Compilation of CORTEX_release_v1.0.5.21 failed in mac OS X 10.9.

[Sang Chul Choi]

Hi, I could not compile CORTEX_release_v1.0.5.21 in a mac with OS X 10.9.  Are there anyone who could have any clue? The following is a tail of the message from "install.sh". 

==================================

cc -O3 -Wall -Wextra -I ../htslib/htslib/ -I ../string_buffer -c seq_sam.c -o seq_sam.o

readlink: illegal option -- f

usage: readlink [-n] [file ...]

ar -csru libseqfile.a seq_file.o seq_common.o seq_fasta.o seq_fastq.o seq_plain.o seq_sam.o

cc -o seq_convert -O3 -Wall -Wextra -I ../htslib/htslib/ -I ../string_buffer seq_convert.c libseqfile.a -L ../htslib/htslib/ -L ../string_buffer -lstrbuf -lhts -lpthread -lz -lm

cc -o seq_file_test -O3 -Wall -Wextra -I ../htslib/htslib/ -I ../string_buffer seq_file_test.c libseqfile.a -L ../htslib/htslib/ -L ../string_buffer -lstrbuf -lhts -lpthread -lz -lm

cd new_api; make HTSLIB=

if [[ '' == '' ]]; \

then echo "Error: Please pass HTSLIB=... with path to htslib"; exit 1; fi

Error: Please pass HTSLIB=... with path to htslib

make[1]: *** [htslib] Error 1

make: *** [all] Error 2

if test -e needleman_wunsch; then rm needleman_wunsch; fi

for file in ; do rm -r $file; done

for file in ; do rm $file; done

gcc -o needleman_wunsch -O3 -fnested-functions -DCOMPILE_TIME='"Wed Feb  5 10:29:28 AKST 2014"' -DSCORE_TYPE='int' -Wall \

-I . -I ./libs/utility_lib -I ./libs/string_buffer \

-I ./libs/bioinf -I ./libs/alignment_scoring \

nw_cmdline.c needleman_wunsch.c \

./libs/alignment_scoring/*.c ./libs/utility_lib/utility_lib.c \

./libs/bioinf/bioinf.c ./libs/string_buffer/string_buffer.c -lz

./libs/bioinf/bioinf.c:593:47: error: expected ';' at end of declaration

  int cmp_chroms(const void *a, const void *b)

                                              ^

                                              ;

1 error generated.

make: *** [all] Error 1

[Zamin Iqbal]

Sorry for the long delay in getting through moderation, somehow the notification that your post was waiting for me got lost.

Sorry for the Mac issue - will take a look

Zam

[Isaac Turner]

Dear Sang Chul Choi,

cortex_var requires GCC, macs come with clang only these days (when you install the developer tools). So you'll need to install GCC through macports, homebrew, fink or some other way.  Also, the default readlink implementation on Mac OS X doesn't take the -f argument, so we'll need to patch a couple of lines.

GCC is required for C nested functions, a GCC extension.

Isaac

--
You received this message because you are subscribed to the Google Groups "cortex_var" group.
To unsubscribe from this group and stop receiving emails from it, send an email to cortex_var+...@googlegroups.com.
For more options, visit https://groups.google.com/groups/opt_out.

[Allison Truhlar]

Hello,

Disclaimer: I'm new to everything command line, so apologies if I leave out critical information.

I'm trying to get Cortex_var up and running on a Mac (OS X 10.11.6) and I seem to have a similar error to the original post.  I have installed the latest Xcode, Xcode command line tools, and GCC, as suggested in this post and elsewhere in this group.  Possibly it's the -f argument mentioned by Isaac that's the problem - I've pasted some of the output from bash install.sh, including the error messages below.  Any advice would be much appreciated.

Thanks in advance,
Allison


cd new_api; make clean
rm -rf bin/*
cd benchmarks; make clean
rm -rf seqtest ktest
cd dev; make clean
rm -rf btest seqcmdline seqstat
cc -O3 -Wall -Wextra -I ../htslib/htslib/ -I ../string_buffer -c seq_file.c -o seq_file.o
cc -O3 -Wall -Wextra -I ../htslib/htslib/ -I ../string_buffer -c seq_common.c -o seq_common.o
cc -O3 -Wall -Wextra -I ../htslib/htslib/ -I ../string_buffer -c seq_fasta.c -o seq_fasta.o
cc -O3 -Wall -Wextra -I ../htslib/htslib/ -I ../string_buffer -c seq_fastq.c -o seq_fastq.o
cc -O3 -Wall -Wextra -I ../htslib/htslib/ -I ../string_buffer -c seq_plain.c -o seq_plain.o

cc -O3 -Wall -Wextra -I ../htslib/htslib/ -I ../string_buffer -c seq_sam.c -o seq_sam.o
readlink: illegal option -- f
usage: readlink [-n] [file ...]
ar -csru libseqfile.a seq_file.o seq_common.o seq_fasta.o seq_fastq.o seq_plain.o seq_sam.o
cc -o seq_convert -O3 -Wall -Wextra -I ../htslib/htslib/ -I ../string_buffer seq_convert.c libseqfile.a -L ../htslib/htslib/ -L ../string_buffer -lstrbuf -lhts -lpthread -lz -lm
cc -o seq_file_test -O3 -Wall -Wextra -I ../htslib/htslib/ -I ../string_buffer seq_file_test.c libseqfile.a -L ../htslib/htslib/ -L ../string_buffer -lstrbuf -lhts -lpthread -lz -lm
cd new_api; make HTSLIB=
if [[ '' == '' ]]; \
    then echo "Error: Please pass HTSLIB=... with path to htslib"; exit 1; fi
Error: Please pass HTSLIB=... with path to htslib
make[1]: *** [htslib] Error 1
make: *** [all] Error 2
if test -e needleman_wunsch; then rm needleman_wunsch; fi
for file in ; do rm -r $file; done
for file in ; do rm $file; done

gcc -o needleman_wunsch -O3 -fnested-functions -DCOMPILE_TIME='"Thu Sep  1 15:58:58 EDT 2016"' -DSCORE_TYPE='int' -Wall \

    -I . -I ./libs/utility_lib -I ./libs/string_buffer \
    -I ./libs/bioinf -I ./libs/alignment_scoring \
    nw_cmdline.c needleman_wunsch.c \
    ./libs/alignment_scoring/*.c ./libs/utility_lib/utility_lib.c \
    ./libs/bioinf/bioinf.c ./libs/string_buffer/string_buffer.c -lz

gcc: error: unrecognized command line option '-fnested-functions'

make: *** [all] Error 1

[Zamin Iqbal]

Hi Allison

I think you need to get a unix person near you to help you follow Isaac's suggestions - looks like that is the issue.

regards

Zam