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aigofaith
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@aigofaith-19249
Last seen 6.0 years ago
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
Thanks I solved it
Good to know you solved it. Please could you tell us how you did so that we could learn from your experience? Thanks.
Hi aigofaith
could you let us know how you could solve it as I faced the same problem best,
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.