src/HisMaker.hh:11:20: fatal error: TFrame.h: No such file or directory

[Babita004]

Hello,

I tried following command to install SVE:

export ROOTSYS=/home/programs export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:$ROOTSYS/lib

git clone --recursive https://github.com/TheJacksonLaboratory/SVE.git cd SVE make

I have got following error:

g++ -std=c++11 -m64 -O3 -DCNVNATOR_VERSION=\"v0.3\" -I/home/Programs/include -Isrc/samtools -c src/cnvnator.cpp -o src/obj/cnvnator.o In file included from src/cnvnator.cpp:8:0: src/HisMaker.hh:11:20: fatal error: TFrame.h: No such file or directory

include

                ^

compilation terminated. make[3]: [src/obj/cnvnator.o] Error 1 make[2]: [cnvnator-multi] Error 2 make[1]: [all] Error 2 make: [speedseq] Error 2

Can you suggest me what I am doing wrong.

Thanks in advance

[Babita004]

After compilation, I have got following error:

gcc -g -Wall -O2 -o bcftools call1.o main.o ../kstring.o ../bgzf.o ../knetfile.o ../bedidx.o -L. -lbcf -lm -lz -lpthread make[5]: Nothing to be done for `all'. g++ -std=c++11 -m64 -O3 -DCNVNATOR_VERSION=\"v0.3\" -o bin/cnvnator-multi src/obj/cnvnator.o src/obj/HisMaker.o src/obj/AliParser.o src/obj/Genotyper.o src/obj/Interval.o src/obj/Genome.o src/obj/TreeBuilder.o src/samtools/libbam.a -lz -pthread -L/home/samir/Programs/root/builddir/lib -lCore -lCint -lRIO -lNet -lHist -lGraf -lGraf3d -lGpad -lTree -lRint -lMatrix -lPhysics -lMathCore -lThread -lGui /usr/bin/ld: cannot find -lCint collect2: error: ld returned 1 exit status make[3]: [cnvnator-multi] Error 1 make[2]: [cnvnator-multi] Error 2 make[1]: [all] Error 2 make: [speedseq] Error 2

Please help me

[lslochov]

Hi @Babita004 , there's no need to use "-lCint" to compile CNVnator, so you can safely remove that option from the Makefile. The TFrame error happens if CNVnator can't find your ROOT installation.

[Babita004]

Can you please suggest me, which makefile used for removing -lCint option. Thanks

On Tuesday, September 3, 2019, 9:21:35 PM GMT+5:30, lslochov <notifications@github.com> wrote:  

Hi @Babita004 , there's no need to use "-lCint" to compile CNVnator, so you can safely remove that option from the Makefile. The TFrame error happens if CNVnator can't find your ROOT installation.

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub, or mute the thread.

[lslochov]

This is on line 5 of the Makefile under "src/speedseq/src/cnvnator/Makefile"

[Babita004]

Hello Sir, I have already post this error previously but here I want to given complete details for understanding the problem. Firstly, I have given following command for root environment and then run make command.

export ROOTSYS=/home/Programs/root/build

export PATH=$PATH:$ROOTSYS/bin

export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:$ROOTSYS/lib

After running, I have got following error;

make

• Unzip svtoolkit_2.00.1736

• Building in htslib checking for gcc... gcc checking whether the C compiler works... yes checking for C compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether we are using the GNU C compiler... yes checking whether gcc accepts -g... yes checking for gcc option to accept ISO C89... none needed checking for ranlib... ranlib checking for special C compiler options needed for large files... no checking for _FILE_OFFSET_BITS value needed for large files... no checking shared library type... plain .so checking how to run the C preprocessor... gcc -E checking for grep that handles long lines and -e... /usr/bin/grep checking for egrep... /usr/bin/grep -E checking for ANSI C header files... yes checking for sys/types.h... yes checking for sys/stat.h... yes checking for stdlib.h... yes checking for string.h... yes checking for memory.h... yes checking for strings.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for unistd.h... yes checking for stdlib.h... (cached) yes checking for unistd.h... (cached) yes checking for sys/param.h... yes checking for getpagesize... yes checking for working mmap... yes checking for gmtime_r... yes checking whether fdatasync is declared... yes checking for fdatasync... yes checking for library containing log... -lm checking for zlib.h... yes checking for inflate in -lz... yes checking for library containing connect... none required checking for bzlib.h... yes checking for BZ2_bzBuffToBuffCompress in -lbz2... yes checking for curl_easy_pause in -lcurl... no checking for curl_easy_init in -lcurl... no configure: WARNING: libcurl not enabled: library not found configure: WARNING: GCS support not enabled: requires libcurl support configure: WARNING: S3 support not enabled: requires libcurl support configure: creating ./config.status config.status: creating config.mk config.status: creating htslib.pc.tmp config.status: creating config.h config.status: config.h is unchanged make --no-print-directory -C /home/Programs/SVE/src/htslib make[1]: Nothing to be done for `all'. samtools-0.1.19/ samtools-0.1.19/bam_lpileup.c samtools-0.1.19/bam2depth.c samtools-0.1.19/bam_rmdupse.c samtools-0.1.19/faidx.h samtools-0.1.19/bamtk.c samtools-0.1.19/Makefile.mingw samtools-0.1.19/razf.c samtools-0.1.19/bedcov.c samtools-0.1.19/khash.h samtools-0.1.19/bam2bcf.h samtools-0.1.19/samtools.1 samtools-0.1.19/bam_cat.c samtools-0.1.19/kaln.h samtools-0.1.19/bam_rmdup.c samtools-0.1.19/cut_target.c samtools-0.1.19/ksort.h samtools-0.1.19/bam_plcmd.c samtools-0.1.19/sample.h samtools-0.1.19/sam.c samtools-0.1.19/INSTALL samtools-0.1.19/bam_reheader.c samtools-0.1.19/bam.c samtools-0.1.19/bam.h samtools-0.1.19/errmod.h samtools-0.1.19/bedidx.c samtools-0.1.19/sample.c samtools-0.1.19/bam_aux.c samtools-0.1.19/Makefile samtools-0.1.19/COPYING samtools-0.1.19/bam_tview.c samtools-0.1.19/knetfile.c samtools-0.1.19/bgzf.c samtools-0.1.19/faidx.c samtools-0.1.19/sam_header.c samtools-0.1.19/bcftools/ samtools-0.1.19/bcftools/bcf.h~ samtools-0.1.19/bcftools/em.c samtools-0.1.19/bcftools/bcf.h samtools-0.1.19/bcftools/kmin.h samtools-0.1.19/bcftools/main.c samtools-0.1.19/bcftools/vcfutils.pl samtools-0.1.19/bcftools/fet.c samtools-0.1.19/bcftools/prob1.h samtools-0.1.19/bcftools/index.c samtools-0.1.19/bcftools/bcf2qcall.c samtools-0.1.19/bcftools/Makefile samtools-0.1.19/bcftools/bcfutils.c samtools-0.1.19/bcftools/README samtools-0.1.19/bcftools/prob1.c samtools-0.1.19/bcftools/vcf.c samtools-0.1.19/bcftools/mut.c samtools-0.1.19/bcftools/bcf.tex samtools-0.1.19/bcftools/bcf.c samtools-0.1.19/bcftools/kfunc.c samtools-0.1.19/bcftools/kmin.c samtools-0.1.19/bcftools/call1.c samtools-0.1.19/examples/ samtools-0.1.19/examples/ex1.fa samtools-0.1.19/examples/chk_indel.c samtools-0.1.19/examples/Makefile samtools-0.1.19/examples/ex1.sam.gz samtools-0.1.19/examples/toy.sam samtools-0.1.19/examples/toy.fa samtools-0.1.19/examples/00README.txt samtools-0.1.19/examples/bam2bed.c samtools-0.1.19/examples/calDepth.c samtools-0.1.19/win32/ samtools-0.1.19/win32/zlib.h samtools-0.1.19/win32/libcurses.a samtools-0.1.19/win32/libz.a samtools-0.1.19/win32/xcurses.h samtools-0.1.19/win32/zconf.h samtools-0.1.19/bam2bcf_indel.c samtools-0.1.19/kstring.c samtools-0.1.19/kstring.h samtools-0.1.19/kaln.c samtools-0.1.19/kseq.h samtools-0.1.19/bgzip.c samtools-0.1.19/bam2bcf.c samtools-0.1.19/bam_sort.c samtools-0.1.19/sam_view.c samtools-0.1.19/razf.h samtools-0.1.19/.gitignore samtools-0.1.19/knetfile.h samtools-0.1.19/bam_color.c samtools-0.1.19/bam_tview_html.c samtools-0.1.19/bam_import.c samtools-0.1.19/ChangeLog.old samtools-0.1.19/bam_endian.h samtools-0.1.19/kprobaln.c samtools-0.1.19/kprobaln.h samtools-0.1.19/razip.c samtools-0.1.19/misc/ samtools-0.1.19/misc/wgsim.c samtools-0.1.19/misc/bowtie2sam.pl samtools-0.1.19/misc/r2plot.lua samtools-0.1.19/misc/vcfutils.lua samtools-0.1.19/misc/novo2sam.pl samtools-0.1.19/misc/samtools.pl samtools-0.1.19/misc/md5.h samtools-0.1.19/misc/psl2sam.pl samtools-0.1.19/misc/varfilter.py samtools-0.1.19/misc/Makefile samtools-0.1.19/misc/maq2sam.c samtools-0.1.19/misc/md5fa.c samtools-0.1.19/misc/export2sam.pl samtools-0.1.19/misc/sam2vcf.pl samtools-0.1.19/misc/soap2sam.pl samtools-0.1.19/misc/HmmGlocal.java samtools-0.1.19/misc/plot-bamcheck samtools-0.1.19/misc/bamcheck.c samtools-0.1.19/misc/md5.c samtools-0.1.19/misc/blast2sam.pl samtools-0.1.19/misc/interpolate_sam.pl samtools-0.1.19/misc/zoom2sam.pl samtools-0.1.19/misc/ace2sam.c samtools-0.1.19/misc/wgsim_eval.pl samtools-0.1.19/bam_mate.c samtools-0.1.19/bam_pileup.c samtools-0.1.19/bam_stat.c samtools-0.1.19/bam_md.c samtools-0.1.19/NEWS samtools-0.1.19/bam_tview_curses.c samtools-0.1.19/bamshuf.c samtools-0.1.19/bam.h~ samtools-0.1.19/phase.c samtools-0.1.19/sam.h samtools-0.1.19/padding.c samtools-0.1.19/errmod.c samtools-0.1.19/AUTHORS samtools-0.1.19/klist.h samtools-0.1.19/bam_index.c samtools-0.1.19/bam_tview.h samtools-0.1.19/sam_header.h samtools-0.1.19/bgzf.h

• Building in bwa make[1]: Nothing to be done for `all'.

• Building in samtools cd ../htslib && make htslib_static.mk sed -n '/^static_libs=/s/[^=]=/HTSLIB_static_LIBS = /p;/^static_ldflags=/s/[^=]=/HTSLIB_static_LDFLAGS = /p' htslib.pc.tmp > htslib_static.mk make[1]: Nothing to be done for `all'.

• Building in samtools-0.1.19 make[3]: Nothing to be done for lib'. make[3]: Nothing to be done forlib'. make[3]: Nothing to be done for lib'. gcc -g -Wall -O2 -o samtools bam_tview.o bam_plcmd.o sam_view.o bam_rmdup.o bam_rmdupse.o bam_mate.o bam_stat.o bam_color.o bamtk.o kaln.o bam2bcf.o bam2bcf_indel.o errmod.o sample.o cut_target.o phase.o bam2depth.o padding.o bedcov.o bamshuf.o bam_tview_curses.o bam_tview_html.o libbam.a -Lbcftools -lbcf -lcurses -lm -lz -lpthread gcc -g -Wall -O2 -o bcftools call1.o main.o ../kstring.o ../bgzf.o ../knetfile.o ../bedidx.o -L. -lbcf -lm -lz -lpthread make[2]: Nothing to be done forall'.

• Building in speedseq sed -i 's#CXX = g++ $(ROOTFLAGS)#CXX = g++ -std=c++11 $(ROOTFLAGS)#g' src/speedseq/src/cnvnator/Makefile make --no-print-directory -C src/speedseq make align make -C src/bwa make[3]: Nothing to be done for all'. cp src/bwa/bwa bin cp src/sambamba bin make -C src/samblaster make[3]: Nothing to be done forSAMBLASTER'. cp src/samblaster/samblaster bin cd src/parallel; ./configure --prefix=/home/Programs/SVE/src/speedseq checking for a BSD-compatible install... /usr/bin/install -c checking whether build environment is sane... yes checking for a thread-safe mkdir -p... /usr/bin/mkdir -p checking for gawk... gawk checking whether make sets $(MAKE)... yes configure: creating ./config.status config.status: creating Makefile config.status: creating src/Makefile config.status: creating config.h config.status: config.h is unchanged make -C src/parallel make all-recursive Making all in src pod2man --release='20131022' --center='parallel' \ --section=1 ./parallel.pod > ./parallel.1 pod2man --release='20131022' --center='parallel' \ --section=1 ./sem.pod > ./sem.1 pod2man --release='20131022' --center='parallel' \ --section=1 ./sql > ./sql.1 pod2man --release='20131022' --center='parallel' \ --section=1 ./niceload.pod > ./niceload.1 pod2man --release='20131022' --center='parallel' \ --section=1 ./parallel_tutorial.pod > ./parallel_tutorial.1 pod2html ./parallel.pod > ./parallel.html rm -f ./pod2htm pod2html ./parallel_tutorial.pod > ./parallel_tutorial.html rm -f ./pod2htm pod2html ./sem.pod > ./sem.html rm -f ./pod2htm pod2html ./sql > ./sql.html rm -f ./pod2htm pod2html ./niceload.pod > ./niceload.html rm -f ./pod2htm pod2pdf --output-file ./parallel.pdf ./parallel.pod --title "GNU Parallel" || true /bin/sh: pod2pdf: command not found pod2pdf --output-file ./parallel_tutorial.pdf ./parallel_tutorial.pod --title "GNU Parallel Tutorial" || true /bin/sh: pod2pdf: command not found cp src/parallel/src/parallel bin make var make -C src/freebayes wget -q http://hypervolu.me/freebayes/build/v0.9.21 & cd src && make DETECTED_VERSION = v0.9.21 CURRENT_VERSION = v0.9.21 cp src/freebayes/bin/freebayes bin make -C src/tabix gcc -g -Wall -O2 -fPIC -o tabix main.o -L. -ltabix -lm -lz cp src/tabix/tabix bin cp src/tabix/bgzip bin cp src/vawk/vawk bin cd src/parallel; ./configure --prefix=/home/Programs/SVE/src/speedseq checking for a BSD-compatible install... /usr/bin/install -c checking whether build environment is sane... yes checking for a thread-safe mkdir -p... /usr/bin/mkdir -p checking for gawk... gawk checking whether make sets $(MAKE)... yes configure: creating ./config.status config.status: creating Makefile config.status: creating src/Makefile config.status: creating config.h config.status: config.h is unchanged make -C src/parallel make all-recursive Making all in src pod2man --release='20131022' --center='parallel' \ --section=1 ./parallel.pod > ./parallel.1 pod2man --release='20131022' --center='parallel' \ --section=1 ./sem.pod > ./sem.1 pod2man --release='20131022' --center='parallel' \ --section=1 ./sql > ./sql.1 pod2man --release='20131022' --center='parallel' \ --section=1 ./niceload.pod > ./niceload.1 pod2man --release='20131022' --center='parallel' \ --section=1 ./parallel_tutorial.pod > ./parallel_tutorial.1 pod2html ./parallel.pod > ./parallel.html rm -f ./pod2htm pod2html ./parallel_tutorial.pod > ./parallel_tutorial.html rm -f ./pod2htm pod2html ./sem.pod > ./sem.html rm -f ./pod2htm pod2html ./sql > ./sql.html rm -f ./pod2htm pod2html ./niceload.pod > ./niceload.html rm -f ./pod2htm pod2pdf --output-file ./parallel.pdf ./parallel.pod --title "GNU Parallel" || true /bin/sh: pod2pdf: command not found pod2pdf --output-file ./parallel_tutorial.pdf ./parallel_tutorial.pod --title "GNU Parallel Tutorial" || true /bin/sh: pod2pdf: command not found cp src/parallel/src/parallel bin make sv make -C src/lumpy-sv [ -d bin ] || mkdir -p bin cp scripts/lumpyexpress bin/lumpyexpress

  bin/lumpyexpress.config which: no samblaster in (/home/Programs/root/build/bin:/home/Programs/root/bin:/root/anaconda2/bin:/root/anaconda3/bin:/root/anaconda2/bin:/root/anaconda3/bin:/home/perl5/perlbrew/bin:/usr/local/bin:/usr/local/sbin:/usr/bin:/usr/sbin:/bin:/sbin:/home/.local/bin:/home/bin:/home/Programs/root/builddir/bin:/home/Programs/root/builddir/bin:/home/Programs/root/builddir/bin) which: no sambamba in (/home/Programs/root/build/bin:/home/Programs/root/bin:/root/anaconda2/bin:/root/anaconda3/bin:/root/anaconda2/bin:/root/anaconda3/bin:/home/perl5/perlbrew/bin:/usr/local/bin:/usr/local/sbin:/usr/bin:/usr/sbin:/bin:/sbin:/home/.local/bin:/home/bin:/home/Programs/root/builddir/bin:/home/Programs/root/builddir/bin:/home/Programs/root/builddir/bin) [ -d obj ] || mkdir -p obj [ -d bin ] || mkdir -p bin Building lumpy:

  • Creating BamTools API

• Building in src/utils/bedFile make[4]: `../../../obj//bedFile.o' is up to date.

• Building in src/utils/version make[4]: Nothing to be done for `all'.

• Building in src/utils/gzstream make[4]: `../../../obj//gzstream.o' is up to date.

• Building in src/utils/fileType make[4]: `../../../obj//fileType.o' is up to date.

• Building in src/utils/bedFilePE make[4]: `../../../obj//bedFilePE.o' is up to date.

• Building in src/utils/genomeFile make[4]: `../../../obj//genomeFile.o' is up to date.

• Building in src/utils/BamTools make[4]: Nothing to be done for `all'.

• Building in src/utils/BamTools-Ancillary make[4]: Nothing to be done for `all'.

• Building in src/utils/sequenceUtilities make[4]: `../../../obj//sequenceUtils.o' is up to date.

• Building in src/utils/sqlite3 make[4]: `../../../obj//sqlite3.o' is up to date.

• Building in src/lumpy

  • linking lumpy

cp src/lumpy-sv/scripts/pairend_distro.py bin cp src/lumpy-sv/bin/lumpy bin cp src/lumpy-sv/bin/lumpyexpress bin cp src/lumpy-sv/scripts/vcfToBedpe bin cp src/sambamba bin make -C src/samblaster make[3]: Nothing to be done for SAMBLASTER'. cp src/samblaster/samblaster bin cp src/vawk/vawk bin cp src/bamkit/bamtofastq.py bin cp src/bamkit/bamheadrg.py bin cp src/bamkit/bamgroupreads.py bin cp src/bamkit/bamfilterrg.py bin cp src/bamkit/bamcleanheader.py bin cp src/bamkit/bamlibs.py bin make -C src/tabix gcc -g -Wall -O2 -fPIC -o tabix main.o -L. -ltabix -lm -lz cp src/tabix/tabix bin cp src/tabix/bgzip bin cp src/svtyper/svtyper bin make -C src/cnvnator make -C src/samtools make[6]: Nothing to be done forlib'. make[6]: Nothing to be done for lib'. make[6]: Nothing to be done forlib'. gcc -g -Wall -O2 -o samtools bam_tview.o bam_plcmd.o sam_view.o bam_rmdup.o bam_rmdupse.o bam_mate.o bam_stat.o bam_color.o bamtk.o kaln.o bam2bcf.o bam2bcf_indel.o errmod.o sample.o cut_target.o phase.o bam2depth.o padding.o bedcov.o bamshuf.o bam_tview_curses.o bam_tview_html.o libbam.a -Lbcftools -lbcf -lcurses -lm -lz -lpthread gcc -g -Wall -O2 -o bcftools call1.o main.o ../kstring.o ../bgzf.o ../knetfile.o ../bedidx.o -L. -lbcf -lm -lz -lpthread make[5]: Nothing to be done for `all'. g++ -std=c++11 -m64 -O3 -DCNVNATOR_VERSION=\"v0.3\" -o bin/cnvnator-multi src/obj/cnvnator.o src/obj/HisMaker.o src/obj/AliParser.o src/obj/Genotyper.o src/obj/Interval.o src/obj/Genome.o src/obj/TreeBuilder.o src/samtools/libbam.a -lz -pthread -L/home/Programs/root/build/lib -lCore -lCint -lRIO -lNet -lHist -lGraf -lGraf3d -lGpad -lTree -lRint -lMatrix -lPhysics -lMathCore -lThread -lGui /usr/bin/ld: cannot find -lCint collect2: error: ld returned 1 exit status make[3]: [cnvnator-multi] Error 1 make[2]: [cnvnator-multi] Error 2 make[1]: [all] Error 2 make: [speedseq] Error 2

I have also removed removed "-lCint" options from src/speedseq/src/cnvnator/Makefile. Unfortunately, I have got similar error.

Please give me suggestions and help me. I don't know what I am doing wrong

Thanks in advance

[lslochov]

Hi, I think what's going on is that running "make" will attempt to install a fresh copy of CNVnator, so you also need to modify a line in the top level Makefile (the one in the SVE folder) so that it uses the existing copy.

On line 109, change this line:

@cd $(SVE_DIR)/$(SRC) && tar -zxvf CNVnator_v0.3.3.tar.gz

to:

@cd $(SVE_DIR)/$(SRC) # && tar -zxvf CNVnator_v0.3.3.tar.gz

Then go to the CNVnator Makefile under Speedseq and remove "-lCint" again. Then trying compiling the whole thing with "make"

[Babita004]

Hello lslochov Thank you so much for your suggestions. Sorry for delay response. I have make changes in the both Makefile and then run the again make command. After your suggestions, previous error is solved but unfortunately following error come again;

Score floating point type: double -- Performing Test CXX11_FLAG0 -- Performing Test CXX11_FLAG0 - Success -- C++11 support enabled via -std=c++11 -- Performing Test CXX11_STDLIB_FLAG0 -- Performing Test CXX11_STDLIB_FLAG0 - Success -- Sufficient C++11 library support found with flag ' ' -- Configuring done -- Generating done -- Build files have been written to: /home/Programs/SVE/src/breakdancer-1.4.5 make[1]: Entering directory /home/Programs/SVE/src/breakdancer-1.4.5/build' make[1]: *** No targets specified and no makefile found. Stop. make[1]: Leaving directory/home/Programs/SVE/src/breakdancer-1.4.5/build' make: *** [breakdancer] Error 2

Please help me and give the suggestions. Thanks in advance

[Babita004]

Hello,

Please help me and give the suggestions. I don't know what I am doing wrong

Thank You