Building BioC packages from source on MacOSX (R-2.3.0)
3
0
Entering edit mode
@benilton-carvalho-1375
Last seen 5.1 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.
• 993 views
ADD COMMENT •
0
Entering edit mode
Seth Falcon ★ 7.4k
@seth-falcon-992
Last seen 10.6 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
ADD COMMENT •
0
Entering edit mode
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
ADD REPLY •
0
Entering edit mode
Seth Falcon ★ 7.4k
@seth-falcon-992
Last seen 10.6 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/...).
ADD COMMENT •
0
Entering edit mode
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 >
ADD REPLY •
0
Entering edit mode
Seth Falcon ★ 7.4k
@seth-falcon-992
Last seen 10.6 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.
ADD COMMENT •
0
Entering edit mode
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 >
ADD REPLY •
0
Entering edit mode
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
ADD REPLY •
0
Entering edit mode
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 >
ADD REPLY •

Login before adding your answer.

Similar Posts
Loading Similar Posts
Traffic: 1055 users visited in the last hour
Content Search
Users
Tags
Badges
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6