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Question: Cannot Install BSgenome.Hsapiens.UCSC.hg19
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gravatar for alongalor
19 months ago by
alongalor10
alongalor10 wrote:

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 Installationhttps://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

ADD COMMENTlink modified 19 months ago • written 19 months ago by alongalor10
2
gravatar for Hervé Pagès
19 months ago by
Hervé Pagès ♦♦ 13k
United States
Hervé Pagès ♦♦ 13k wrote:

Hi,

The BSgenome packages depend on rtracklayer and the rtracklayer Mac binary that we distribute as part of BioC 3.5 is currently broken. You should be able to reproduce the above error by just trying to load rtracklayer with library(rtracklayer). This is a known issue and we are working on it. See A: "minfi" loading problem because of couldn't "bumphunter" load for a workaround.

Sorry for the inconvenience,

H.

ADD COMMENTlink written 19 months ago by Hervé Pagès ♦♦ 13k

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

ADD REPLYlink written 19 months ago by alongalor10
1

Yep, I recognize this warning:

  Warning in file.append(to[okay], from[okay]):
    write error during file append

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 by file.copy() which is called by R CMD INSTALL, which is called by installed.packages(), which is called by biocLite()) 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.

ADD REPLYlink modified 19 months ago • written 19 months ago by Hervé Pagès ♦♦ 13k

You guys are unreal! Cant believe it finally worked! Thanks a ton for the help!

ADD REPLYlink written 19 months ago by alongalor10

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.

ADD REPLYlink written 18 months ago by Hervé Pagès ♦♦ 13k
0
gravatar for alongalor
19 months ago by
alongalor10
alongalor10 wrote:

removeddddd

ADD COMMENTlink modified 19 months ago • written 19 months ago by alongalor10
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