[Bioc-devel] SSL support in Docker images?

Tim Triche, Jr. tim.triche at gmail.com
Sat Jun 27 00:12:26 CEST 2015

Hi all,

I was looking to see whether my proposed DMRcate changes would run smoothly
within the devel_microarray Docker image, and ran into this blocker
(below).  So I can't use install_github to see whether the addition of the
changes I've proposed will integrate smoothly with the devel docker
images.  This is a nice sanity check for me, and I'd like to be able to use
it... any idea of whether SSL, git2r, and devtools will be possible soon?

> install.packages(c("git2r"))
Installing package into ‘/usr/local/lib/R/site-library’
(as ‘lib’ is unspecified)
trying URL 'http://cran.rstudio.com/src/contrib/git2r_0.10.1.tar.gz'
Content type 'application/x-gzip' length 1014817 bytes (991 KB)
downloaded 991 KB

Bioconductor version 3.1 (BiocInstaller 1.18.3), ?biocLite for help
* installing *source* package ‘git2r’ ...
** package ‘git2r’ successfully unpacked and MD5 sums checked
checking build system type... x86_64-unknown-linux-gnu
checking host system type... x86_64-unknown-linux-gnu
checking for gcc... gcc
checking whether the C compiler works... yes
checking for C compiler default output file name... a.out
checking for suffix of executables...
checking whether we are cross compiling... no
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 for library containing inflate... -lz
checking for library containing SSL_library_init... no
configure: error: in `/tmp/RtmpQMHf20/R.INSTALLa7236dd394b/git2r':
configure: error: OpenSSL library required
See `config.log' for more details
ERROR: configuration failed for package ‘git2r’
* removing ‘/usr/local/lib/R/site-library/git2r’

The downloaded source packages are in
Warning message:
In install.packages(c("git2r")) :
  installation of package ‘git2r’ had non-zero exit status

I suppose I could add to the Dockerfile but I'm not 100% sure where it is
in SVN.



Statistics is the grammar of science.
Karl Pearson <http://en.wikipedia.org/wiki/The_Grammar_of_Science>

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