Building BioC packages from source on MacOSX (R-2.3.0)
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@benilton-carvalho-1375
Last seen 4.0 years ago
Brazil/Campinas/UNICAMP
Hi All, i've been trying to build BioC packages on macosx, but i can't get it to work. i got rid of fink and installed the g77 that comes with R binary. then i built and installed the latest devel version of R using the sequence ./configure && make && make install i built R-2.3.0 from the source, but when I try: R CMD build Biobase/ from my svn dir, this is what i get: ** arch - Frameworks /Library/Frameworks/R.framework/Resources/share/make/shlib.mk:3: /Library/Frameworks/R.framework/Resources/etc/Frameworks/Makeconf: No such file or directory make: *** No rule to make target `/Library/Frameworks/R.framework/Resources/etc/Frameworks/Makeconf'. Stop. chmod: /private/tmp/Rinst1800553001/Biobase/libs/Frameworks/*: No such file or directory suggestions on how to proceed? thanks, b.
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Seth Falcon ★ 7.4k
@seth-falcon-992
Last seen 9.6 years ago
Hi Benilton, Benilton Carvalho <bcarvalh at="" jhsph.edu=""> writes: > i've been trying to build BioC packages on macosx, but i can't get it to > work. i got rid of fink and installed the g77 that comes with R binary. > then i built and installed the latest devel version of R using the > sequence ./configure && make && make install > > i built R-2.3.0 from the source, but when I try: > > R CMD build Biobase/ > > from my svn dir, this is what i get: > > ** arch - Frameworks > /Library/Frameworks/R.framework/Resources/share/make/shlib.mk:3: > /Library/Frameworks/R.framework/Resources/etc/Frameworks/Makeconf: No such > file or directory > make: *** No rule to make target > `/Library/Frameworks/R.framework/Resources/etc/Frameworks/Makeconf'. Is the R you built on your PATH? Can you verify: * Try just starting R and looking at the version info it prints. Is it the R you are expecting? * Try the R CMD build command specifying the _absolute_ path to R. You might also ask this question on the R-sig-mac list where there are a higher concentration of mac experts. + seth
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Hi Seth, The R I built is the one in my PATH. Starting R and checking the version confirms that. The same error is produced even when I use absolute paths. :( thanks, b
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Seth Falcon ★ 7.4k
@seth-falcon-992
Last seen 9.6 years ago
Benilton Carvalho <bcarvalh at="" jhsph.edu=""> writes: > The R I built is the one in my PATH. Starting R and checking the > version confirms that. The same error is produced even when I use > absolute paths. :( That is strange. Do you have ~/.Rprofile, ~/.Renviron or anything like that? I _think_ what is happening is that R is picking up a config file left from an old binary install (hence the error messges including paths from /Library/...).
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i do have a .Rprofile, which sets the pager and the editor. Even upon its removal i get the same error. is there a way i can make sure R is (not) picking up an old config file? i was positive i deleted everything before (re)trying, but i might have missed something. b. On Mon, 10 Apr 2006, Seth Falcon wrote: > Benilton Carvalho <bcarvalh at="" jhsph.edu=""> writes: >> The R I built is the one in my PATH. Starting R and checking the >> version confirms that. The same error is produced even when I use >> absolute paths. :( > > That is strange. Do you have ~/.Rprofile, ~/.Renviron or anything > like that? I _think_ what is happening is that R is picking up a > config file left from an old binary install (hence the error messges > including paths from /Library/...). > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor >
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Seth Falcon ★ 7.4k
@seth-falcon-992
Last seen 9.6 years ago
Benilton Carvalho <bcarvalh at="" jhsph.edu=""> writes: > i do have a .Rprofile, which sets the pager and the editor. Even upon > its removal i get the same error. > > is there a way i can make sure R is (not) picking up an old config > file? i was positive i deleted everything before (re)trying, but i > might have missed something. The error message you reported has this in it: ** arch - Frameworks /Library/Frameworks/R.framework/Resources/share/make/shlib.mk:3: /Library/Frameworks/R.framework/Resources/etc/Frameworks/Makeconf: No such file or directory make: *** No rule to make target So I would try nuking /Library/Frameworks/R.framework But I'm still quite puzzled. For example, I have such a directory from a binary install of R, but it does not interfere with my from source R build.
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Hi Seth, I removed the binary R that I had and the /Library/Frameworks/R.framework directory. I also rebuilt R from the source and I get the same error. I'll keep trying and if I have any success, I'll let you know. thanks for your help, b On Mon, 10 Apr 2006, Seth Falcon wrote: > Benilton Carvalho <bcarvalh at="" jhsph.edu=""> writes: > >> i do have a .Rprofile, which sets the pager and the editor. Even upon >> its removal i get the same error. >> >> is there a way i can make sure R is (not) picking up an old config >> file? i was positive i deleted everything before (re)trying, but i >> might have missed something. > > The error message you reported has this in it: > > ** arch - Frameworks > /Library/Frameworks/R.framework/Resources/share/make/shlib.mk:3: > /Library/Frameworks/R.framework/Resources/etc/Frameworks/Makeconf: No such file > or directory > make: *** No rule to make target > > So I would try nuking /Library/Frameworks/R.framework > But I'm still quite puzzled. For example, I have such a directory > from a binary install of R, but it does not interfere with my from > source R build. > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor >
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I think Benilton did a make install after he compiled R. Benilton: I believe most of us just compiles R, stopping after the make step and then just do R-devel/bin/R CMD ...., ie. running R directly from the build directory instead of installing it on the system. Given that you have already build R, it should be a 2 sec. test :) Of course, that may not help at all.... /Kasper On Apr 10, 2006, at 9:25 AM, Seth Falcon wrote: > Benilton Carvalho <bcarvalh at="" jhsph.edu=""> writes: > >> i do have a .Rprofile, which sets the pager and the editor. Even upon >> its removal i get the same error. >> >> is there a way i can make sure R is (not) picking up an old config >> file? i was positive i deleted everything before (re)trying, but i >> might have missed something. > > The error message you reported has this in it: > > ** arch - Frameworks > /Library/Frameworks/R.framework/Resources/share/make/shlib.mk:3: > /Library/Frameworks/R.framework/Resources/etc/Frameworks/ > Makeconf: No such file > or directory > make: *** No rule to make target > > So I would try nuking /Library/Frameworks/R.framework > But I'm still quite puzzled. For example, I have such a directory > from a binary install of R, but it does not interfere with my from > source R build. > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/ > gmane.science.biology.informatics.conductor
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That was the case. If the preference is to make a system-wide instal., then it also suffices to use ./configure --disable-R-framework :) Thanks Kasper. b. On Mon, 10 Apr 2006, Kasper Daniel Hansen wrote: > I think Benilton did a > make install > after he compiled R. Benilton: I believe most of us just compiles R, > stopping after the make step and then just do R-devel/bin/R CMD ...., > ie. running R directly from the build directory instead of installing > it on the system. Given that you have already build R, it should be a > 2 sec. test :) Of course, that may not help at all.... > > /Kasper > > On Apr 10, 2006, at 9:25 AM, Seth Falcon wrote: > >> Benilton Carvalho <bcarvalh at="" jhsph.edu=""> writes: >> >>> i do have a .Rprofile, which sets the pager and the editor. Even upon >>> its removal i get the same error. >>> >>> is there a way i can make sure R is (not) picking up an old config >>> file? i was positive i deleted everything before (re)trying, but i >>> might have missed something. >> >> The error message you reported has this in it: >> >> ** arch - Frameworks >> /Library/Frameworks/R.framework/Resources/share/make/shlib.mk:3: >> /Library/Frameworks/R.framework/Resources/etc/Frameworks/ >> Makeconf: No such file >> or directory >> make: *** No rule to make target >> >> So I would try nuking /Library/Frameworks/R.framework >> But I'm still quite puzzled. For example, I have such a directory >> from a binary install of R, but it does not interfere with my from >> source R build. >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor at stat.math.ethz.ch >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: http://news.gmane.org/ >> gmane.science.biology.informatics.conductor > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor >
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