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:[EMAIL PROTECTED] Sent: 2007年2月14日 10:07 To: Mao, Jean (NIH/CIT) [E] Cc: [EMAIL PROTECTED] 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 _______________________________________________ EMBOSS mailing list [email protected] http://lists.open-bio.org/mailman/listinfo/emboss
