* Re: Re: mingw/math.h not found while compiling R packages @ 2013-07-11 17:20 Enrico Ferrero 2013-07-11 20:28 ` marco atzeri 0 siblings, 1 reply; 7+ messages in thread From: Enrico Ferrero @ 2013-07-11 17:20 UTC (permalink / raw) To: cygwin Hi Larry, Thank you for your reply and advice. > If you are using the R from Cygwin Ports, it must be an old package since > R is no longer offered there. I suggest you install the R package from the > Cygwin distribution instead and retry. Since this list supports the Cygwin > distribution only, this would put your issue firmly on-topic for this list > if you can still reproduce it. For Cygwin Ports packages, they are > supported through the Ports site: > <http://sourceware.org/cygwinports/> > If you have a package from that site and have questions, problems, or > comments, it's best to consult the mailing list there. > -- > Larry I got confused in my first email for some reason, but I'm definitely using R (version 2.15.1) from the Cygwin distribution, not the ports. I just made a clean R installation just to make sure and I still get the same error message: >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’ I've read there are some other problems with MinGW these days, maybe this one is related? In any case, is there anything I can do to try to solve the issue? Bioconductor is vital to me and using R from within Windows is causing me a lot of headaches. Thanks! Best, Enrico -- Problem reports: http://cygwin.com/problems.html FAQ: http://cygwin.com/faq/ Documentation: http://cygwin.com/docs.html Unsubscribe info: http://cygwin.com/ml/#unsubscribe-simple ^ permalink raw reply [flat|nested] 7+ messages in thread
* Re: mingw/math.h not found while compiling R packages 2013-07-11 17:20 Re: mingw/math.h not found while compiling R packages Enrico Ferrero @ 2013-07-11 20:28 ` marco atzeri 2013-07-11 22:15 ` Enrico Ferrero 0 siblings, 1 reply; 7+ messages in thread From: marco atzeri @ 2013-07-11 20:28 UTC (permalink / raw) To: cygwin Il 7/11/2013 6:35 PM, Enrico Ferrero ha scritto: > Hi Larry, > > Thank you for your reply and advice. > >> If you are using the R from Cygwin Ports, it must be an old package since >> R is no longer offered there. I suggest you install the R package from the >> Cygwin distribution instead and retry. Since this list supports the Cygwin >> distribution only, this would put your issue firmly on-topic for this list >> if you can still reproduce it. For Cygwin Ports packages, they are >> supported through the Ports site: >> <http://sourceware.org/cygwinports/> >> If you have a package from that site and have questions, problems, or >> comments, it's best to consult the mailing list there. >> -- >> Larry > > I got confused in my first email for some reason, but I'm definitely > using R (version 2.15.1) from the Cygwin distribution, not the ports. > I just made a clean R installation just to make sure and I still get > the same error message: > >> 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’ > > I've read there are some other problems with MinGW these days, maybe > this one is related? > In any case, is there anything I can do to try to solve the issue? > Bioconductor is vital to me and using R from within Windows is causing > me a lot of headaches. > > Thanks! > Best, > > Enrico > Hi Enrico, could you clarify your issue with the R cygwin package ? Are you trying to compile some addon ? How ? Regards Marco -- Problem reports: http://cygwin.com/problems.html FAQ: http://cygwin.com/faq/ Documentation: http://cygwin.com/docs.html Unsubscribe info: http://cygwin.com/ml/#unsubscribe-simple ^ permalink raw reply [flat|nested] 7+ messages in thread
* Re: mingw/math.h not found while compiling R packages 2013-07-11 20:28 ` marco atzeri @ 2013-07-11 22:15 ` Enrico Ferrero 2013-07-11 23:04 ` marco atzeri 0 siblings, 1 reply; 7+ messages in thread From: Enrico Ferrero @ 2013-07-11 22:15 UTC (permalink / raw) To: cygwin Hi, Thanks for your help, I'll try to make things clearer. I have a full installation of Cygwin, including R version 2.15.1, running on my Windows XP box at work. Bioconductor [1] is a a collection of packages for computational biologists that is installed by compiling its packages within the R environment. To install the base packages (and reproduce what I believe is a bug), one just has to type at the R prompt: >source("http://bioconductor.org/biocLite.R") >biocLite() During the compilation of the IRanges package [2], I get the following error: > 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 So, apparently, R needs the math.h library to compile IRanges but can't find it for some reason. As far as I understand, in Cygwin, math.h is provided by the mingw-runtime package, part of the MinGW suite [3]. According to this page [4] on the Cygwin website, math.h is indeed installed by the mingw-runtime package, so I'm trying to figure out why R can't access it. Maybe it's a path or symbolic links-related problem? Maybe it has to do with the recently mentioned issues affecting MinGW packages in Cygwin [5]? Any help is very appreciated, thank you. [1] http://www.bioconductor.org [2] http://www.bioconductor.org/packages/2.12/bioc/html/IRanges.html [3] http://www.mingw.org/ [4] http://cygwin.com/cgi-bin2/package-cat.cgi?file=mingw-runtime%2Fmingw-runtime-3.18-3&grep=math.h [5] http://cygwin.com/ml/cygwin/2013-07/msg00196.html On 11 July 2013 18:28, marco atzeri <marco.atzeri@gmail.com> wrote: > Il 7/11/2013 6:35 PM, Enrico Ferrero ha scritto: > >> Hi Larry, >> >> Thank you for your reply and advice. >> >>> If you are using the R from Cygwin Ports, it must be an old package since >>> R is no longer offered there. I suggest you install the R package from >>> the >>> Cygwin distribution instead and retry. Since this list supports the >>> Cygwin >>> distribution only, this would put your issue firmly on-topic for this >>> list >>> if you can still reproduce it. For Cygwin Ports packages, they are >>> supported through the Ports site: >>> <http://sourceware.org/cygwinports/> >>> If you have a package from that site and have questions, problems, or >>> comments, it's best to consult the mailing list there. >>> -- >>> Larry >> >> >> I got confused in my first email for some reason, but I'm definitely >> using R (version 2.15.1) from the Cygwin distribution, not the ports. >> I just made a clean R installation just to make sure and I still get >> the same error message: >> >>> 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’ >> >> >> I've read there are some other problems with MinGW these days, maybe >> this one is related? >> In any case, is there anything I can do to try to solve the issue? >> Bioconductor is vital to me and using R from within Windows is causing >> me a lot of headaches. >> >> Thanks! >> Best, >> >> Enrico >> > > > Hi Enrico, > could you clarify your issue with the R cygwin package ? > Are you trying to compile some addon ? How ? > > > > Regards > Marco > > > > -- > Problem reports: http://cygwin.com/problems.html > FAQ: http://cygwin.com/faq/ > Documentation: http://cygwin.com/docs.html > Unsubscribe info: http://cygwin.com/ml/#unsubscribe-simple > -- Enrico -- Problem reports: http://cygwin.com/problems.html FAQ: http://cygwin.com/faq/ Documentation: http://cygwin.com/docs.html Unsubscribe info: http://cygwin.com/ml/#unsubscribe-simple ^ permalink raw reply [flat|nested] 7+ messages in thread
* Re: mingw/math.h not found while compiling R packages 2013-07-11 22:15 ` Enrico Ferrero @ 2013-07-11 23:04 ` marco atzeri 2013-07-12 7:33 ` marco atzeri 0 siblings, 1 reply; 7+ messages in thread From: marco atzeri @ 2013-07-11 23:04 UTC (permalink / raw) To: cygwin Il 7/11/2013 10:51 PM, Enrico Ferrero ha scritto: > Hi, > > Thanks for your help, I'll try to make things clearer. > > I have a full installation of Cygwin, including R version 2.15.1, > running on my Windows XP box at work. > Bioconductor [1] is a a collection of packages for computational > biologists that is installed by compiling its packages within the R > environment. > To install the base packages (and reproduce what I believe is a bug), > one just has to type at the R prompt: > >> source("http://bioconductor.org/biocLite.R") >> biocLite() as you are not using R-3.x the last should be biocLite(NULL) > > During the compilation of the IRanges package [2], I get the following error: > >> 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 > > So, apparently, R needs the math.h library to compile IRanges but > can't find it for some reason. likely the package is broken and incorrectly identify cygwin for mingw. > As far as I understand, in Cygwin, math.h is provided by the > mingw-runtime package, part of the MinGW suite [3]. > According to this page [4] on the Cygwin website, math.h is indeed > installed by the mingw-runtime package, so I'm trying to figure out > why R can't access it. Maybe it's a path or symbolic links-related > problem? Maybe it has to do with the recently mentioned issues > affecting MinGW packages in Cygwin [5]? wrong, cygwin have its own math.h $ cygcheck -f /usr/include/math.h cygwin-1.7.20-1 > > Any help is very appreciated, thank you. I am building biocLite, it will take some time... > > [1] http://www.bioconductor.org > [2] http://www.bioconductor.org/packages/2.12/bioc/html/IRanges.html > [3] http://www.mingw.org/ > [4] http://cygwin.com/cgi-bin2/package-cat.cgi?file=mingw-runtime%2Fmingw-runtime-3.18-3&grep=math.h > [5] http://cygwin.com/ml/cygwin/2013-07/msg00196.html > Marco -- Problem reports: http://cygwin.com/problems.html FAQ: http://cygwin.com/faq/ Documentation: http://cygwin.com/docs.html Unsubscribe info: http://cygwin.com/ml/#unsubscribe-simple ^ permalink raw reply [flat|nested] 7+ messages in thread
* Re: mingw/math.h not found while compiling R packages 2013-07-11 23:04 ` marco atzeri @ 2013-07-12 7:33 ` marco atzeri 2013-07-12 8:51 ` Enrico Ferrero 0 siblings, 1 reply; 7+ messages in thread From: marco atzeri @ 2013-07-12 7:33 UTC (permalink / raw) To: cygwin Il 7/12/2013 12:02 AM, marco atzeri ha scritto: > Il 7/11/2013 10:51 PM, Enrico Ferrero ha scritto: >> Hi, >> > > I am building biocLite, it will take some time... > Enrico, As I was thinking the package is broken. I don't know why they put a wrong and useless #include directive If you download the package and patch the source as ------------------------------------------------------- --- 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 --------------------------------------------------------- after repacking you can then install the local file with something like install.packages("/tmp/IRanges_1.16.6.tar.gz") I put the already patched file here if you are interested: http://matzeri.altervista.org/works/R/ Regards Marco -- Problem reports: http://cygwin.com/problems.html FAQ: http://cygwin.com/faq/ Documentation: http://cygwin.com/docs.html Unsubscribe info: http://cygwin.com/ml/#unsubscribe-simple ^ permalink raw reply [flat|nested] 7+ messages in thread
* Re: mingw/math.h not found while compiling R packages 2013-07-12 7:33 ` marco atzeri @ 2013-07-12 8:51 ` Enrico Ferrero 2013-07-12 10:43 ` marco atzeri 0 siblings, 1 reply; 7+ messages in thread From: Enrico Ferrero @ 2013-07-12 8:51 UTC (permalink / raw) To: cygwin Hi Marco, Thanks a lot for your help. I downloaded your patched package and it compiles without any issues. Since the bug is in Bioconductor and not Cygwin at the end of the day, it would probably be a good idea to file a bug report there. If you're OK with it, I can CC you and link to your patch, just let me know. Again, thank you! Best, Enrico On 12 July 2013 04:48, marco atzeri <marco.atzeri@gmail.com> wrote: > Il 7/12/2013 12:02 AM, marco atzeri ha scritto: >> >> Il 7/11/2013 10:51 PM, Enrico Ferrero ha scritto: >>> >>> Hi, >>> >> >> I am building biocLite, it will take some time... >> > > Enrico, > As I was thinking the package is broken. > I don't know why they put a wrong and useless #include directive > > If you download the package and patch the source as > > ------------------------------------------------------- > --- 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 > --------------------------------------------------------- > > after repacking > you can then install the local file with something like > install.packages("/tmp/IRanges_1.16.6.tar.gz") > > I put the already patched file here if you are interested: > http://matzeri.altervista.org/works/R/ > > Regards > > Marco > > > -- > Problem reports: http://cygwin.com/problems.html > FAQ: http://cygwin.com/faq/ > Documentation: http://cygwin.com/docs.html > Unsubscribe info: http://cygwin.com/ml/#unsubscribe-simple > -- Problem reports: http://cygwin.com/problems.html FAQ: http://cygwin.com/faq/ Documentation: http://cygwin.com/docs.html Unsubscribe info: http://cygwin.com/ml/#unsubscribe-simple ^ permalink raw reply [flat|nested] 7+ messages in thread
* Re: mingw/math.h not found while compiling R packages 2013-07-12 8:51 ` Enrico Ferrero @ 2013-07-12 10:43 ` marco atzeri 0 siblings, 0 replies; 7+ messages in thread From: marco atzeri @ 2013-07-12 10:43 UTC (permalink / raw) To: cygwin Il 7/12/2013 10:01 AM, Enrico Ferrero ha scritto: > Hi Marco, > > Thanks a lot for your help. I downloaded your patched package and it > compiles without any issues. > > Since the bug is in Bioconductor and not Cygwin at the end of the day, > it would probably be a good idea to file a bug report there. > > If you're OK with it, I can CC you and link to your patch, just let me know. > > Again, thank you! > Best, > > Enrico > fine for me. Ciao Marco -- Problem reports: http://cygwin.com/problems.html FAQ: http://cygwin.com/faq/ Documentation: http://cygwin.com/docs.html Unsubscribe info: http://cygwin.com/ml/#unsubscribe-simple ^ permalink raw reply [flat|nested] 7+ messages in thread
end of thread, other threads:[~2013-07-12 8:51 UTC | newest] Thread overview: 7+ messages (download: mbox.gz / follow: Atom feed) -- links below jump to the message on this page -- 2013-07-11 17:20 Re: mingw/math.h not found while compiling R packages Enrico Ferrero 2013-07-11 20:28 ` marco atzeri 2013-07-11 22:15 ` Enrico Ferrero 2013-07-11 23:04 ` marco atzeri 2013-07-12 7:33 ` marco atzeri 2013-07-12 8:51 ` Enrico Ferrero 2013-07-12 10:43 ` marco atzeri
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