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opencb / hpg-aligner

HPG Aligner is an ultrafast and highly sensitive Next-Generation Sequencing (NGS) mapper which supoprts both DNA and RNA alignment
GNU General Public License v2.0
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Missing libsubunit in some SConscript to build master branch #18

Open julien-nc opened 8 years ago

julien-nc commented 8 years ago

I'm running Ubuntu 16.04 and installed those packages with apt : zlib-devel libcurl-devel libxml2-devel ncurses-devel gsl-devel check-devel scons Then I did : 

git clone https://github.com/opencb/hpg-aligner.git
cd hpg-aligner
git submodule update --init

cd lib/hpg-libs
git checkout master
cd ../..
git checkout master
scons

and it failed at some point with : 

gcc -o lib/hpg-libs/bioinfo-libs/bioformats/features/region/test/parse_regions_vcf.test -fopenmp -fopenmp lib/hpg-libs/bioinfo-libs/bioformats/features/region/test/test_parse_regions.o lib/hpg-libs/common-libs/libcommon.a lib/hpg-libs/bioinfo-libs/libbioinfo.a -Llib/hpg-libs/common-libs -Llib/hpg-libs/bioinfo-libs -L/usr/lib -L/usr/lib -L/usr/local/lib -Llibs -Llib/hpg-libs/common-libs -lxml2 -lm -lz -lcurl -ldl -lbioinfo -lcommon -lcheck -lcommon -lcurl -ldl -lm -lrt -lz
/usr/lib/gcc/x86_64-linux-gnu/5/../../../x86_64-linux-gnu/libcheck.a(check_log.o): In function `subunit_lfun':
(.text+0x584): undefined reference to `subunit_test_start'
/usr/lib/gcc/x86_64-linux-gnu/5/../../../x86_64-linux-gnu/libcheck.a(check_log.o): In function `subunit_lfun':
(.text+0x63f): undefined reference to `subunit_test_fail'
/usr/lib/gcc/x86_64-linux-gnu/5/../../../x86_64-linux-gnu/libcheck.a(check_log.o): In function `subunit_lfun':
(.text+0x654): undefined reference to `subunit_test_pass'
/usr/lib/gcc/x86_64-linux-gnu/5/../../../x86_64-linux-gnu/libcheck.a(check_log.o): In function `subunit_lfun':
(.text+0x66f): undefined reference to `subunit_test_error'
collect2: error: ld returned 1 exit status
scons: *** [lib/hpg-libs/bioinfo-libs/bioformats/features/region/test/parse_regions_vcf.test] Error 1
scons: building terminated because of errors.

Link to libsubunit is missing. First i modified the makefiles to add -lsubunit but it is overwritten or overridden by scons so I modified those scons files :

to add libsubunit by changing this kind of line :

LIBS = ['check', 'common', 'curl', 'dl', 'm', 'rt', 'z'],

in

LIBS = ['check', 'subunit', 'common', 'curl', 'dl', 'm', 'rt', 'z'],

And it works like a charm.

I wonder how this can work without this modification. Maybe libsubunit is included in some versions of static libcheck. Anyway, don't you think subunit should be added to scons files ?

sumudu-rangika commented 8 years ago

Hi,

I'm getting the following error when I run scons to build hpg-aligner.

parasit@parasit-OptiPlex-3020:~/hpg-aligner$ scons scons: Reading SConscript files ... scons: done reading SConscript files. scons: Building targets ... gcc -o lib/hpg-libs/bioinfo-libs/bioformats/features/region/test/parse_regions_vcf.test -fopenmp -fopenmp lib/hpg-libs/bioinfo-libs/bioformats/features/region/test/test_parse_regions.o lib/hpg-libs/common-libs/libcommon.a lib/hpg-libs/bioinfo-libs/libbioinfo.a -Llib/hpg-libs/common-libs -Llib/hpg-libs/bioinfo-libs -L/usr/lib -L/usr/lib -L/usr/local/lib -Llibs -Llib/hpg-libs/common-libs -lxml2 -lm -lz -lcurl -ldl -lbioinfo -lcommon -lcheck -lcommon -lcurl -ldl -lm -lrt -lz /usr/lib/gcc/x86_64-linux-gnu/5/../../../x86_64-linux-gnu/libcheck.a(check_log.o): In function subunit_lfun': (.text+0x584): undefined reference tosubunit_test_start' /usr/lib/gcc/x86_64-linux-gnu/5/../../../x86_64-linux-gnu/libcheck.a(check_log.o): In function subunit_lfun': (.text+0x63f): undefined reference tosubunit_test_fail' /usr/lib/gcc/x86_64-linux-gnu/5/../../../x86_64-linux-gnu/libcheck.a(check_log.o): In function subunit_lfun': (.text+0x654): undefined reference tosubunit_test_pass' /usr/lib/gcc/x86_64-linux-gnu/5/../../../x86_64-linux-gnu/libcheck.a(check_log.o): In function subunit_lfun': (.text+0x66f): undefined reference tosubunit_test_error' collect2: error: ld returned 1 exit status scons: *\ [lib/hpg-libs/bioinfo-libs/bioformats/features/region/test/parse_regions_vcf.test] Error 1 scons: building terminated because of errors.

I'm using Ubuntu 16.04LTS and I tried your solution but it doesn't work. Can you give a solution to this.