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
Thanks Aaron! Works great now.