Hi friends! Am having some trouble installing BSgenome.Hsapiens.UCSC.hg19!
When executing the following command
> biocLite("BSgenome.Hsapiens.UCSC.hg19")
I get an error: "installation of package ‘BSgenome.Hsapiens.UCSC.hg19’ had non-zero exit status"
I followed the instructions offered in several previous posts for similar issues (including Problem in BSgenome.Hsapiens.UCSC.hg19 Installation, https://support.bioconductor.org/p/79513/) without success.
Here is the full output I get upon executing the command
> biocLite("BSgenome.Hsapiens.UCSC.hg19")
BioC_mirror: https://bioconductor.org
Using Bioconductor 3.5 (BiocInstaller 1.26.0), R 3.4.0 (2017-04-21).
Installing package(s) ‘BSgenome.Hsapiens.UCSC.hg19’
installing the source package ‘BSgenome.Hsapiens.UCSC.hg19’
trying URL 'https://bioconductor.org/packages/3.5/data/annotation/src/contrib/BSgenome.Hsapiens.UCSC.hg19_1.4.0.tar.gz'
Content type 'application/x-gzip' length 688190187 bytes (656.3 MB)
==================================================
downloaded 656.3 MB
* installing *source* package ‘BSgenome.Hsapiens.UCSC.hg19’ ...
** R
** inst
** preparing package for lazy loading
Error: package or namespace load failed for ‘rtracklayer’ in dyn.load(file, DLLpath = DLLpath, ...):
unable to load shared object '/Library/Frameworks/R.framework/Versions/3.4/Resources/library/rtracklayer/libs/rtracklayer.so':
dlopen(/Library/Frameworks/R.framework/Versions/3.4/Resources/library/rtracklayer/libs/rtracklayer.so, 6): Library not loaded: /usr/local/opt/openssl/lib/libssl.1.0.0.dylib
Referenced from: /Library/Frameworks/R.framework/Versions/3.4/Resources/library/rtracklayer/libs/rtracklayer.so
Reason: image not found
Error : package ‘rtracklayer’ could not be loaded
ERROR: lazy loading failed for package ‘BSgenome.Hsapiens.UCSC.hg19’
* removing ‘/Library/Frameworks/R.framework/Versions/3.4/Resources/library/BSgenome.Hsapiens.UCSC.hg19’
The downloaded source packages are in
‘/private/var/folders/qn/2fg7k8n904b6dpg9jgsm_j0m0000gn/T/RtmpS066ev/downloaded_packages’
Warning message:
In install.packages(pkgs = doing, lib = lib, ...) :
installation of package ‘BSgenome.Hsapiens.UCSC.hg19’ had non-zero exit status
> sessionInfo()
R version 3.4.0 (2017-04-21)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: macOS Sierra 10.12.1
Matrix products: default
BLAS: /Library/Frameworks/R.framework/Versions/3.4/Resources/lib/libRblas.0.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/3.4/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] stats4 parallel stats graphics grDevices utils datasets methods base
other attached packages:
[1] annotate_1.54.0 XML_3.98-1.7 AnnotationDbi_1.38.0 IRanges_2.10.1 S4Vectors_0.14.1
[6] BiocParallel_1.10.1 GSE5859_1.0 devtools_1.13.1 Biobase_2.36.2 BiocGenerics_0.22.0
[11] BiocInstaller_1.26.0
loaded via a namespace (and not attached):
[1] Rcpp_0.12.10 xtable_1.8-2 R6_2.2.1 httr_1.2.1 tools_3.4.0 DBI_0.6-1 git2r_0.18.0 withr_1.0.2
[9] digest_0.6.12 bitops_1.0-6 RCurl_1.95-4.8 curl_2.6 memoise_1.1.0 RSQLite_1.1-2 compiler_3.4.0 jsonlite_1.4
>
Thanks in advance for any help :)
Alon
Hi Hervé! Thanks so much for your help!
I followed the instructions in the article you provided and managed to install rtracklayer:
> library(rtracklayer)
Loading required package: GenomicRanges
Loading required package: GenomeInfoDb
But unfortunately I still run into an error when attempting to install BSgenome.Hsapiens.UCSC.hg19:
> biocLite("BSgenome.Hsapiens.UCSC.hg19")
BioC_mirror: https://bioconductor.org
Using Bioconductor 3.5 (BiocInstaller 1.26.0), R 3.4.0 (2017-04-21).
Installing package(s) ‘BSgenome.Hsapiens.UCSC.hg19’
installing the source package ‘BSgenome.Hsapiens.UCSC.hg19’
trying URL 'https://bioconductor.org/packages/3.5/data/annotation/src/contrib/BSgenome.Hsapiens.UCSC.hg19_1.4.0.tar.gz'
Content type 'application/x-gzip' length 688190187 bytes (656.3 MB)
==================================================
downloaded 656.3 MB
* installing *source* package ‘BSgenome.Hsapiens.UCSC.hg19’ ...
** R
** inst
Warning in file.append(to[okay], from[okay]) :
write error during file append
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
Warning in .seqlengths_TwoBitFile(x) : End of file reading 4 bytes
Error: package or namespace load failed for ‘BSgenome.Hsapiens.UCSC.hg19’:
.onLoad failed in loadNamespace() for 'BSgenome.Hsapiens.UCSC.hg19', details:
call: .seqlengths_TwoBitFile(x)
error: UCSC library operation failed
Error: loading failed
Execution halted
ERROR: loading failed
* removing ‘/Library/Frameworks/R.framework/Versions/3.4/Resources/library/BSgenome.Hsapiens.UCSC.hg19’
The downloaded source packages are in
‘/private/var/folders/qn/2fg7k8n904b6dpg9jgsm_j0m0000gn/T/RtmpS066ev/downloaded_packages’
Warning message:
In install.packages(pkgs = doing, lib = lib, ...) :
installation of package ‘BSgenome.Hsapiens.UCSC.hg19’ had non-zero exit status
Might you have any sugguestions? Thanks so much!
Alon
Yep, I recognize this warning:
I had it once while I was trying to install a big package (was not a BSgenome data package), and, after scratching my head for a while, it turned out that I had consumed my disk quota on the server where I was trying to install the package (no space left on device). So make sure you have enough disk space!
I wish that
file.append()(which is called byfile.copy()which is called byR CMD INSTALL, which is called byinstalled.packages(), which is called bybiocLite()) would error with a more informative error message than the current warning message when running out of disk space. But that's another story...H.
You guys are unreal! Cant believe it finally worked! Thanks a ton for the help!
There is a new rtracklayer Mac binary that addresses this issue. See edit to my answer here A: "minfi" loading problem because of couldn't "bumphunter" load
H.