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jts / sga

de novo sequence assembler using string graphs
http://genome.cshlp.org/content/22/3/549
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COMPILE error: BamTools has not been declared #48

Closed apelin20 closed 11 years ago

apelin20 commented 11 years ago

Hello,

Issue occurs at make step:

... Making all in GraphDiff make[2]: Entering directory /shared/reads/velvet_1.2.07/contrib/VelvetOptimiser-2.2.0/pseudoloma/sga/sga/src/GraphDiff' g++ -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Util -I../StringGraph -I../SQG -I../SuffixTools -I../Thirdparty -I../Algorithm -I../Concurrency -fopenmp -I../../bamtools//include -I../../bamtools//include/bamtools -Wall -Wextra -Werror -Wno-unknown-pragmas -O3 -MT libgraphdiff_a-DindelUtil.o -MD -MP -MF .deps/libgraphdiff_a-DindelUtil.Tpo -c -o libgraphdiff_a-DindelUtil.otest -f 'DindelUtil.cpp' || echo './'DindelUtil.cpp In file included from DindelUtil.h:14, from DindelUtil.cpp:11: GraphCompare.h:31:27: error: api/BamWriter.h: No such file or directory In file included from DindelUtil.h:14, from DindelUtil.cpp:11: GraphCompare.h:234: error: \u2018BamTools\u2019 has not been declared GraphCompare.h:234: error: ISO C++ forbids declaration of \u2018BamWriter\u2019 with no type GraphCompare.h:234: error: expected \u2018;\u2019 before \u2018m_evidenceBamFile\u2019 make[2]: *** [libgraphdiff_a-DindelUtil.o] Error 1 make[2]: Leaving directory/shared/reads/velvet_1.2.07/contrib/VelvetOptimiser-2.2.0/pseudoloma/sga/sga/src/GraphDiff' make[1]: * [all-recursive] Error 1 make[1]: Leaving directory `/shared/reads/velvet_1.2.07/contrib/VelvetOptimiser-2.2.0/pseudoloma/sga/sga/src' make: * [all] Error 2

$ gcc --version gcc (GCC) 4.4.6 20120305 (Red Hat 4.4.6-4) Copyright (C) 2010 Free Software Foundation, Inc. This is free software; see the source for copying conditions. There is NO warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.

$ uname -a Linux BioPower 2.6.32-279.5.1.el6.x86_64 #1 SMP Tue Aug 14 16:11:42 CDT 2012 x86_64 x86_64 x86_64 GNU/Linux

Bamtools: bamtools-2.2.3 Config cmd: $ ./configure --with-bamtools=../../bamtools/ --with-jemalloc=../../jemalloc/lib ... checking api/BamReader.h usability... yes checking api/BamReader.h presence... yes checking for api/BamReader.h... yes configure: creating ./config.status config.status: creating Makefile config.status: creating bin/Makefile config.status: creating Thirdparty/Makefile config.status: creating Util/Makefile config.status: creating SQG/Makefile config.status: creating Bigraph/Makefile config.status: creating Algorithm/Makefile config.status: creating StringGraph/Makefile config.status: creating Concurrency/Makefile config.status: creating SuffixTools/Makefile config.status: creating GraphDiff/Makefile config.status: creating Scaffold/Makefile config.status: creating SGA/Makefile config.status: creating config.h config.status: config.h is unchanged config.status: executing depfiles commands

Any thoughts would be appreciated, Adrian

jts commented 11 years ago

Can you try to compile using the absolute path to bamtools instead of the relative path?

apelin20 commented 11 years ago

Indeed, it works.

jts commented 11 years ago

I'm glad to hear it.