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I am trying to install DESeq2. It seems to install ok, but crashes out when I try to load it with "library(DESeq2)" command. Here are my commands and sessionInfo():
> BiocManager::install("DESeq2")
Bioconductor version 3.10 (BiocManager 1.30.10), R 3.6.2 (2019-12-12)
Installing package(s) 'DESeq2'
trying URL 'https://bioconductor.org/packages/3.10/bioc/bin/macosx/el-capitan/contrib/3.6/DESeq2_1.26.0.tgz'
Content type 'application/x-gzip' length 4052218 bytes (3.9 MB)
==================================================
downloaded 3.9 MB
The downloaded binary packages are in
/var/folders/gh/2d3ryrbn071_thmpcb_86w_w0000gn/T//RtmpwyYBDn/downloaded_packages
> library(DESeq2)
Loading required package: S4Vectors
Loading required package: stats4
Loading required package: BiocGenerics
Loading required package: parallel
Attaching package: ‘BiocGenerics’
The following objects are masked from ‘package:parallel’:
clusterApply, clusterApplyLB, clusterCall, clusterEvalQ, clusterExport, clusterMap, parApply,
parCapply, parLapply, parLapplyLB, parRapply, parSapply, parSapplyLB
The following objects are masked from ‘package:stats’:
IQR, mad, sd, var, xtabs
The following objects are masked from ‘package:base’:
anyDuplicated, append, as.data.frame, basename, cbind, colnames, dirname, do.call, duplicated,
eval, evalq, Filter, Find, get, grep, grepl, intersect, is.unsorted, lapply, Map, mapply,
match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, Position, rank, rbind, Reduce,
rownames, sapply, setdiff, sort, table, tapply, union, unique, unsplit, which, which.max,
which.min
Attaching package: ‘S4Vectors’
The following object is masked from ‘package:base’:
expand.grid
Loading required package: IRanges
Loading required package: GenomicRanges
Loading required package: GenomeInfoDb
Error: package or namespace load failed for ‘GenomeInfoDb’ in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]):
there is no package called ‘GenomeInfoDbData’
Error: package ‘GenomeInfoDb’ could not be loaded
*> BiocManager::install("GenomeInfoDb")
Bioconductor version 3.10 (BiocManager 1.30.10), R 3.6.2 (2019-12-12)
Installing package(s) 'GenomeInfoDb'
also installing the dependency ‘GenomeInfoDbData’
trying URL 'https://bioconductor.org/packages/3.10/bioc/bin/macosx/el-capitan/contrib/3.6/GenomeInfoDb_1.22.0.tgz'
Content type 'application/x-gzip' length 3794448 bytes (3.6 MB)
==================================================
downloaded 3.6 MB
The downloaded binary packages are in
/var/folders/gh/2d3ryrbn071_thmpcb_86w_w0000gn/T//RtmpwyYBDn/downloaded_packages
installing the source package ‘GenomeInfoDbData’
trying URL 'https://bioconductor.org/packages/3.10/data/annotation/src/contrib/GenomeInfoDbData_1.2.2.tar.gz'
Content type 'application/x-gzip' length 10194482 bytes (9.7 MB)
==================================================
downloaded 9.7 MB
Error in library(BiocInstaller) :
there is no package called ‘BiocInstaller’
Execution halted
The downloaded source packages are in
‘/private/var/folders/gh/2d3ryrbn071_thmpcb_86w_w0000gn/T/RtmpwyYBDn/downloaded_packages’
Warning message:
In install.packages(...) :
installation of package ‘GenomeInfoDbData’ had non-zero exit status
> BiocManager::install("BiocInstaller")
Bioconductor version 3.10 (BiocManager 1.30.10), R 3.6.2 (2019-12-12)
Installing package(s) 'BiocInstaller'
Warning message:
package ‘BiocInstaller’ is not available (for R version 3.6.2)*
> sessionInfo()
R version 3.6.2 (2019-12-12)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: macOS High Sierra 10.13.6
Matrix products: default
BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libRlapack.dylib
locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
attached base packages:
[1] parallel stats4 stats graphics grDevices utils datasets methods base
other attached packages:
[1] IRanges_2.20.1 S4Vectors_0.24.1 BiocGenerics_0.32.0
loaded via a namespace (and not attached):
[1] BiocManager_1.30.10 compiler_3.6.2 tools_3.6.2 RCurl_1.95-4.12 bitops_1.0-6
Nope, didn't work (I have edited the main post, i.e. added attempt to install 'GenomeInfoDb')
The mystery is where the need to install 'BiocInstaller' comes from. Make sure that you are using a 'vanilla' version of R (no .Rprofile loaded, e.g., by using a terminal and launching
R --vanilla). TryBiocManager::install("GenomeInfoDbData"). Check alsoBiocManager::valid(). If that fails, I suspect that you have multiple installations of GenomeInfoDbData (and perhaps other packages); you could look at.libPaths()andinstalled.packages()to find out, e.g.,and then remove all copies of duplicated packages (some are perhaps installed by an 'administrator'; the right think to do, on a personal work station, is NOT to install packages as administrator) and re-install using
BiocManager::install()So, I did the following:
So we're making progress? If this were an installation of R from CRAN, then it would be installing binaries on macOS, rather than source, and it would not need to find a clang able to build binaries. My guess is that you're using something else, maybe bioconda, and if the later that you should restrict yourself to using conda-based installation practices (rather than mixing conda and Bioconductor practices; actually my recommendation would be to stick with Bioconductor practices...)
The compiler error may be due to reliance on apple's clang. see https://cran.r-project.org/bin/macosx/tools/ for a version of the compiler that might be better -- although I cannot vouch for this if indeed you are mixing conda and Bioc installation practices.
Thanks, that helped to figure out the problem! I installed a fresh version of the compiler and re-installed R.