[Bioc-devel] GSVA/configure.ac problem

Hervé Pagès hpages at fhcrc.org
Thu Nov 10 03:15:07 CET 2011

Hi Robert,

On 11-11-07 10:30 AM, Robert Castelo wrote:
> dear core developers at BioC,
> as you might have seen in a message at BioC, the package GSVA (which i
> collaborate maintaining it) requires GSL version>= 1.6, however current
> GSL version is 1.15 (see http://www.gnu.org/s/gsl) and in fact the
> original version of the package we submitted required version>= 1.12
> according to the svn log, the core development of BioC decided to
> replace the configure.ac file by other one more appropriate for building
> the package in windows and apple machines, so i guess that this 1.6
> version requirement change might have been introduced at that point.

Yes "the core development of BioC" (and in that case it was me) fixed
the configure script a couple of days before the release because it was
not working properly on our Mac OS X build machine. I must confess I'm
not an expert with configure scripts either so what I did was copy
the configure.ac file from another package that links to the GSL, and
did very minor modifications to it (if you do diff GSVA/configure.ac
flowClust/configure.ac you'll be surprised how little different those
files are). I forgot to replace >= 1.6 by >= 1.12 though, sorry.

> i must confess i'm not an expert with configure scripts, so i'd like to
> double check with you whether i could solve this issue by simple
> replacing all the 1.6 values by 1.12 values.

That seems to work (I just tested this on my Linux laptop). Don't
forget to rerun autoconf.

> i currently cannot verify
> whether that works because in fact the configure script seems to by pass
> that requirement, but the message pops up when GSL is not available and
> confuses the user about what GSL should be installed in the system.

The configure script will fail when GSL is not found on the system OR
when it is found but has an inappropriate version. In the latter case,
you'll get something like:

hpages at latitude:~/svn/Rpacks_2_9$ R-2.14 CMD INSTALL GSVA
* installing to library ‘/home/hpages/R-2.14.0/library’
* installing *source* package ‘GSVA’ ...
checking for pkg-config... /usr/bin/pkg-config
checking pkg-config is at least version 0.9.0... yes
checking for GSL... no
checking for gcc... gcc -std=gnu99
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 -std=gnu99 accepts -g... yes
checking for gcc -std=gnu99 option to accept ISO C89... none needed
checking for gsl-config... /usr/bin/gsl-config
checking for GSL - version >= 1.12...
*** 'gsl-config --version' returned 1.9.0, but the minimum version
*** of GSL required is 1.12.0. If gsl-config is correct, then it is
*** best to upgrade to the required version.
*** If gsl-config was wrong, set the environment variable GSL_CONFIG
*** to point to the correct copy of gsl-config, and remove the file
*** config.cache before re-running configure
configure: error: Cannot find the Gnu Scientific Library >= 1.12
ERROR: configuration failed for package ‘GSVA’
* removing ‘/home/hpages/R-2.14.0/library/GSVA’
* restoring previous ‘/home/hpages/R-2.14.0/library/GSVA’

> additionally, our former configure script had the options
> --with-gsl-lib
> --with-gsl-include
> in order to allow the user to have a non-system-wide installation of
> GSL. i understand that this should be now handled differently to ensure
> across-platform compatibility and it depends whether the gsl-config
> script is on the PATH variable. would it be possible to add some option
> to the configure script to tell where exactly the gsl-config script is??
> (in case the user cannot or does not want to have a system-wide
> installation of GSL).

Even for a non system-wide installation of GSL, the user can always
(and should) have the gsl-config script in his/her PATH. It's reasonable
to assume that if s/he was able to install his/her own private GSL, s/he
also knows how to modify his/her PATH to point to it. Alternatively, as
displayed by the error message above, s/he can set the environment
variable GSL_CONFIG to point to his/her private copy of
gsl-config. Does that make sense?


> thanks!!!!
> robert.
> _______________________________________________
> Bioc-devel at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel

Hervé Pagès

Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N, M1-B514
P.O. Box 19024
Seattle, WA 98109-1024

E-mail: hpages at fhcrc.org
Phone:  (206) 667-5791
Fax:    (206) 667-1319

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