IRanges is broken in Cygwin (mingw/math.h)
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enricoferrero ▴ 660
@enricoferrero-6037
Last seen 3.1 years ago
Switzerland
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
IRanges IRanges • 1.9k views
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@michael-lawrence-3846
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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 > [[alternative HTML version deleted]]
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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 at="" 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 at="" 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 at 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 at gen.cam.ac.uk http://flypress.gen.cam.ac.uk/
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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/ > [[alternative HTML version deleted]]
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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/contri b/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/ [[alternative HTML version deleted]]
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Hi Enrico, On Mon, Jul 15, 2013 at 1:10 AM, Enrico Ferrero <enricoferrero86 at="" gmail.com=""> wrote: > 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): [snip] > 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? Yes you are. You need to be running R-3.0.x in order to use bioc 2.12, as is pointed out in the intro of the Bioconductor installation page: http://bioconductor.org/install/ HTH, -steve -- Steve Lianoglou Computational Biologist Bioinformatics and Computational Biology Genentech
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Hi Steve, Thanks for the clarification. I guess it's a matter of waiting for the Cygwin devs to update to R 3.0.1 then. In the meanwhile, may I ask (Michael?) to also patch the latest version of IRanges (I am guessing 1.16.6, according to my logs) for R 2.15.1? Thanks! Best, On 15 July 2013 09:17, Steve Lianoglou <lianoglou.steve@gene.com> wrote: > Hi Enrico, > > On Mon, Jul 15, 2013 at 1:10 AM, Enrico Ferrero > <enricoferrero86@gmail.com> wrote: > > 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): > [snip] > > 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? > > Yes you are. > > You need to be running R-3.0.x in order to use bioc 2.12, as is > pointed out in the intro of the Bioconductor installation page: > > http://bioconductor.org/install/ > > HTH, > > -steve > > -- > Steve Lianoglou > Computational Biologist > Bioinformatics and Computational Biology > Genentech > -- 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/ [[alternative HTML version deleted]]
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Sorry Enrico, Bioc 2.11 is obsolete and no longer maintained. IRanges works fine natively on Windows; I guess there is some really good reason for using Cygwin? Michael On Mon, Jul 15, 2013 at 1:23 AM, Enrico Ferrero <enricoferrero86@gmail.com>wrote: > Hi Steve, > > Thanks for the clarification. I guess it's a matter of waiting for the > Cygwin devs to update to R 3.0.1 then. > > In the meanwhile, may I ask (Michael?) to also patch the latest version of > IRanges (I am guessing 1.16.6, according to my logs) for R 2.15.1? > > Thanks! > Best, > > > On 15 July 2013 09:17, Steve Lianoglou <lianoglou.steve@gene.com> wrote: > >> Hi Enrico, >> >> On Mon, Jul 15, 2013 at 1:10 AM, Enrico Ferrero >> <enricoferrero86@gmail.com> wrote: >> > 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): >> [snip] >> > 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? >> >> Yes you are. >> >> You need to be running R-3.0.x in order to use bioc 2.12, as is >> pointed out in the intro of the Bioconductor installation page: >> >> http://bioconductor.org/install/ >> >> HTH, >> >> -steve >> >> -- >> Steve Lianoglou >> Computational Biologist >> Bioinformatics and Computational Biology >> Genentech >> > > > > -- > 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/ > > > [[alternative HTML version deleted]]
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On 07/15/2013 01:23 AM, Enrico Ferrero wrote: > Hi Steve, > > Thanks for the clarification. I guess it's a matter of waiting for the > Cygwin devs to update to R 3.0.1 then. > > In the meanwhile, may I ask (Michael?) to also patch the latest version of > IRanges (I am guessing 1.16.6, according to my logs) for R 2.15.1? Michael won't be able to do that. Or rather, he'll be able to patch it but the Bioconductor build machines will not build it -- only current and devel versions of Bioconductor packages are built. I guess I'll ask the obvious, and I guess you've got a good answer, but is there a reason that you're using R on cygwin? I would have thought that you could install and manage R under Windows, and used the Windows executable from cygwin? If not in general, then at least for your use cases that involve IRanges? Martin > > Thanks! > Best, > > > On 15 July 2013 09:17, Steve Lianoglou <lianoglou.steve at="" gene.com=""> wrote: > >> Hi Enrico, >> >> On Mon, Jul 15, 2013 at 1:10 AM, Enrico Ferrero >> <enricoferrero86 at="" gmail.com=""> wrote: >>> 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): >> [snip] >>> 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? >> >> Yes you are. >> >> You need to be running R-3.0.x in order to use bioc 2.12, as is >> pointed out in the intro of the Bioconductor installation page: >> >> http://bioconductor.org/install/ >> >> HTH, >> >> -steve >> >> -- >> Steve Lianoglou >> Computational Biologist >> Bioinformatics and Computational Biology >> Genentech >> > > > -- Computational Biology / Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109 Location: Arnold Building M1 B861 Phone: (206) 667-2793
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Dear Michael and Martin, First of all apologies to everybody else for hijacking the discussion, I guess it's not very relevant to the Bioconductor list at this point. Maybe we can keep the next emails off the list? The main reason for using R/Bioconductor within Cygwin is convenience. I work almost exclusively from a Cygwin terminal and using the R console or the Rscript command from within my Cygwin terminal is a lot more convenient than having to fire up Windows' Rgui. However, I'm still new to Cygwin (new job!), so I wasn't even aware that it was possible to use Windows R from Cygwin. May I ask how? Thank you. Best, On 15 July 2013 12:53, Martin Morgan <mtmorgan@fhcrc.org> wrote: > On 07/15/2013 01:23 AM, Enrico Ferrero wrote: > >> Hi Steve, >> >> Thanks for the clarification. I guess it's a matter of waiting for the >> Cygwin devs to update to R 3.0.1 then. >> >> In the meanwhile, may I ask (Michael?) to also patch the latest version of >> IRanges (I am guessing 1.16.6, according to my logs) for R 2.15.1? >> > > Michael won't be able to do that. Or rather, he'll be able to patch it but > the Bioconductor build machines will not build it -- only current and devel > versions of Bioconductor packages are built. > > I guess I'll ask the obvious, and I guess you've got a good answer, but is > there a reason that you're using R on cygwin? I would have thought that you > could install and manage R under Windows, and used the Windows executable > from cygwin? If not in general, then at least for your use cases that > involve IRanges? > > Martin > > > >> Thanks! >> Best, >> >> >> On 15 July 2013 09:17, Steve Lianoglou <lianoglou.steve@gene.com> wrote: >> >> Hi Enrico, >>> >>> On Mon, Jul 15, 2013 at 1:10 AM, Enrico Ferrero >>> <enricoferrero86@gmail.com> wrote: >>> >>>> 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): >>>> >>> [snip] >>> >>>> 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? >>>> >>> >>> Yes you are. >>> >>> You need to be running R-3.0.x in order to use bioc 2.12, as is >>> pointed out in the intro of the Bioconductor installation page: >>> >>> http://bioconductor.org/**install/ <http: bioconductor.org="" install=""/> >>> >>> HTH, >>> >>> -steve >>> >>> -- >>> Steve Lianoglou >>> Computational Biologist >>> Bioinformatics and Computational Biology >>> Genentech >>> >>> >> >> >> > > -- > Computational Biology / Fred Hutchinson Cancer Research Center > 1100 Fairview Ave. N. > PO Box 19024 Seattle, WA 98109 > > Location: Arnold Building M1 B861 > Phone: (206) 667-2793 > -- 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/ [[alternative HTML version deleted]]
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On 7/15/2013 8:59 AM, Enrico Ferrero wrote: > Dear Michael and Martin, > > First of all apologies to everybody else for hijacking the discussion, I guess > it's not very relevant to the Bioconductor list at this point. Maybe we can keep > the next emails off the list? > > The main reason for using R/Bioconductor within Cygwin is convenience. I work > almost exclusively from a Cygwin terminal and using the R console or the Rscript > command from within my Cygwin terminal is a lot more convenient than having to > fire up Windows' Rgui. > However, I'm still new to Cygwin (new job!), so I wasn't even aware that it was > possible to use Windows R from Cygwin. May I ask how? Probably I spoke too quickly; I'm not a cygwin user, other than casually and mostly as an ssh client. It's straight-forward to start R from cygwin -- Rterm --vanilla or Rgui or Rscript, assuming R is on your (cygwin's) PATH. Rgui launches the R GUI which is as functional as ever; Rterm --vanilla get the terminal version but it's not really usable -- X11 isn't available so plots go to Rplots.pdf and errors break to the shell. I'm not an Rscript user so don't know what functionalities are missing. You never know what expertise lurks out there so I'll leave this on the mailing list. Martin > > Thank you. > Best, > > > On 15 July 2013 12:53, Martin Morgan <mtmorgan at="" fhcrc.org=""> <mailto:mtmorgan at="" fhcrc.org="">> wrote: > > On 07/15/2013 01:23 AM, Enrico Ferrero wrote: > > Hi Steve, > > Thanks for the clarification. I guess it's a matter of waiting for the > Cygwin devs to update to R 3.0.1 then. > > In the meanwhile, may I ask (Michael?) to also patch the latest version of > IRanges (I am guessing 1.16.6, according to my logs) for R 2.15.1? > > > Michael won't be able to do that. Or rather, he'll be able to patch it but > the Bioconductor build machines will not build it -- only current and devel > versions of Bioconductor packages are built. > > I guess I'll ask the obvious, and I guess you've got a good answer, but is > there a reason that you're using R on cygwin? I would have thought that you > could install and manage R under Windows, and used the Windows executable > from cygwin? If not in general, then at least for your use cases that > involve IRanges? > > Martin > > > > Thanks! > Best, > > > On 15 July 2013 09:17, Steve Lianoglou <lianoglou.steve at="" gene.com=""> <mailto:lianoglou.steve at="" gene.com="">> wrote: > > Hi Enrico, > > On Mon, Jul 15, 2013 at 1:10 AM, Enrico Ferrero > <enricoferrero86 at="" gmail.com="" <mailto:enricoferrero86="" at="" gmail.com="">> wrote: > > 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): > > [snip] > > 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? > > > Yes you are. > > You need to be running R-3.0.x in order to use bioc 2.12, as is > pointed out in the intro of the Bioconductor installation page: > > http://bioconductor.org/__install/ <http: bioconductor.org="" install=""/> > > HTH, > > -steve > > -- > Steve Lianoglou > Computational Biologist > Bioinformatics and Computational Biology > Genentech > > > > > > > -- > Computational Biology / Fred Hutchinson Cancer Research Center > 1100 Fairview Ave. N. > PO Box 19024 Seattle, WA 98109 > > Location: Arnold Building M1 B861 > Phone: (206) 667-2793 > > > > > -- > Enrico Ferrero > PhD Student > Steve Russell Lab - Department of Genetics > FlyChip - Cambridge Systems Biology Centre > University of Cambridge > > e.ferrero at gen.cam.ac.uk <mailto:e.ferrero at="" gen.cam.ac.uk=""> > http://flypress.gen.cam.ac.uk/ > > -- Dr. Martin Morgan, PhD Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109
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Il 7/15/2013 1:53 PM, Martin Morgan ha scritto: > On 07/15/2013 01:23 AM, Enrico Ferrero wrote: >> Hi Steve, >> >> Thanks for the clarification. I guess it's a matter of waiting for the >> Cygwin devs to update to R 3.0.1 then. >> >> In the meanwhile, may I ask (Michael?) to also patch the latest >> version of >> IRanges (I am guessing 1.16.6, according to my logs) for R 2.15.1? > > Michael won't be able to do that. Or rather, he'll be able to patch it > but the Bioconductor build machines will not build it -- only current > and devel versions of Bioconductor packages are built. > > I guess I'll ask the obvious, and I guess you've got a good answer, but > is there a reason that you're using R on cygwin? interation with other tools available on cygwin and not in general on plain windows ? > I would have thought > that you could install and manage R under Windows, and used the Windows > executable from cygwin? If not in general, then at least for your use > cases that involve IRanges? > > Martin > please note that also debian stable is at 2.15.1, and R-3.0.0 is only 6 months old, same age of 2.15.3 So you could not expect that everyone is on R-3.0.x series. As support policy, supporting only 3.x is a bit courious I will look on building 3.0.x, but no promise on it Regards Marco
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On Mon, Jul 15, 2013 at 5:11 PM, marco atzeri <marco.atzeri@gmail.com>wrote: > Il 7/15/2013 1:53 PM, Martin Morgan ha scritto: > > On 07/15/2013 01:23 AM, Enrico Ferrero wrote: >> >>> Hi Steve, >>> >>> Thanks for the clarification. I guess it's a matter of waiting for the >>> Cygwin devs to update to R 3.0.1 then. >>> >>> In the meanwhile, may I ask (Michael?) to also patch the latest >>> version of >>> IRanges (I am guessing 1.16.6, according to my logs) for R 2.15.1? >>> >> >> Michael won't be able to do that. Or rather, he'll be able to patch it >> but the Bioconductor build machines will not build it -- only current >> and devel versions of Bioconductor packages are built. >> >> I guess I'll ask the obvious, and I guess you've got a good answer, but >> is there a reason that you're using R on cygwin? >> > > interation with other tools available on cygwin and not in general > on plain windows ? > > > I would have thought >> that you could install and manage R under Windows, and used the Windows >> executable from cygwin? If not in general, then at least for your use >> cases that involve IRanges? >> >> Martin >> >> > please note that also debian stable is at 2.15.1, and > R-3.0.0 is only 6 months old, same age of 2.15.3 > So you could not expect that everyone is on R-3.0.x series. > As support policy, supporting only 3.x is a bit courious > Nevertheless, this is the policy adapted by the project. The version of Bioconductor you are trying to use is from October last year and that is eons ago in this field. Also, note that a Bioconductor release is a simultaneous release of many inter-dependent packages, and that we did a new release in March, so you are one stable release behind. The choice to only support Bioc on the newest stable release of R at the time of Bioc release can certainly be debated. In general Bioc is amongst the earliest adapters of new features of R, which makes this a necessity, much more than for a normal CRAN R package. Best, Kasper > ______________________________**_________________ > Bioconductor mailing list > Bioconductor@r-project.org > https://stat.ethz.ch/mailman/**listinfo/bioconductor<https: stat.et="" hz.ch="" mailman="" listinfo="" bioconductor=""> > Search the archives: http://news.gmane.org/gmane.** > science.biology.informatics.**conductor<http: news.gmane.org="" gmane.="" science.biology.informatics.conductor=""> > [[alternative HTML version deleted]]
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Just to summarize, it really comes down to: (a) limited resources and (b) science moves faster than Debian stable. On Tue, Jul 16, 2013 at 5:32 AM, Kasper Daniel Hansen < kasperdanielhansen@gmail.com> wrote: > On Mon, Jul 15, 2013 at 5:11 PM, marco atzeri <marco.atzeri@gmail.com>wrote: > >> Il 7/15/2013 1:53 PM, Martin Morgan ha scritto: >> >> On 07/15/2013 01:23 AM, Enrico Ferrero wrote: >>> >>>> Hi Steve, >>>> >>>> Thanks for the clarification. I guess it's a matter of waiting for the >>>> Cygwin devs to update to R 3.0.1 then. >>>> >>>> In the meanwhile, may I ask (Michael?) to also patch the latest >>>> version of >>>> IRanges (I am guessing 1.16.6, according to my logs) for R 2.15.1? >>>> >>> >>> Michael won't be able to do that. Or rather, he'll be able to patch it >>> but the Bioconductor build machines will not build it -- only current >>> and devel versions of Bioconductor packages are built. >>> >>> I guess I'll ask the obvious, and I guess you've got a good answer, but >>> is there a reason that you're using R on cygwin? >>> >> >> interation with other tools available on cygwin and not in general >> on plain windows ? >> >> >> I would have thought >>> that you could install and manage R under Windows, and used the Windows >>> executable from cygwin? If not in general, then at least for your use >>> cases that involve IRanges? >>> >>> Martin >>> >>> >> please note that also debian stable is at 2.15.1, and >> R-3.0.0 is only 6 months old, same age of 2.15.3 >> So you could not expect that everyone is on R-3.0.x series. >> As support policy, supporting only 3.x is a bit courious >> > > Nevertheless, this is the policy adapted by the project. The version of > Bioconductor you are trying to use is from October last year and that is > eons ago in this field. Also, note that a Bioconductor release is a > simultaneous release of many inter-dependent packages, and that we did a > new release in March, so you are one stable release behind. > > The choice to only support Bioc on the newest stable release of R at the > time of Bioc release can certainly be debated. In general Bioc is amongst > the earliest adapters of new features of R, which makes this a necessity, > much more than for a normal CRAN R package. > > Best, > Kasper > > > > >> ______________________________**_________________ >> Bioconductor mailing list >> Bioconductor@r-project.org >> https://stat.ethz.ch/mailman/**listinfo/bioconductor<https: stat.e="" thz.ch="" mailman="" listinfo="" bioconductor=""> >> Search the archives: http://news.gmane.org/gmane.** >> science.biology.informatics.**conductor<http: news.gmane.org="" gmane="" .science.biology.informatics.conductor=""> >> > > [[alternative HTML version deleted]]
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When in doubt, compile it yourself. ________________________________________ From: bioconductor-bounces@r-project.org [bioconductor- bounces@r-project.org] on behalf of Michael Lawrence [lawrence.michael@gene.com] Sent: Tuesday, July 16, 2013 10:44 AM To: Kasper Daniel Hansen Cc: Michael Lawrence; marco atzeri; Steve Lianoglou; bioconductor at r-project.org Subject: Re: [BioC] IRanges is broken in Cygwin (mingw/math.h) Just to summarize, it really comes down to: (a) limited resources and (b) science moves faster than Debian stable.
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Il 7/12/2013 2:38 PM, Enrico Ferrero ha scritto: > 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, > Michael, just to be clear: We are not violating the license. See http://www.perlfoundation.org/artistic_license_2_0 at point 4 and 4a, the distribution of modified version is allowed. Anyway, I have no interest what's so ever in distributing the package itself. I was just helping Enrico in my role cygwin package manager for R. Regards Marco
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On Fri, Jul 12, 2013 at 5:58 AM, marco atzeri <marco.atzeri@gmail.com>wrote: > Il 7/12/2013 2:38 PM, Enrico Ferrero ha scritto: > > 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, >> >> > Michael, > just to be clear: We are not violating the license. > > See http://www.perlfoundation.org/**artistic_license_2_0<http: www.="" perlfoundation.org="" artistic_license_2_0=""> > > at point 4 and 4a, the distribution of modified version is allowed. > > Ok, thanks for clarifying. I've recently been trying to understand these licenses. Thanks for your help. > Anyway, I have no interest what's so ever in distributing the package > itself. > I was just helping Enrico in my role cygwin package manager for R. > > Regards > Marco > > > > [[alternative HTML version deleted]]
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