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Last seen 9.6 years ago
I am encountering a problem with trying to install Rsamtools from the
latest release of Bioconductor. I am using R version 2.14 but the
latest release of Bioconductor is for R version 2.15. I am new to R
and Bioconductor so I am wondering if these installation errors are
due to the wrong version of R. Unfortunately, I tried updating R (in
Ubuntu 12.04) but my version of R still remains 2.14.
I will continue try to update to R (ver 2.15) but can someone tell me
if there is another potential problem based on the errors in my
session output. Thanks.
-- output of sessionInfo():
> source("http://bioconductor.org/biocLite.R")
> biocLite("Rsamtools")
BioC_mirror: 'http://www.bioconductor.org'
Using R version 2.14, BiocInstaller version 1.2.1.
Installing package(s) 'Rsamtools'
Installing package(s) into ???/usr/local/lib/R/site-library???
(as ???lib??? is unspecified)
also installing the dependencies ???RCurl???, ???XML???,
???rtracklayer???
trying URL 'http://cran.fhcrc.org/src/contrib/RCurl_1.95-3.tar.gz'
Content type 'application/x-gzip' length 868491 bytes (848 Kb)
opened URL
==================================================
downloaded 848 Kb
trying URL 'http://cran.fhcrc.org/src/contrib/XML_3.95-0.1.tar.gz'
Content type 'application/x-gzip' length 1724282 bytes (1.6 Mb)
opened URL
==================================================
downloaded 1.6 Mb
trying URL 'http://www.bioconductor.org/packages/2.9/bioc/src/contrib/
rtracklayer_1.14.4.tar.gz'
Content type 'application/x-gzip' length 1606020 bytes (1.5 Mb)
opened URL
==================================================
downloaded 1.5 Mb
trying URL 'http://www.bioconductor.org/packages/2.9/bioc/src/contrib/
Rsamtools_1.6.3.tar.gz'
Content type 'application/x-gzip' length 2088820 bytes (2.0 Mb)
opened URL
==================================================
downloaded 2.0 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 ???/usr/local/lib/R/site-library/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
No ability to remove finalizers on externalptr objects in this verison
of R
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 ???/usr/local/lib/R/site-library/XML???
ERROR: dependencies ???RCurl???, ???XML??? are not available for
package ???rtracklayer???
* removing ???/usr/local/lib/R/site-library/rtracklayer???
ERROR: dependency ???rtracklayer??? is not available for package
???Rsamtools???
* removing ???/usr/local/lib/R/site-library/Rsamtools???
The downloaded packages are in
???/tmp/RtmpGSb3No/downloaded_packages???
Warning messages:
1: In install.packages(pkgs = pkgs, repos = repos, ...) :
installation of package ???RCurl??? had non-zero exit status
2: In install.packages(pkgs = pkgs, repos = repos, ...) :
installation of package ???XML??? had non-zero exit status
3: In install.packages(pkgs = pkgs, repos = repos, ...) :
installation of package ???rtracklayer??? had non-zero exit status
4: In install.packages(pkgs = pkgs, repos = repos, ...) :
installation of package ???Rsamtools??? had non-zero exit status
>
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