biocLite() fails to install with R3.4.4 in Ubuntu 18
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Entering edit mode
@joeemendobio-16578
Last seen 5.7 years ago

R doesn't seem to have privileges to install bioconductor packages. Can someone help me out? I'm opening in Ubuntu 18 with sudo R and it should have privileges from what I can tell.

 

> biocLite("BSgenome")
BioC_mirror: https://bioconductor.org
Using Bioconductor 3.6 (BiocInstaller 1.28.0), R 3.4.4 (2018-03-15).
Installing package(s) ‘BSgenome’
also installing the dependencies ‘SummarizedExperiment’, ‘RCurl’, ‘XML’, ‘GenomicAlignments’, ‘GenomeInfoDb’, ‘GenomicRanges’, ‘rtracklayer’, ‘Rsamtools’

trying URL 'https://bioconductor.org/packages/3.6/bioc/src/contrib/SummarizedExperiment_1.8.1.tar.gz'
Content type 'application/x-gzip' length 1204201 bytes (1.1 MB)
==================================================
downloaded 1.1 MB

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://cloud.r-project.org/src/contrib/XML_3.98-1.12.tar.gz'
Content type 'application/x-gzip' length 1599591 bytes (1.5 MB)
==================================================
downloaded 1.5 MB

trying URL 'https://bioconductor.org/packages/3.6/bioc/src/contrib/GenomicAlignments_1.14.2.tar.gz'
Content type 'application/x-gzip' length 2315965 bytes (2.2 MB)
==================================================
downloaded 2.2 MB

trying URL 'https://bioconductor.org/packages/3.6/bioc/src/contrib/GenomeInfoDb_1.14.0.tar.gz'
Content type 'application/x-gzip' length 3402862 bytes (3.2 MB)
==================================================
downloaded 3.2 MB

trying URL 'https://bioconductor.org/packages/3.6/bioc/src/contrib/GenomicRanges_1.30.3.tar.gz'
Content type 'application/x-gzip' length 1116094 bytes (1.1 MB)
==================================================
downloaded 1.1 MB

trying URL 'https://bioconductor.org/packages/3.6/bioc/src/contrib/rtracklayer_1.38.3.tar.gz'
Content type 'application/x-gzip' length 1379677 bytes (1.3 MB)
==================================================
downloaded 1.3 MB

trying URL 'https://bioconductor.org/packages/3.6/bioc/src/contrib/Rsamtools_1.30.0.tar.gz'
Content type 'application/x-gzip' length 3065535 bytes (2.9 MB)
==================================================
downloaded 2.9 MB

trying URL 'https://bioconductor.org/packages/3.6/bioc/src/contrib/BSgenome_1.46.0.tar.gz'
Content type 'application/x-gzip' length 6064527 bytes (5.8 MB)
==================================================
downloaded 5.8 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/joe/R/x86_64-pc-linux-gnu-library/3.4/RCurl’
* installing *source* package ‘XML’ ...
** package ‘XML’ successfully unpacked and MD5 sums checked
checking for gcc... gcc
checking for C compiler default output file name... a.out
checking whether the C compiler works... yes
checking whether we are cross compiling... no
checking for suffix of executables... 
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether gcc accepts -g... yes
checking for gcc option to accept ISO C89... none needed
checking how to run the C preprocessor... gcc -E
checking for sed... /bin/sed
checking for pkg-config... /usr/bin/pkg-config
checking for xml2-config... no
Cannot find xml2-config
ERROR: configuration failed for package ‘XML’
* removing ‘/home/joe/R/x86_64-pc-linux-gnu-library/3.4/XML’
ERROR: dependency ‘RCurl’ is not available for package ‘GenomeInfoDb’
* removing ‘/home/joe/R/x86_64-pc-linux-gnu-library/3.4/GenomeInfoDb’
ERROR: dependency ‘GenomeInfoDb’ is not available for package ‘GenomicRanges’
* removing ‘/home/joe/R/x86_64-pc-linux-gnu-library/3.4/GenomicRanges’
ERROR: dependencies ‘GenomicRanges’, ‘GenomeInfoDb’ are not available for package ‘SummarizedExperiment’
* removing ‘/home/joe/R/x86_64-pc-linux-gnu-library/3.4/SummarizedExperiment’
ERROR: dependencies ‘GenomeInfoDb’, ‘GenomicRanges’ are not available for package ‘Rsamtools’
* removing ‘/home/joe/R/x86_64-pc-linux-gnu-library/3.4/Rsamtools’
ERROR: dependencies ‘GenomeInfoDb’, ‘GenomicRanges’, ‘SummarizedExperiment’, ‘Rsamtools’ are not available for package ‘GenomicAlignments’
* removing ‘/home/joe/R/x86_64-pc-linux-gnu-library/3.4/GenomicAlignments’
ERROR: dependencies ‘GenomicRanges’, ‘XML’, ‘GenomeInfoDb’, ‘RCurl’, ‘Rsamtools’, ‘GenomicAlignments’ are not available for package ‘rtracklayer’
* removing ‘/home/joe/R/x86_64-pc-linux-gnu-library/3.4/rtracklayer’
ERROR: dependencies ‘GenomeInfoDb’, ‘GenomicRanges’, ‘rtracklayer’, ‘Rsamtools’ are not available for package ‘BSgenome’
* removing ‘/home/joe/R/x86_64-pc-linux-gnu-library/3.4/BSgenome’

The downloaded source packages are in
	‘/tmp/RtmpLwNEs5/downloaded_packages’
installation path not writeable, unable to update packages: cluster,
  foreign, MASS, Matrix, mgcv, nlme, survival
Warning messages:
1: In install.packages(pkgs = doing, lib = lib, ...) :
  installation of package ‘RCurl’ had non-zero exit status
2: In install.packages(pkgs = doing, lib = lib, ...) :
  installation of package ‘XML’ had non-zero exit status
3: In install.packages(pkgs = doing, lib = lib, ...) :
  installation of package ‘GenomeInfoDb’ had non-zero exit status
4: In install.packages(pkgs = doing, lib = lib, ...) :
  installation of package ‘GenomicRanges’ had non-zero exit status
5: In install.packages(pkgs = doing, lib = lib, ...) :
  installation of package ‘SummarizedExperiment’ had non-zero exit status
6: In install.packages(pkgs = doing, lib = lib, ...) :
  installation of package ‘Rsamtools’ had non-zero exit status
7: In install.packages(pkgs = doing, lib = lib, ...) :
  installation of package ‘GenomicAlignments’ had non-zero exit status
8: In install.packages(pkgs = doing, lib = lib, ...) :
  installation of package ‘rtracklayer’ had non-zero exit status
9: In install.packages(pkgs = doing, lib = lib, ...) :
  installation of package ‘BSgenome’ had non-zero exit status
bioconductor • 1.4k views
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Entering edit mode
Aaron Lun ★ 28k
@alun
Last seen 1 hour ago
The city by the bay

Look at your error log, in particular the lines "Cannot find curl-config" and "Cannot find xml2-config". All of the other errors derive from these two. A bit of Googling reveals a number of solutions:

https://askubuntu.com/questions/359267/cannot-find-curl-config-in-ubuntu-13-04

https://stackoverflow.com/questions/7765429/unable-to-install-r-package-in-ubuntu-11-04

... so install the relevant system libraries and try again.

P.S. The latest version of Bioconductor is now running on R 3.5.0. Up-to-date versions of Bioconductor packages will not be installed on R 3.4.4, and we (i.e., package developers) will not be providing bugfixes for older versions. So you really should upgrade to the latest version of R.

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0
Entering edit mode

Thanks Aaron! Works great now.

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