NA → 1.5.2 ) [CRAN]
pkgmaker (NA → 0.32.2 ) [CRAN]
scran (NA → 1.26.2 ) [CRAN]
NMF (NA → 0.24.0 ) [CRAN]
snowfall (NA → 1.84-6.1) [CRAN]
Installing 27 packages: formatR, futile.options, lambda.r, snow, futile.logger, RcppHNSW, BiocNeighbors, BiocParallel, beachmat, rsvd, ScaledMatrix, sparseMatrixStats, locfit, DelayedMatrixStats, registry, metapod, bluster, BiocSingular, statmod, edgeR, scuttle, gridBase, rngtools, pkgmaker, scran, NMF, snowfall
Warning message:
“dependency ‘Matrix (>= 1.5.0)’ is not available”
Warning message in i.p(…):
“installation of package ‘DelayedMatrixStats’ had non-zero exit status”
Warning message in i.p(…):
“installation of package ‘scuttle’ had non-zero exit status”
Warning message in i.p(…):
“installation of package ‘scran’ had non-zero exit status”
- checking for file ‘/tmp/Rtmp6tQ3CV/remotes16b72b1d6904/Danko-Lab-BayesPrism-1ad3e82/BayesPrism/DESCRIPTION’ … OK
- preparing ‘BayesPrism’:
- checking DESCRIPTION meta-information … OK
- checking for LF line-endings in source and make files and shell scripts
- checking for empty or unneeded directories
- building ‘BayesPrism_2.0.tar.gz’
Warning message in i.p(…):
“installation of package ‘/tmp/Rtmp6tQ3CV/file16b7302681db/BayesPrism_2.0.tar.gz’ had non-zero exit status”
Thank you very much !
Best,
Alexandre Coudray
PhD student at EPFL