Question: Problem installing GenomicRanges package
0
gravatar for aigofaith
10 months ago by
aigofaith10
aigofaith10 wrote:

Hey Could someone help with this

> if (!requireNamespace("BiocManager", quietly = TRUE))
+     install.packages("BiocManager")
> BiocManager::install("GenomicRanges", version = "3.8")
Bioconductor version 3.8 (BiocManager 1.30.4), R 3.5.2
  (2018-12-20)
Installing package(s) 'GenomicRanges'
also installing the dependencies ‘RCurl’, ‘GenomeInfoDb’

trying URL 'https://cloud.r-project.org/src/contrib/RCurl_1.95-4.11.tar.gz'
Content type 'application/x-gzip' length 916667 bytes (895 KB)
==================================================
downloaded 895 KB

trying URL 'https://bioconductor.org/packages/3.8/bioc/src/contrib/GenomeInfoDb_1.18.1.tar.gz'
Content type 'application/x-gzip' length 3404522 bytes (3.2 MB)
==================================================
downloaded 3.2 MB

trying URL 'https://bioconductor.org/packages/3.8/bioc/src/contrib/GenomicRanges_1.34.0.tar.gz'
Content type 'application/x-gzip' length 1159067 bytes (1.1 MB)
==================================================
downloaded 1.1 MB

* installing *source* package ‘RCurl’ ...
** package ‘RCurl’ successfully unpacked and MD5 sums checked
checking for curl-config... no
Cannot find curl-config
ERROR: configuration failed for package ‘RCurl’
* removing ‘/home/ms/R/x86_64-pc-linux-gnu-library/3.5/RCurl’
ERROR: dependency ‘RCurl’ is not available for package ‘GenomeInfoDb’
* removing ‘/home/ms/R/x86_64-pc-linux-gnu-library/3.5/GenomeInfoDb’
ERROR: dependency ‘GenomeInfoDb’ is not available for package ‘GenomicRanges’
* removing ‘/home/ms/R/x86_64-pc-linux-gnu-library/3.5/GenomicRanges’

The downloaded source packages are in
    ‘/tmp/RtmpV1CUHO/downloaded_packages’
installation path not writeable, unable to update packages:
  foreign
Warning messages:
1: In install.packages(pkgs = doing, lib = lib, repos = repos, ...) :
  installation of package ‘RCurl’ had non-zero exit status
2: In install.packages(pkgs = doing, lib = lib, repos = repos, ...) :
  installation of package ‘GenomeInfoDb’ had non-zero exit status
3: In install.packages(pkgs = doing, lib = lib, repos = repos, ...) :
  installation of package ‘GenomicRanges’ had non-zero exit status

> sessionInfo()
R version 3.5.2 (2018-12-20)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 18.04.1 LTS

Matrix products: default
BLAS: /usr/lib/x86_64-linux-gnu/openblas/libblas.so.3
LAPACK: /usr/lib/x86_64-linux-gnu/libopenblasp-r0.2.20.so

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C               LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8    
 [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8    LC_PAPER=en_US.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C             LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       

attached base packages:
[1] stats4    parallel  stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] IRanges_2.16.0      S4Vectors_0.20.1    BiocGenerics_0.28.0 BiocManager_1.30.4 

loaded via a namespace (and not attached):
[1] compiler_3.5.2 tools_3.5.2
software error • 552 views
ADD COMMENTlink written 10 months ago by aigofaith10
1

Thanks I solved it

ADD REPLYlink written 10 months ago by aigofaith10
1

Good to know you solved it. Please could you tell us how you did so that we could learn from your experience? Thanks.

ADD REPLYlink written 6 months ago by gracechy10

Hi aigofaith

could you let us know how you could solve it as I faced the same problem best,

ADD REPLYlink written 4 months ago by hanan_albegali0

usually this means that you need to install libcurl using your operating system management software such as yum or apt get; you need to install the version with headers, e.g., libcurl-dev. People who need to install libcurl also often need to install libxml2-dev.

ADD REPLYlink written 4 months ago by Martin Morgan ♦♦ 24k
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