guanchangge / mosaik-aligner

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Unable to make on rhel6 #108

Open GoogleCodeExporter opened 8 years ago

GoogleCodeExporter commented 8 years ago
What steps will reproduce the problem?
1.Download  Mosaik-1.1.0021-Linux-x64.tar 
2. cd src
3. make

What is the expected output? What do you see instead?

Expect successful compilation but...

Building MOSAIK for the following platform: linux
=========================================================
- Building in CommonSource
- Building in AssemblyFormats
make[2]: Nothing to be done for `all'.

- Building in DataStructures
make[2]: Nothing to be done for `all'.

- Building in ExternalReadFormats
make[2]: Nothing to be done for `all'.

- Building in MosaikReadFormat
make[2]: Nothing to be done for `all'.

- Building in PairwiseAlignment
make[2]: Nothing to be done for `all'.

- Building in Utilities
make[2]: Nothing to be done for `all'.

- Building in MosaikBuild
  * linking MosaikBuild
/usr/bin/ld: cannot find -lz
collect2: ld returned 1 exit status
make[1]: *** [MosaikBuild] Error 1

- Building in MosaikAligner
  * linking MosaikAligner
/usr/bin/ld: cannot find -lm
collect2: ld returned 1 exit status
make[1]: *** [MosaikAligner] Error 1

- Building in MosaikSort
  * linking MosaikSort
/usr/bin/ld: cannot find -lpthread
collect2: ld returned 1 exit status
make[1]: *** [MosaikSort] Error 1

- Building in MosaikMerge
  * linking MosaikMerge
/usr/bin/ld: cannot find -lpthread
collect2: ld returned 1 exit status
make[1]: *** [MosaikMerge] Error 1

- Building in MosaikAssembler
  * linking MosaikAssembler
/usr/bin/ld: cannot find -lpthread
collect2: ld returned 1 exit status
make[1]: *** [MosaikAssembler] Error 1
What version of the product are you using? On what operating system?
Redhat Enterprise Linux 6 64 bit
Mosaik-1.1.0021-Linux-x64

Please provide any additional information below.
We believe we have appropriate devel libraries installed. I believe we can fix 
the lpthread by substituting -pthread but I am too much of a newby to figure 
out the other fixes. Is there a chance for a build that will work out of the 
box?
Thanks! Claire

Original issue reported on code.google.com by claire.w...@sydney.edu.au on 12 Oct 2011 at 4:37

GoogleCodeExporter commented 8 years ago
I am getting this same issue with Centos 6.5 on our Rocks cluster...

Original comment by glen.new...@gmail.com on 25 Jul 2014 at 9:29

GoogleCodeExporter commented 8 years ago
Sorry: with MOSAIK-2.2.3

Original comment by glen.new...@gmail.com on 25 Jul 2014 at 9:30

GoogleCodeExporter commented 8 years ago
I am having this problem as well, MOSAIK-2.2.3

Original comment by map.208...@gmail.com on 18 Aug 2015 at 9:40