[Bioc-devel] SSL support in Docker images?

[Dan Tenenbaum]

----- Original Message -----
> From: "Tim Triche, Jr." <tim.triche at gmail.com>
> To: bioc-devel at r-project.org
> Cc: "Dan Tenenbaum" <dtenenba at fredhutch.org>
> Sent: Friday, June 26, 2015 3:12:26 PM
> Subject: SSL support in Docker images?
> 
> 
> 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
> ‘/tmp/RtmpLHhGwv/downloaded_packages’
> Warning message:
> In install.packages(c("git2r")) :
> installation of package ‘git2r’ had non-zero exit status
> 
> 
> 

I can't repro this problem; are you using the latest bioconductor/devel_microarray:latest?

Try 

docker pull bioconductor/devel_microarray

After doing that I was able to install git2r and devtools without issues.

Dan


> 
> 
> 
> I suppose I could add to the Dockerfile but I'm not 100% sure where
> it is in SVN.
> 
> 
> Thnaks,
> 
> 
> --t
> 
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> 
> Statistics is the grammar of science.
> Karl Pearson