Hi, I am trying to create a formula for exonerate, which is a popular sequence alignment tool (http://www.ebi.ac.uk/~guy/exonerate/). When I unpack the tarball manually, and issue the following commands: ./configure --disable-debug --disable-dependency-tracking make the package builds without a problem. But when I try to build using my Homebrew formula, the build breaks. The formula is available here: https://gist.github.com/774656 The broken output is available here: https://gist.github.com/774661 Note, I changed the default formula from just issuing system "make install" to issuing both system "make" system "make install" and there is the same problem. Any ideas why this may be occuring? Thanks! Uri ................................................................................... Uri Laserson Graduate Student, Biomedical Engineering Harvard-MIT Division of Health Sciences and Technology M +1 917 742 8019 laserson@mit.edu
On 11 January 2011 16:44, Uri Laserson <laserson@mit.edu> wrote: > Any ideas why this may be occuring? You snipped out the error. Please paste the entire installation output into the gist. It could be a parallelism issue but can't tell for sure until you gist the full brew install -v output. Thanks! -- Mike McQuaid http://mikemcquaid.com
The output for the successful build is here: http://web.mit.edu/laserson/Public/good_output.txt ................................................................................... Uri Laserson Graduate Student, Biomedical Engineering Harvard-MIT Division of Health Sciences and Technology M +1 917 742 8019 laserson@mit.edu On Tue, Jan 11, 2011 at 11:47, Mike McQuaid <mike@mikemcquaid.com> wrote: > On 11 January 2011 16:44, Uri Laserson <laserson@mit.edu> wrote: > > Any ideas why this may be occuring? > You snipped out the error. Please paste the entire installation output > into the gist. It could be a parallelism issue but can't tell for sure > until you gist the full brew install -v output. > > Thanks! > > -- > Mike McQuaid > http://mikemcquaid.com >
The output is too long for gist. You can get the full output here (~1 MB): http://web.mit.edu/laserson/Public/broken_output.txt ................................................................................... Uri Laserson Graduate Student, Biomedical Engineering Harvard-MIT Division of Health Sciences and Technology M +1 917 742 8019 laserson@mit.edu On Tue, Jan 11, 2011 at 11:47, Mike McQuaid <mike@mikemcquaid.com> wrote: > On 11 January 2011 16:44, Uri Laserson <laserson@mit.edu> wrote: > > Any ideas why this may be occuring? > You snipped out the error. Please paste the entire installation output > into the gist. It could be a parallelism issue but can't tell for sure > until you gist the full brew install -v output. > > Thanks! > > -- > Mike McQuaid > http://mikemcquaid.com >
The error suggests the Makefile can't handle more than one job at a time. Try ENV.j1. If that doesn't work may I recommend the troubleshooting wiki? > The output is too long for gist. You can get the full output here (~1 MB): > http://web.mit.edu/laserson/Public/broken_output.txt > > > > Any ideas why this may be occuring? > > > > You snipped out the error. Please paste the entire installation output > > into the gist. It could be a parallelism issue but can't tell for sure > > until you gist the full brew install -v output. > > > > > > >
Thanks! I'll try it out. Can you explain what that does? I am not a ruby programmer, and am not an expert on make/autotools. Uri ................................................................................... Uri Laserson Graduate Student, Biomedical Engineering Harvard-MIT Division of Health Sciences and Technology M +1 917 742 8019 laserson@mit.edu On Tue, Jan 11, 2011 at 12:00, Max Howell <max@methylblue.com> wrote: > The error suggests the Makefile can't handle more than one job at a time. > > Try ENV.j1. > > If that doesn't work may I recommend the troubleshooting wiki? > > The output is too long for gist. You can get the full output here (~1 MB): > http://web.mit.edu/laserson/Public/broken_output.txt > > > Any ideas why this may be occuring? > You snipped out the error. Please paste the entire installation output > into the gist. It could be a parallelism issue but can't tell for sure > until you gist the full brew install -v output. > >
I added the ENV.j1 to the formula, but is still has MAKEFLAGS -j2 as you can see below. Could I be overriding this somewhere? laserson@hobbes:~$ brew install -v exonerate ==> Build Environment CC: /usr/bin/cc => /usr/bin/gcc-4.2 CXX: /usr/bin/c++ => /usr/bin/c++-4.2 LD: /usr/bin/cc => /usr/bin/gcc-4.2 CFLAGS: -O3 -march=core2 -w -pipe CXXFLAGS: -O3 -march=core2 -w -pipe MACOSX_DEPLOYMENT_TARGET: 10.6 MAKEFLAGS: -j2 ==> Downloading http://www.ebi.ac.uk/~guy/exonerate/exonerate-2.2.0.tar.gz File already downloaded and cached to /Users/laserson/Library/Caches/Homebrew /usr/bin/tar xf /Users/laserson/Library/Caches/Homebrew/exonerate-2.2.0.tar.gz ................................................................................... Uri Laserson Graduate Student, Biomedical Engineering Harvard-MIT Division of Health Sciences and Technology M +1 917 742 8019 laserson@mit.edu On Tue, Jan 11, 2011 at 12:03, Uri Laserson <laserson@mit.edu> wrote: > Thanks! I'll try it out. Can you explain what that does? I am not a ruby > programmer, and am not an expert on make/autotools. > > Uri > > > ................................................................................... > Uri Laserson > Graduate Student, Biomedical Engineering > Harvard-MIT Division of Health Sciences and Technology > M +1 917 742 8019 > laserson@mit.edu > > > On Tue, Jan 11, 2011 at 12:00, Max Howell <max@methylblue.com> wrote: > >> The error suggests the Makefile can't handle more than one job at a >> time. >> >> Try ENV.j1. >> >> If that doesn't work may I recommend the troubleshooting wiki? >> >> The output is too long for gist. You can get the full output here (~1 >> MB): >> http://web.mit.edu/laserson/Public/broken_output.txt >> >> > Any ideas why this may be occuring? >> You snipped out the error. Please paste the entire installation output >> into the gist. It could be a parallelism issue but can't tell for sure >> until you gist the full brew install -v output. >> >> >
Your suggestion worked perfectly. Thanks again for the help! Uri ................................................................................... Uri Laserson Graduate Student, Biomedical Engineering Harvard-MIT Division of Health Sciences and Technology M +1 917 742 8019 laserson@mit.edu On Tue, Jan 11, 2011 at 12:10, Uri Laserson <laserson@mit.edu> wrote: > I added the ENV.j1 to the formula, but is still has MAKEFLAGS -j2 as you > can see below. Could I be overriding this somewhere? > > laserson@hobbes:~$ brew install -v exonerate > ==> Build Environment > CC: /usr/bin/cc => /usr/bin/gcc-4.2 > CXX: /usr/bin/c++ => /usr/bin/c++-4.2 > LD: /usr/bin/cc => /usr/bin/gcc-4.2 > CFLAGS: -O3 -march=core2 -w -pipe > CXXFLAGS: -O3 -march=core2 -w -pipe > MACOSX_DEPLOYMENT_TARGET: 10.6 > MAKEFLAGS: -j2 > ==> Downloading http://www.ebi.ac.uk/~guy/exonerate/exonerate-2.2.0.tar.gz > File already downloaded and cached to > /Users/laserson/Library/Caches/Homebrew > /usr/bin/tar xf > /Users/laserson/Library/Caches/Homebrew/exonerate-2.2.0.tar.gz > > > > ................................................................................... > Uri Laserson > Graduate Student, Biomedical Engineering > Harvard-MIT Division of Health Sciences and Technology > M +1 917 742 8019 > laserson@mit.edu > > > On Tue, Jan 11, 2011 at 12:03, Uri Laserson <laserson@mit.edu> wrote: > >> Thanks! I'll try it out. Can you explain what that does? I am not a >> ruby programmer, and am not an expert on make/autotools. >> >> Uri >> >> >> ................................................................................... >> Uri Laserson >> Graduate Student, Biomedical Engineering >> Harvard-MIT Division of Health Sciences and Technology >> M +1 917 742 8019 >> laserson@mit.edu >> >> >> On Tue, Jan 11, 2011 at 12:00, Max Howell <max@methylblue.com> wrote: >> >>> The error suggests the Makefile can't handle more than one job at a >>> time. >>> >>> Try ENV.j1. >>> >>> If that doesn't work may I recommend the troubleshooting wiki? >>> >>> The output is too long for gist. You can get the full output here (~1 >>> MB): >>> http://web.mit.edu/laserson/Public/broken_output.txt >>> >>> > Any ideas why this may be occuring? >>> You snipped out the error. Please paste the entire installation output >>> into the gist. It could be a parallelism issue but can't tell for sure >>> until you gist the full brew install -v output. >>> >>> >> >