Problem installing hpg-aligner

[sumudu-rangika]

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 .
Please advice.
Thanks
Sumudu

[jotasi]

Hi,

I know this thread is ancient but I had the same problem on Debian and so I'm leaving this here for future reference. The problem is a linking error, which arises due to the omission of the subunit library in the list of libraries that is passed to the linker. To fix it, you just have to add subunit to the list of libraries in the specification of the build environment by adding it in this line:

hpg-aligner/SConstruct

Line 26 in df95cd2

LIBS = ['curl', 'dl', 'gsl', 'gslcblas', 'm', 'xml2', 'z'],

I am not sure if there is still active development here as the last commit is from 2015 but if a corresponding PR would be welcome, please let me know.