-rdynamic problem for Mac OS 10.10.5

[top1214]

$ make install
gcc -rdynamic  -o bcftools main.o vcfindex.o tabix.o vcfstats.o vcfisec.o vcfmerge.o vcfquery.o vcffilter.o filter.o vcfsom.o vcfnorm.o vcfgtcheck.o vcfview.o vcfannotate.o vcfroh.o vcfconcat.o vcfcall.o mcall.o vcmp.o gvcf.o reheader.o convert.o vcfconvert.o tsv2vcf.o vcfcnv.o HMM.o vcfplugin.o consensus.o ploidy.o version.o ccall.o em.o prob1.o kmin.o  htslib-1.3/libhts.a -lpthread -lz -lm -ldl  
gcc: error: unrecognized command line option ‘-rdynamic’
make: *** [bcftools] Error 1

I tried removing that flag from the makefile, and this happened

$ make install
gcc   -o bcftools main.o vcfindex.o tabix.o vcfstats.o vcfisec.o vcfmerge.o vcfquery.o vcffilter.o filter.o vcfsom.o vcfnorm.o vcfgtcheck.o vcfview.o vcfannotate.o vcfroh.o vcfconcat.o vcfcall.o mcall.o vcmp.o gvcf.o reheader.o convert.o vcfconvert.o tsv2vcf.o vcfcnv.o HMM.o vcfplugin.o consensus.o ploidy.o version.o ccall.o em.o prob1.o kmin.o  htslib-1.3/libhts.a -lpthread -lz -lm -ldl  
mkdir -p -m 755 /usr/local/bin /usr/local/share/man/man1 /usr/local/libexec/bcftools
mkdir: /usr/local/bin: Operation not permitted
mkdir: /usr/local/share/man/man1: Operation not permitted
mkdir: /usr/local/libexec/bcftools: Permission denied
make: *** [install] Error 1

[top1214]

OK, i manually made /usr/local/libexec/bcftools, then removed from the makefile
$(INSTALL_DIR) $(DESTDIR)$(bindir) $(DESTDIR)$(man1dir) $(DESTDIR)$(plugindir)
and I guess it worked

$ make install
install -p bcftools plot-vcfstats vcfutils.pl plugins/color-chrs.pl /usr/local/bin
Installing BAMToGASV and GASV...
Buildfile: build.xml does not exist!
Build failed
Creating pipeline scripts...
cp: src/GASVPro-HQ.sh: No such file or directory
cp: src/GASVPro.sh: No such file or directory
/Users/johnsonlab/gasv//install: line 10: cd: src: No such file or directory
chmod: GASVPro-HQ.sh: No such file or directory
chmod: GASVPro.sh: No such file or directory
Installing GASVPro-CC...
g++: error: src/gasvPro/GASVPro-cc.cpp: No such file or directory
g++: fatal error: no input files
compilation terminated.
Installing GASVPro-graph...
g++: error: src/gasvPro/GASVPro-graph.cpp: No such file or directory
g++: fatal error: no input files
compilation terminated.
Installing GASVPro-mcmc...
g++: error: src/gasvPro/GASVPro-mcmc.cpp: No such file or directory
g++: fatal error: no input files
compilation terminated.
Installing Cluster Converter...
g++: error: src/gasvPro/convertClusters.cpp: No such file or directory
g++: fatal error: no input files
compilation terminated.
Installation complete. Check for errors.
install -p -m 644 doc/bcftools.1 /usr/local/share/man/man1
Installing BAMToGASV and GASV...
mkdir: bin: File exists
Buildfile: build.xml does not exist!
Build failed
Creating pipeline scripts...
cp: src/GASVPro-HQ.sh: No such file or directory
cp: src/GASVPro.sh: No such file or directory
/Users/johnsonlab/gasv//install: line 10: cd: src: No such file or directory
chmod: GASVPro-HQ.sh: No such file or directory
chmod: GASVPro.sh: No such file or directory
Installing GASVPro-CC...
g++: error: src/gasvPro/GASVPro-cc.cpp: No such file or directory
g++: fatal error: no input files
compilation terminated.
Installing GASVPro-graph...
g++: error: src/gasvPro/GASVPro-graph.cpp: No such file or directory
g++: fatal error: no input files
compilation terminated.
Installing GASVPro-mcmc...
g++: error: src/gasvPro/GASVPro-mcmc.cpp: No such file or directory
g++: fatal error: no input files
compilation terminated.
Installing Cluster Converter...
g++: error: src/gasvPro/convertClusters.cpp: No such file or directory
g++: fatal error: no input files
compilation terminated.
Installation complete. Check for errors.
install -p plugins/*.so /usr/local/libexec/bcftools
Installing BAMToGASV and GASV...
mkdir: bin: File exists
Buildfile: build.xml does not exist!
Build failed
Creating pipeline scripts...
cp: src/GASVPro-HQ.sh: No such file or directory
cp: src/GASVPro.sh: No such file or directory
/Users/johnsonlab/gasv/install: line 10: cd: src: No such file or directory
chmod: GASVPro-HQ.sh: No such file or directory
chmod: GASVPro.sh: No such file or directory
Installing GASVPro-CC...
g++: error: src/gasvPro/GASVPro-cc.cpp: No such file or directory
g++: fatal error: no input files
compilation terminated.
Installing GASVPro-graph...
g++: error: src/gasvPro/GASVPro-graph.cpp: No such file or directory
g++: fatal error: no input files
compilation terminated.
Installing GASVPro-mcmc...
g++: error: src/gasvPro/GASVPro-mcmc.cpp: No such file or directory
g++: fatal error: no input files
compilation terminated.
Installing Cluster Converter...
g++: error: src/gasvPro/convertClusters.cpp: No such file or directory
g++: fatal error: no input files
compilation terminated.
Installation complete. Check for errors.

[jrandall]

@top1214 could you send us the output of gcc --version ? It seems likely that your problem involves having an older version of gcc

[top1214]

gcc (GCC) 4.9.2 20141029 (prerelease)

Guess it's time to update then.

[jmarshall]

See also https://sourceforge.net/p/samtools/mailman/message/34699333/