Hi,
I hoping someone might be able to help me get cufflinks working on our system. I have cufflinks v0.8.1 working (using the provided executables) but every version released since then all three executables (64bit) have just crashed with a floating point exception when I tried to call them.
Our system's kernel is Linux 2.6.16.60-0.21-smp x86_64.
To try to get around this, I've tried to build a version on our system using the provided sources. I've installed the boost libraries and during the configuration everything goes fine until it gets to the check for bamlib, which it says is not installed. Thats no problem, except I can't find it anywhere to install, the error refers me to a site: http://randspringer.de/bam which doesn;t exist anymore.
After hours searching I hadto give up, but the version of cufflinks I have running is crashing on a large dataset I'm trying to run, so its becoming urgent that I update.
Can anyone point me in the right direction for either getting the executables working on my system (I'm not sure that's possible), or point me to where I can find these Bam libraries so I can build the executables myself.
Any help would be greatly appreciated. I attach the "./configure" output for reference, maybe its just that I'm doing something stupid.
Thanks,
Chris.
I hoping someone might be able to help me get cufflinks working on our system. I have cufflinks v0.8.1 working (using the provided executables) but every version released since then all three executables (64bit) have just crashed with a floating point exception when I tried to call them.
Our system's kernel is Linux 2.6.16.60-0.21-smp x86_64.
To try to get around this, I've tried to build a version on our system using the provided sources. I've installed the boost libraries and during the configuration everything goes fine until it gets to the check for bamlib, which it says is not installed. Thats no problem, except I can't find it anywhere to install, the error refers me to a site: http://randspringer.de/bam which doesn;t exist anymore.
After hours searching I hadto give up, but the version of cufflinks I have running is crashing on a large dataset I'm trying to run, so its becoming urgent that I update.
Can anyone point me in the right direction for either getting the executables working on my system (I'm not sure that's possible), or point me to where I can find these Bam libraries so I can build the executables myself.
Any help would be greatly appreciated. I attach the "./configure" output for reference, maybe its just that I'm doing something stupid.
Thanks,
Chris.
cufflinks-0.8.4> ./configure
checking for a BSD-compatible install... /usr/bin/install -c
checking whether build environment is sane... yes
checking for a thread-safe mkdir -p... /bin/mkdir -p
checking for gawk... gawk
checking whether make sets $(MAKE)... yes
checking for gawk... (cached) gawk
checking for g++... g++
checking for C++ compiler default output file name... a.out
checking whether the C++ compiler works... yes
checking whether we are cross compiling... no
checking for suffix of executables...
checking for suffix of object files... o
checking whether we are using the GNU C++ compiler... yes
checking whether g++ accepts -g... yes
checking for style of include used by make... GNU
checking dependency style of g++... gcc3
checking for gcc... gcc
checking whether we are using the GNU C compiler... yes
checking whether gcc accepts -g... yes
checking for gcc option to accept ISO C89... none needed
checking dependency style of gcc... gcc3
checking whether make sets $(MAKE)... (cached) yes
checking for ranlib... ranlib
checking for a BSD-compatible install... /usr/bin/install -c
checking for boostlib >= 1.38.0... yes
checking for bamlib... configure: error: We could not detect the bam libraries (version or higher). If you have a staged bam library (still not installed) please specify $BAM_ROOT in your environment and do not give a PATH to --with-bam option. If you are sure you have bam installed, then check your version number looking in <bam/version.hpp>. See http://randspringer.de/bam for more documentation.
checking for a BSD-compatible install... /usr/bin/install -c
checking whether build environment is sane... yes
checking for a thread-safe mkdir -p... /bin/mkdir -p
checking for gawk... gawk
checking whether make sets $(MAKE)... yes
checking for gawk... (cached) gawk
checking for g++... g++
checking for C++ compiler default output file name... a.out
checking whether the C++ compiler works... yes
checking whether we are cross compiling... no
checking for suffix of executables...
checking for suffix of object files... o
checking whether we are using the GNU C++ compiler... yes
checking whether g++ accepts -g... yes
checking for style of include used by make... GNU
checking dependency style of g++... gcc3
checking for gcc... gcc
checking whether we are using the GNU C compiler... yes
checking whether gcc accepts -g... yes
checking for gcc option to accept ISO C89... none needed
checking dependency style of gcc... gcc3
checking whether make sets $(MAKE)... (cached) yes
checking for ranlib... ranlib
checking for a BSD-compatible install... /usr/bin/install -c
checking for boostlib >= 1.38.0... yes
checking for bamlib... configure: error: We could not detect the bam libraries (version or higher). If you have a staged bam library (still not installed) please specify $BAM_ROOT in your environment and do not give a PATH to --with-bam option. If you are sure you have bam installed, then check your version number looking in <bam/version.hpp>. See http://randspringer.de/bam for more documentation.
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