error during compilation - code may need update with gcc 10.2.0?

[kinestetika]

While making pullseq with gcc 10.2.0, I got the following error during linking: ... gcc -g -O2 -o pullseq hash.o output.o size_filter.o search_header.o file_read.o pull_by_re.o pull_by_name.o pull_by_size.o pullseq.o -lpcre -lz /usr/bin/ld: output.o:/home/kinestetika/bin/util/pullseq/src/global.h:27: multiple definition of QUALITY_SCORE'; hash.o:/home/kinestetika/bin/util/pullseq/src/global.h:27: first defined here /usr/bin/ld: output.o:/home/kinestetika/bin/util/pullseq/src/global.h:28: multiple definition of verbose_flag'; hash.o:/home/kinestetika/bin/util/pullseq/src/global.h:28: first defined here /usr/bin/ld: output.o:/home/kinestetika/bin/util/pullseq/src/global.h:26: multiple definition of progname'; hash.o:/home/kinestetika/bin/util/pullseq/src/global.h:26: first defined here /usr/bin/ld: size_filter.o:/home/kinestetika/bin/util/pullseq/src/global.h:28: multiple definition of verbose_flag'; hash.o:/home/kinestetika/bin/util/pullseq/src/global.h:28: first defined here /usr/bin/ld: size_filter.o:/home/kinestetika/bin/util/pullseq/src/global.h:27: multiple definition of QUALITY_SCORE'; hash.o:/home/kinestetika/bin/util/pullseq/src/global.h:27: first defined here /usr/bin/ld: size_filter.o:/home/kinestetika/bin/util/pullseq/src/global.h:26: multiple definition of progname'; hash.o:/home/kinestetika/bin/util/pullseq/src/global.h:26: first defined here /usr/bin/ld: search_header.o:/home/kinestetika/bin/util/pullseq/src/global.h:28: multiple definition of verbose_flag'; hash.o:/home/kinestetika/bin/util/pullseq/src/global.h:28: first defined here /usr/bin/ld: search_header.o:/home/kinestetika/bin/util/pullseq/src/global.h:27: multiple definition of QUALITY_SCORE'; hash.o:/home/kinestetika/bin/util/pullseq/src/global.h:27: first defined here /usr/bin/ld: search_header.o:/home/kinestetika/bin/util/pullseq/src/global.h:26: multiple definition of progname'; hash.o:/home/kinestetika/bin/util/pullseq/src/global.h:26: first defined here /usr/bin/ld: file_read.o:/home/kinestetika/bin/util/pullseq/src/global.h:28: multiple definition of verbose_flag'; hash.o:/home/kinestetika/bin/util/pullseq/src/global.h:28: first defined here /usr/bin/ld: file_read.o:/home/kinestetika/bin/util/pullseq/src/global.h:27: multiple definition of QUALITY_SCORE'; hash.o:/home/kinestetika/bin/util/pullseq/src/global.h:27: first defined here /usr/bin/ld: file_read.o:/home/kinestetika/bin/util/pullseq/src/global.h:26: multiple definition of progname'; hash.o:/home/kinestetika/bin/util/pullseq/src/global.h:26: first defined here /usr/bin/ld: pull_by_re.o:/home/kinestetika/bin/util/pullseq/src/global.h:28: multiple definition of verbose_flag'; hash.o:/home/kinestetika/bin/util/pullseq/src/global.h:28: first defined here /usr/bin/ld: pull_by_re.o:/home/kinestetika/bin/util/pullseq/src/global.h:26: multiple definition of progname'; hash.o:/home/kinestetika/bin/util/pullseq/src/global.h:26: first defined here /usr/bin/ld: pull_by_re.o:/home/kinestetika/bin/util/pullseq/src/global.h:27: multiple definition of QUALITY_SCORE'; hash.o:/home/kinestetika/bin/util/pullseq/src/global.h:27: first defined here /usr/bin/ld: pull_by_name.o:/home/kinestetika/bin/util/pullseq/src/global.h:28: multiple definition of verbose_flag'; hash.o:/home/kinestetika/bin/util/pullseq/src/global.h:28: first defined here /usr/bin/ld: pull_by_name.o:/home/kinestetika/bin/util/pullseq/src/global.h:26: multiple definition of progname'; hash.o:/home/kinestetika/bin/util/pullseq/src/global.h:26: first defined here /usr/bin/ld: pull_by_name.o:/home/kinestetika/bin/util/pullseq/src/global.h:27: multiple definition of QUALITY_SCORE'; hash.o:/home/kinestetika/bin/util/pullseq/src/global.h:27: first defined here /usr/bin/ld: pull_by_size.o:/home/kinestetika/bin/util/pullseq/src/global.h:28: multiple definition of verbose_flag'; hash.o:/home/kinestetika/bin/util/pullseq/src/global.h:28: first defined here /usr/bin/ld: pull_by_size.o:/home/kinestetika/bin/util/pullseq/src/global.h:26: multiple definition of progname'; hash.o:/home/kinestetika/bin/util/pullseq/src/global.h:26: first defined here /usr/bin/ld: pull_by_size.o:/home/kinestetika/bin/util/pullseq/src/global.h:27: multiple definition of QUALITY_SCORE'; hash.o:/home/kinestetika/bin/util/pullseq/src/global.h:27: first defined here /usr/bin/ld: pullseq.o:/home/kinestetika/bin/util/pullseq/src/global.h:26: multiple definition of progname'; hash.o:/home/kinestetika/bin/util/pullseq/src/global.h:26: first defined here /usr/bin/ld: pullseq.o:/home/kinestetika/bin/util/pullseq/src/global.h:28: multiple definition of verbose_flag'; hash.o:/home/kinestetika/bin/util/pullseq/src/global.h:28: first defined here /usr/bin/ld: pullseq.o:/home/kinestetika/bin/util/pullseq/src/global.h:27: multiple definition of QUALITY_SCORE'; hash.o:/home/kinestetika/bin/util/pullseq/src/global.h:27: first defined here collect2: error: ld returned 1 exit status make[2]: *** [Makefile:376: pullseq] Error 1 make[2]: Leaving directory '/home/kinestetika/bin/util/pullseq/src' make[1]: *** [Makefile:283: all] Error 2 make[1]: Leaving directory '/home/kinestetika/bin/util/pullseq/src' make: *** [Makefile:344: all-recursive] Error 1

[ItIsI-Orient]

Adding -fcommon to CFLAGS resolved this issue for me

[GerardTromp]

Modern C standards require declaration of the variables in a header (.h) file as extern <variable> and then only define the variables in one code (.c) file.

Here is a patch file that cleans this up -- the final code still needs the commented out variable deleted to make it really clean. I left them in as a learning tool for my student(s).

I have modified the patchfile, it was causing some hiccups when applying. patch -s -p0 < pullseq20230119.patch now works flawlessly. pullseq20230119.patch