[EMBOSS] problem compiling EMBOSS-4.0.0
Jean Mao
maoj at helix.nih.gov
Wed Feb 14 15:53:09 UTC 2007
Based on the conversation I had below with Peter, I grep that patch and put
into $EMBOSS/ajax, make clean, make install and got the following this time
, Thank you for your help :
gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\"
-DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"EMBOSS\"
-DVERSION=\"4.0.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1
-DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1
-DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1
-DHAVE_DLFCN_H=1 -DHAVE_DIRENT_H=1 -DSTDC_HEADERS=1 -DHAVE_UNISTD_H=1
-DGETPGRP_VOID=1 -DHAVE_STRFTIME=1 -DHAVE_UNISTD_H=1 -DHAVE_FORK=1
-DHAVE_VFORK=1 -DHAVE_WORKING_VFORK=1 -DHAVE_WORKING_FORK=1 -DHAVE_VPRINTF=1
-DHAVE_MEMMOVE=1 -DHAVE_LIBM=1 -DPLD_png=1 -I. -I.
-DAJAX_FIXED_ROOT=\"/usr/local/EMBOSS-4.0.0.fix1-23/emboss\"
-DPREFIX=\"/usr/local/EMBOSS-4.0.0.fix1-23\" -I../plplot
-DPOSIX_MALLOC_THRESHOLD=10 -DAJ_LinuxLF -D_FILE_OFFSET_BITS=64
-D_LARGEFILE_SOURCE -D_LARGEFILE64_SOURCE -DLENDIAN -DNO_AUTH -O2
-D__amd64__ -MT ajreport.lo -MD -MP -MF .deps/ajreport.Tpo -c ajreport.c
-fPIC -DPIC -o .libs/ajreport.o
ajreport.c:2375: error: conflicting types for 'ajReportWrite'
ajreport.h:122: error: previous declaration of 'ajReportWrite' was here
ajreport.c:2375: error: conflicting types for 'ajReportWrite'
ajreport.h:122: error: previous declaration of 'ajReportWrite' was here
ajreport.c: In function `ajReportWrite':
ajreport.c:2390: error: structure has no member named `MaxHitAll'
ajreport.c:2392: error: structure has no member named `MaxHitAll'
ajreport.c:2399: error: structure has no member named `MaxHitSeq'
ajreport.c:2401: error: structure has no member named `MaxHitAll'
ajreport.c:2402: error: structure has no member named `MaxHitSeq'
ajreport.c:2402: error: structure has no member named `MaxHitSeq'
ajreport.c:2404: error: structure has no member named `MaxHitSeq'
ajreport.c:2409: error: structure has no member named `MaxHitSeq'
ajreport.c:2409: error: structure has no member named `MaxHitAll'
ajreport.c:2423: warning: assignment makes pointer from integer without a
cast
ajreport.c: In function `ajReportWriteHeader':
ajreport.c:2569: error: structure has no member named `MaxHitAll'
ajreport.c:2571: error: structure has no member named `MaxHitAll'
ajreport.c:2572: error: structure has no member named `MaxHitSeq'
ajreport.c:2574: error: structure has no member named `MaxHitSeq'
ajreport.c: In function `ajReportWriteTail':
ajreport.c:2723: error: structure has no member named `MaxHitAll'
ajreport.c:2724: error: structure has no member named `MaxHitAll'
ajreport.c: At top level:
ajreport.c:3061: error: conflicting types for 'ajReportAppendSubTail'
ajreport.c:2420: error: previous implicit declaration of
'ajReportAppendSubTail' was here
make[1]: *** [ajreport.lo] Error 1
make[1]: Leaving directory `/usr/local/EMBOSS-4.0.0.fix1-23/ajax'
make: *** [install-recursive] Error 1
-----Original Message-----
From: Peter Rice [mailto:pmr at ebi.ac.uk]
Sent: 2007年2月14日 10:07
To: Mao, Jean (NIH/CIT) [E]
Cc: emboss-bug at emboss.open-bio.org
Subject: 4.0 patch problem
Hi Jean
> I am working on patching EMBOSS 4.0 right now and run into some problems.
On my Linux machine:
>
> downloaded the patch1-23.gz file from your ftp site. then copy my
> current emboss tree to a different name. cd to that dir, then
>
> gunzip -c /somewhere/patch-1-X.gz | patch -p1
>
> I answered 'y' to all questions for those patches I previously applied.
>
> Then I modify the install directory in the configure file,
>
> ./configure
> make clean
> make install
>
> later, the following error appears. I attached the three files in case you
need them. Thank you very much!
>
> if /bin/sh ../libtool --tag=CC --mode=compile gcc -DPACKAGE_NAME=\"\"
-DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\"
-DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"EMBOSS\" -DVERSION=\"4.0.0\"
-DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1
-DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1
-DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DHAVE_DIRENT_H=1
-DSTDC_HEADERS=1 -DHAVE_UNISTD_H=1 -DGETPGRP_VOID=1 -DHAVE_STRFTIME=1
-DHAVE_UNISTD_H=1 -DHAVE_FORK=1 -DHAVE_VFORK=1 -DHAVE_WORKING_VFORK=1
-DHAVE_WORKING_FORK=1 -DHAVE_VPRINTF=1 -DHAVE_MEMMOVE=1 -DHAVE_LIBM=1
-DPLD_png=1 -I. -I.
-DAJAX_FIXED_ROOT=\"/usr/local/EMBOSS-4.0.0.fix1-23/emboss\"
-DPREFIX=\"/usr/local/EMBOSS-4.0.0.fix1-23\" -I../plplot
-DPOSIX_MALLOC_THRESHOLD=10 -DAJ_LinuxLF -D_FILE_OFFSET_BITS=64
-D_LARGEFILE_SOURCE -D_LARGEFILE64_SOURCE -DLENDIAN -DNO_AUTH -O2
-D__amd64__ -MT ajreport.lo -MD -MP -MF ".deps/ajreport.Tpo" -c -o ajreport.
lo
ajreport.c; \
> then mv -f ".deps/ajreport.Tpo" ".deps/ajreport.Plo"; else rm -f
> ".deps/ajreport.Tpo"; exit 1; fi gcc -DPACKAGE_NAME=\"\"
> -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\"
> -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"EMBOSS\" -DVERSION=\"4.0.0\"
> -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1
> -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1
> -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1
> -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DHAVE_DIRENT_H=1 -DSTDC_HEADERS=1
> -DHAVE_UNISTD_H=1 -DGETPGRP_VOID=1 -DHAVE_STRFTIME=1 -DHAVE_UNISTD_H=1
> -DHAVE_FORK=1 -DHAVE_VFORK=1 -DHAVE_WORKING_VFORK=1
> -DHAVE_WORKING_FORK=1 -DHAVE_VPRINTF=1 -DHAVE_MEMMOVE=1 -DHAVE_LIBM=1
> -DPLD_png=1 -I. -I.
> -DAJAX_FIXED_ROOT=\"/usr/local/EMBOSS-4.0.0.fix1-23/emboss\"
> -DPREFIX=\"/usr/local/EMBOSS-4.0.0.fix1-23\" -I../plplot
> -DPOSIX_MALLOC_THRESHOLD=10 -DAJ_LinuxLF -D_FILE_OFFSET_BITS=64
> -D_LARGEFILE_SOURCE -D_LARGEFILE64_SOURCE -DLENDIAN -DNO_AUTH -O2
> -D__amd64__ -MT ajreport.lo -MD -MP -MF .deps/ajreport.Tpo -c
> ajreport.c -fPIC -DPIC -o .libs/ajreport.o
> ajreport.c:137: warning: excess elements in struct initializer
> ajreport.c:137: warning: (near initialization for `reportFormat[0]')
> ajreport.c:139: warning: excess elements in struct initializer
> ajreport.c:139: warning: (near initialization for `reportFormat[1]')
> ajreport.c:141: warning: excess elements in struct initializer
> ajreport.c:141: warning: (near initialization for `reportFormat[2]')
> ajreport.c:143: warning: excess elements in struct initializer
> ajreport.c:143: warning: (near initialization for `reportFormat[3]')
> ajreport.c:145: warning: excess elements in struct initializer
> ajreport.c:145: warning: (near initialization for `reportFormat[4]')
> ajreport.c:148: warning: initialization makes pointer from integer
> without a cast
> ajreport.c:148: warning: excess elements in struct initializer
> ajreport.c:148: warning: (near initialization for `reportFormat[5]')
> ajreport.c:151: warning: initialization makes pointer from integer
> without a cast
> ajreport.c:151: warning: excess elements in struct initializer
> ajreport.c:151: warning: (near initialization for `reportFormat[6]')
> ajreport.c:154: warning: initialization makes pointer from integer
> without a cast
> ajreport.c:154: warning: excess elements in struct initializer
> ajreport.c:154: warning: (near initialization for `reportFormat[7]')
> ajreport.c:156: warning: initialization makes pointer from integer
> without a cast
> ajreport.c:156: warning: excess elements in struct initializer
> ajreport.c:156: warning: (near initialization for `reportFormat[8]')
> ajreport.c:161: warning: excess elements in struct initializer
> ajreport.c:161: warning: (near initialization for `reportFormat[9]')
> ajreport.c:163: warning: excess elements in struct initializer
> ajreport.c:163: warning: (near initialization for `reportFormat[10]')
> ajreport.c:165: warning: initialization makes pointer from integer
> without a cast
> ajreport.c:165: warning: excess elements in struct initializer
> ajreport.c:165: warning: (near initialization for `reportFormat[11]')
> ajreport.c:167: warning: initialization makes pointer from integer
> without a cast
> ajreport.c:167: warning: excess elements in struct initializer
> ajreport.c:167: warning: (near initialization for `reportFormat[12]')
> ajreport.c:169: warning: initialization makes pointer from integer
> without a cast
> ajreport.c:169: warning: excess elements in struct initializer
> ajreport.c:169: warning: (near initialization for `reportFormat[13]')
> ajreport.c:171: warning: initialization makes pointer from integer
> without a cast
> ajreport.c:171: warning: excess elements in struct initializer
> ajreport.c:171: warning: (near initialization for `reportFormat[14]')
> ajreport.c:173: warning: initialization makes pointer from integer
> without a cast
> ajreport.c:173: warning: excess elements in struct initializer
> ajreport.c:173: warning: (near initialization for `reportFormat[15]')
> ajreport.c:175: warning: initialization makes pointer from integer
> without a cast
> ajreport.c:175: warning: excess elements in struct initializer
> ajreport.c:175: warning: (near initialization for `reportFormat[16]')
> ajreport.c:177: warning: initialization makes pointer from integer
> without a cast
> ajreport.c:177: warning: excess elements in struct initializer
> ajreport.c:177: warning: (near initialization for `reportFormat[17]')
> ajreport.c:179: warning: initialization makes pointer from integer
> without a cast
> ajreport.c:179: warning: excess elements in struct initializer
> ajreport.c:179: warning: (near initialization for `reportFormat[18]')
> ajreport.c:180: warning: excess elements in struct initializer
> ajreport.c:180: warning: (near initialization for `reportFormat[19]')
> ajreport.c: In function `ajReportNew':
> ajreport.c:2342: error: structure has no member named `Count'
> ajreport.c: In function `ajReportWriteHeader':
> ajreport.c:2488: error: structure has no member named `Count'
> make[1]: *** [ajreport.lo] Error 1
> make[1]: Leaving directory `/usr/local/EMBOSS-4.0.0.fix1-23/ajax'
> make: *** [install-recursive] Error 1
ajax/ajreport.h and ajax/ajreport.c do not match. Perhaps one patch did not
get applied.
I think ajreport.c is out of date. The structure should have CountSeq and
CountHit. In the original 4.0.0 it only had Count.
You will find a new ajreport.c on the ftp server, or you can try to reapply
the patches.
Hope that helps. I am away for the next few days so please mail emboss-bug
in case I have problems getting to my email.
regards,
Peter
More information about the EMBOSS
mailing list