I can't build hpg-aligner

[yocra3]

Hi,

In order to install hpg-aligner, I have followed the instructions of wiki.

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

However, when I call scons:

scons: Reading SConscript files ...
scons: done reading SConscript files.
scons: Building targets ...
gcc -o src/breakpoint.o -c -Wall -std=c99 -D_XOPEN_SOURCE=600 -D_GNU_SOURCE -fopenmp -D_REENTRANT -O3 -DNODEBUG -mssse3 -DD_TIME_DEBUG -I. -Isrc -Isrc/tools/bam -Ilib/hpg-libs/bioinfo-libs -Ilib/hpg-libs/common-libs -Ilib/hpg-libs/common-libs/commons/argtable -Ilib/hpg-libs/common-libs/commons/config -I/usr/include -I/usr/include/libxml2 src/breakpoint.c
gcc -o src/buffers.o -c -Wall -std=c99 -D_XOPEN_SOURCE=600 -D_GNU_SOURCE -fopenmp -D_REENTRANT -O3 -DNODEBUG -mssse3 -DD_TIME_DEBUG -I. -Isrc -Isrc/tools/bam -Ilib/hpg-libs/bioinfo-libs -Ilib/hpg-libs/common-libs -Ilib/hpg-libs/common-libs/commons/argtable -Ilib/hpg-libs/common-libs/commons/config -I/usr/include -I/usr/include/libxml2 src/buffers.c
gcc -o src/bwt_server_cpu.o -c -Wall -std=c99 -D_XOPEN_SOURCE=600 -D_GNU_SOURCE -fopenmp -D_REENTRANT -O3 -DNODEBUG -mssse3 -DD_TIME_DEBUG -I. -Isrc -Isrc/tools/bam -Ilib/hpg-libs/bioinfo-libs -Ilib/hpg-libs/common-libs -Ilib/hpg-libs/common-libs/commons/argtable -Ilib/hpg-libs/common-libs/commons/config -I/usr/include -I/usr/include/libxml2 src/bwt_server_cpu.c
gcc -o src/cal_seeker.o -c -Wall -std=c99 -D_XOPEN_SOURCE=600 -D_GNU_SOURCE -fopenmp -D_REENTRANT -O3 -DNODEBUG -mssse3 -DD_TIME_DEBUG -I. -Isrc -Isrc/tools/bam -Ilib/hpg-libs/bioinfo-libs -Ilib/hpg-libs/common-libs -Ilib/hpg-libs/common-libs/commons/argtable -Ilib/hpg-libs/common-libs/commons/config -I/usr/include -I/usr/include/libxml2 src/cal_seeker.c
gcc -o src/pair_server.o -c -Wall -std=c99 -D_XOPEN_SOURCE=600 -D_GNU_SOURCE -fopenmp -D_REENTRANT -O3 -DNODEBUG -mssse3 -DD_TIME_DEBUG -I. -Isrc -Isrc/tools/bam -Ilib/hpg-libs/bioinfo-libs -Ilib/hpg-libs/common-libs -Ilib/hpg-libs/common-libs/commons/argtable -Ilib/hpg-libs/common-libs/commons/config -I/usr/include -I/usr/include/libxml2 src/pair_server.c
gcc -o src/rna/rna_aligner.o -c -Wall -std=c99 -D_XOPEN_SOURCE=600 -D_GNU_SOURCE -fopenmp -D_REENTRANT -O3 -DNODEBUG -mssse3 -DD_TIME_DEBUG -I. -Isrc -Isrc/tools/bam -Ilib/hpg-libs/bioinfo-libs -Ilib/hpg-libs/common-libs -Ilib/hpg-libs/common-libs/commons/argtable -Ilib/hpg-libs/common-libs/commons/config -I/usr/include -I/usr/include/libxml2 src/rna/rna_aligner.c
gcc -o src/rna/rna_server.o -c -Wall -std=c99 -D_XOPEN_SOURCE=600 -D_GNU_SOURCE -fopenmp -D_REENTRANT -O3 -DNODEBUG -mssse3 -DD_TIME_DEBUG -I. -Isrc -Isrc/tools/bam -Ilib/hpg-libs/bioinfo-libs -Ilib/hpg-libs/common-libs -Ilib/hpg-libs/common-libs/commons/argtable -Ilib/hpg-libs/common-libs/commons/config -I/usr/include -I/usr/include/libxml2 src/rna/rna_server.c
gcc -o bin/hpg-aligner -fopenmp src/adapter.o src/batch_writer.o src/breakpoint.o src/buffers.o src/bwt_server_cpu.o src/cal_seeker.o src/hpg-aligner.o src/options.o src/pair_server.o src/region_seeker.o src/statistics.o src/sw_server.o src/timing.o src/workflow_functions.o src/tools/bam/aux/aux_bam.o src/tools/bam/aux/aux_cigar.o src/tools/bam/aux/aux_math.o src/tools/bam/aux/aux_misc.o src/tools/bam/aux/aux_nucleotide.o src/tools/bam/aux/aux_quality.o src/tools/bam/aux/aux_vector.o src/tools/bam/aux/timestats.o src/tools/bam/bfwork/bam_file_ops.o src/tools/bam/bfwork/bam_region.o src/tools/bam/bfwork/bfwork.o src/tools/bam/bfwork/dummy_wander.o src/tools/bam/recalibrate/bam_recal.o src/tools/bam/recalibrate/data_collector.o src/tools/bam/recalibrate/recal_structs.o src/tools/bam/aligner/alig.o src/tools/bam/aligner/alig_region.o src/build-index/index_builder.o src/dna/clasp_v1_1/bintree.o src/dna/clasp_v1_1/container.o src/dna/clasp_v1_1/debug.o src/dna/clasp_v1_1/fileio.o src/dna/clasp_v1_1/info.o src/dna/clasp_v1_1/list.o src/dna/clasp_v1_1/manopt.o src/dna/clasp_v1_1/mathematics.o src/dna/clasp_v1_1/memman.o src/dna/clasp_v1_1/queue.o src/dna/clasp_v1_1/rangetree.o src/dna/clasp_v1_1/slchain.o src/dna/clasp_v1_1/sltypes.o src/dna/clasp_v1_1/sort.o src/dna/clasp_v1_1/stack.o src/dna/clasp_v1_1/stringutils.o src/dna/clasp_v1_1/vebtree.o src/dna/clasp_v1_1/vqueue.o src/dna/clasp_v1_1/vstack.o src/dna/clasp_v1_1/vtprogressbar.o src/dna/dna_aligner.o src/dna/doscadfun.o src/dna/sa_dna_commons.o src/dna/sa_io_stages.o src/dna/sa_mapper_stage.o src/dna/suffix_mng.o src/rna/rna_aligner.o src/rna/rna_server.o src/rna/rna_splice.o src/rna/sa_rna_mapper.o src/rna/sw.o src/rna/workflow_scheduler_SA.o src/sa/sa_index3.o src/sa/sa_search.o src/sa/sa_tools.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 -lxml2 -lm -lz -lcurl -ldl -lbioinfo -lcommon
gcc -o lib/hpg-libs/bioinfo-libs/bioformats/features/region/test/test_parse_regions.o -c -Wall -std=c99 -D_XOPEN_SOURCE=600 -D_GNU_SOURCE -fopenmp -D_REENTRANT -O3 -O3 -I. -Isrc -Isrc/tools/bam -Ilib/hpg-libs/bioinfo-libs -Ilib/hpg-libs/common-libs -Ilib/hpg-libs/common-libs/commons/argtable -Ilib/hpg-libs/common-libs/commons/config -I/usr/include -I/usr/include/libxml2 lib/hpg-libs/bioinfo-libs/bioformats/features/region/test/test_parse_regions.c
lib/hpg-libs/bioinfo-libs/bioformats/features/region/test/test_parse_regions.c:3:19: error: check.h: No such file or directory
lib/hpg-libs/bioinfo-libs/bioformats/features/region/test/test_parse_regions.c:10: error: expected '=', ',', ';', 'asm' or 'attribute' before '' token
lib/hpg-libs/bioinfo-libs/bioformats/features/region/test/test_parse_regions.c:34: warning: return type defaults to 'int'
lib/hpg-libs/bioinfo-libs/bioformats/features/region/test/test_parse_regions.c: In function 'START_TEST':
lib/hpg-libs/bioinfo-libs/bioformats/features/region/test/test_parse_regions.c:33: warning: type of 'gff_file_chromosomes' defaults to 'int'
lib/hpg-libs/bioinfo-libs/bioformats/features/region/test/test_parse_regions.c:36: warning: implicit declaration of function 'fail_unless'
lib/hpg-libs/bioinfo-libs/bioformats/features/region/test/test_parse_regions.c: At top level:
lib/hpg-libs/bioinfo-libs/bioformats/features/region/test/test_parse_regions.c:45: error: expected '=', ',', ';', 'asm' or 'attribute' before 'START_TEST'
lib/hpg-libs/bioinfo-libs/bioformats/features/region/test/test_parse_regions.c:114: error: expected '=', ',', ';', 'asm' or 'attribute' before 'int'
lib/hpg-libs/bioinfo-libs/bioformats/features/region/test/test_parse_regions.c:125: error: expected '=', ',', ';', 'asm' or 'attribute' before '' token
scons: *** [lib/hpg-libs/bioinfo-libs/bioformats/features/region/test/test_parse_regions.o] Error 1
scons: building terminated because of errors.

Can you help me?

Thank you,

Carlos Ruiz

[jtarraga]

Hi Carlos,

You need to install some libraries (e.g., zlib1g-dev libcurl4-gnutls-dev libxml2-dev libncurses5-dev libgsl0-dev check) before compiling the HPG Aligner. I've updated the wiki pages, and I've moved the 'Prerequisites' section before the 'Downloading' section.

https://github.com/opencb/hpg-aligner/wiki/Download-and-building

Cheers

Joaquín

[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 .