Hi Michael,

I can't seem to install the latest version of IRanges.
For some reason, bioLite() still tries to pull an old version of IRanges,
(that still contains the bug):

> biocLite("IRanges")
> BioC_mirror: http://mirrors.ebi.ac.uk/bioconductor/
> Using Bioconductor version 2.11 (BiocInstaller 1.8.3), R version 2.15.
> Installing package(s) 'IRanges'
> trying URL '
> http://mirrors.ebi.ac.uk/bioconductor//packages/2.11/bioc/src/contrib/IRanges_1.16.6.tar.gz
> '
> Content type 'application/gz' length 699298 bytes (682 Kb)
> opened URL
> ==================================================
> downloaded 682 Kb
> Your Bioconductor is out-of-date, upgrade to version 2.12 by following
> instructions at http://bioconductor.org/install.
> Bioconductor version 2.11 (BiocInstaller 1.8.3), ?biocLite for help
>    Welcome to R!
> * installing *source* package ‘IRanges’ ...
> ** libs
> gcc -I/usr/lib/R/include -DNDEBUG        -g -O2 -pipe  -std=gnu99  -c
> AEbufs.c -o AEbufs.o
> gcc -I/usr/lib/R/include -DNDEBUG        -g -O2 -pipe  -std=gnu99  -c
> CompressedIRangesList_class.c -o CompressedIRangesList_class.o
> gcc -I/usr/lib/R/include -DNDEBUG        -g -O2 -pipe  -std=gnu99  -c
> CompressedList_class.c -o CompressedList_class.o
> gcc -I/usr/lib/R/include -DNDEBUG        -g -O2 -pipe  -std=gnu99  -c
> DataFrame_class.c -o DataFrame_class.o
> gcc -I/usr/lib/R/include -DNDEBUG        -g -O2 -pipe  -std=gnu99  -c
> GappedRanges_class.c -o GappedRanges_class.o
> gcc -I/usr/lib/R/include -DNDEBUG        -g -O2 -pipe  -std=gnu99  -c
> Grouping_class.c -o Grouping_class.o
> gcc -I/usr/lib/R/include -DNDEBUG        -g -O2 -pipe  -std=gnu99  -c
> Hits_class.c -o Hits_class.o
> gcc -I/usr/lib/R/include -DNDEBUG        -g -O2 -pipe  -std=gnu99  -c
> IRanges_class.c -o IRanges_class.o
> gcc -I/usr/lib/R/include -DNDEBUG        -g -O2 -pipe  -std=gnu99  -c
> IRanges_constructor.c -o IRanges_constructor.o
> gcc -I/usr/lib/R/include -DNDEBUG        -g -O2 -pipe  -std=gnu99  -c
> IRanges_utils.c -o IRanges_utils.o
> gcc -I/usr/lib/R/include -DNDEBUG        -g -O2 -pipe  -std=gnu99  -c
> IntervalTree.c -o IntervalTree.o
> In file included from IntervalTree.c:3:0:
> common.h:59:24: fatal error: mingw/math.h: No such file or directory
> compilation terminated.
> /usr/lib/R/etc/Makeconf:121: recipe for target `IntervalTree.o' failed
> make: *** [IntervalTree.o] Error 1
> ERROR: compilation failed for package ‘IRanges’
> * removing ‘/usr/lib/R/site-library/IRanges’
> * restoring previous ‘/usr/lib/R/site-library/IRanges’
> The downloaded source packages are in
>         ‘/tmp/RtmpjGjAeB/downloaded_packages’
> Warning message:
> In install.packages(pkgs = pkgs, lib = lib, repos = repos, ...) :
>   installation of package ‘IRanges’ had non-zero exit status


I'm currently on R version 2.15.1 and Bioconductor version 2.11, trying to
upgrade to 2.12.
Am I doing something wrong?

Thank you.
Best,


On 12 July 2013 13:46, Michael Lawrence <lawrence.michael@gene.com> wrote:

> Hi Enrico,
>
> I ported it to release. Look for 1.18.2.
>
>
> On Fri, Jul 12, 2013 at 5:38 AM, Enrico Ferrero <enricoferrero86@gmail.com
> > wrote:
>
>> Hi Michael,
>>
>> Thanks a lot for your help.
>> I'm not the author of the patch, Marco (CC'ed) is.
>>
>> I'm sorry if the patched package violates the license, it was actually
>> just meant to be a quick way to test if the patch worked. I'm sure
>> Marco will remove it asap.
>>
>> I'm not very familiar with Bioconductor development process, what does
>> the patch being in devel mean? The update will be pushed soon to
>> Bionductor 2.12 or it will only be part of Bioconductor's next release
>> (2.13)?
>>
>> Thanks for the clarification!
>> Best,
>>
>>
>>
>> On 12 July 2013 13:16, Michael Lawrence <lawrence.michael@gene.com>
>> wrote:
>> > Hi Enrico,
>> >
>> > Thanks a lot for this patch. I went ahead and committed it to devel.
>> Also
>> > fixed the same problem in rtracklayer, in case you're aiming for that
>> next
>> > ;)
>> >
>> > Btw, I'm wondering if it's a good thing to distribute pre-patched
>> versions
>> > of IRanges. I'm not an expert, but it's probably a violation of the
>> Artistic
>> > 2.0 license. More practically, it doesn't seem like a good thing to have
>> > multiple IRanges floating around. So in the future you might save
>> yourself
>> > the effort and just send a patch.
>> >
>> > Thanks again,
>> > Michael
>> >
>> >
>> >
>> > On Fri, Jul 12, 2013 at 4:24 AM, Enrico Ferrero <
>> enricoferrero86@gmail.com>
>> > wrote:
>> >>
>> >> Hi,
>> >>
>> >> Installation of Bioconductor fails on Cygwin because of a compilation
>> >> error in the IRanges package:
>> >>
>> >> > In file included from IntervalTree.c:3:0:
>> >> > common.h:59:24: fatal error: mingw/math.h: No such file or directory
>> >> > compilation terminated.
>> >> > /usr/lib/R/etc/Makeconf:121: recipe for target `IntervalTree.o'
>> failed
>> >> > make: *** [IntervalTree.o] Error 1
>> >> > ERROR: compilation failed for package =91IRanges=92
>> >>
>> >> I got some help to fix this from Marco Atzeri in the Cygwin mailing
>> >> list and the problem seems to be a perhaps unnecessary '#include
>> >> <mingw/math.h>' directive.
>> >>
>> >> This patch by Marco fixes the problem, allowing compilation of IRanges
>> >> on Cygwin:
>> >>
>> >> -------------------------------------------------------
>> >> --- orig/IRanges/src/common.h   2013-02-22 04:36:50.000000000 +0100
>> >> +++ IRanges/src/common.h        2013-07-12 00:19:05.922405200 +0200
>> >> @@ -55,10 +55,6 @@
>> >>  #endif
>> >>  #endif
>> >>
>> >> -#ifdef __CYGWIN32__
>> >> -#include <mingw/math.h>
>> >> -#endif
>> >> -
>> >>  #ifndef NAN
>> >>  #define NAN (0.0 / 0.0)
>> >>  #endif
>> >> ---------------------------------------------------------
>> >>
>> >> The patch (and a handy patched package) can also be found at:
>> >> http://matzeri.altervista.org/works/R/
>> >>
>> >> Can this be fixed upstream?
>> >> Thank you.
>> >>
>> >> Best,
>> >>
>> >> --
>> >> Enrico Ferrero
>> >>
>> >> _______________________________________________
>> >> Bioconductor mailing list
>> >> Bioconductor@r-project.org
>> >> https://stat.ethz.ch/mailman/listinfo/bioconductor
>> >> Search the archives:
>> >> http://news.gmane.org/gmane.science.biology.informatics.conductor
>> >
>> >
>>
>>
>>
>> --
>> Enrico Ferrero
>> PhD Student
>> Steve Russell Lab - Department of Genetics
>> FlyChip - Cambridge Systems Biology Centre
>> University of Cambridge
>>
>> e.ferrero@gen.cam.ac.uk
>> http://flypress.gen.cam.ac.uk/
>>
>
>


-- 
Enrico Ferrero
PhD Student
Steve Russell Lab - Department of Genetics
FlyChip - Cambridge Systems Biology Centre
University of Cambridge

e.ferrero@gen.cam.ac.uk
http://flypress.gen.cam.ac.uk/

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