[ome-users] Compilation problem...

Claude Bonnard cbonnard at isrec-sg1.unil.ch
Thu Feb 23 12:51:31 GMT 2006


Hello,

Installing Stable release 2.4.0 did not temrinate smoothly, but correction of
the problem is not obvious for me...

Help!...
...and thanks!

Claude

Enclosed: BinaryBuilds.log

-- 
Claude Bonnard Ph.D.
ISREC (Swiss Institute for Experimental Cancer Research)
Microscopy, Imaging and Morphology Core Facility [MIM] 
Lab F216
Ch des Boveresses 155
CH-1066 Epalinges
Switzerland
email: claude.bonnard at isrec.unil.ch
phone: [41-21]-692-5891
  fax: [41-21]-652-6933
-------------- next part --------------
COMPILING MODULE -- 'make'
SUCCESS -- OUTPUT: "make -C cgrayce
 make[1]: Entering directory `/home/ome/OME/src/C/cgrayce'
 make[1]: Nothing to be done for `all'.
 make[1]: Leaving directory `/home/ome/OME/src/C/cgrayce'
"

INSTALLING MODULE -- 'make install'
SUCCESS -- OUTPUT: "install -d /OME
 install -d /OME/bin
 install -d /OME/bin/findSpots
 install -c findSpotsOME /OME/bin/findSpots/findSpotsOME
 install -c findSpotsOME /OME/bin/findSpots/findSpots
 install -d /OME/bin/BinarizeGlobal
 install -c BinarizeGlobal /OME/bin/BinarizeGlobal/BinarizeGlobal
 install -c DumpTIFFheader /OME/bin/DumpTIFFheader
 install -c DumpTIFFstats /OME/bin/DumpTIFFstats
 install -c OME_Image_XYZ_stats /OME/bin/OME_Image_XYZ_stats
 install -c OME_Image_XYZ_fastStats /OME/bin/OME_Image_XYZ_fastStats
 install -c OME_Image_XY_stats /OME/bin/OME_Image_XY_stats
 install -c OME_Image_XY_sums /OME/bin/OME_Image_XY_sums
 install -c SoftWorxSlice /OME/bin/SoftWorxSlice
 install -c DumpSoftWorxHeader /OME/bin/DumpSoftWorxHeader
 install -c DumpSoftWorxExHeader /OME/bin/DumpSoftWorxExHeader
 install -c DumpSoftWorxStats /OME/bin/DumpSoftWorxStats
 install -c maxIntensity /OME/bin/maxIntensity
 install -d /usr/local/bin
 install -c DumpDV /usr/local/bin/DumpDV
 install -c SetDVwave /usr/local/bin/SetDVwave
 make -C cgrayce install
 make[1]: Entering directory `/home/ome/OME/src/C/cgrayce'
 install -c ome_cccp /OME/bin/ome_cccp
 install -c ome_tmcp /OME/bin/ome_tmcp
 make[1]: Leaving directory `/home/ome/OME/src/C/cgrayce'
"

USING C CONFIGURE SCRIPT -- './configure --prefix=/OME --with-omeis-root=/OME/OMEIS'
SUCCESS -- OUTPUT: "checking for a BSD-compatible install... /usr/bin/install -c
 checking whether build environment is sane... yes
 checking for gawk... gawk
 checking whether make sets $(MAKE)... yes
 checking build system type... i686-pc-linux-gnu
 checking host system type... i686-pc-linux-gnu
 checking for gcc... gcc
 checking for C compiler default output file name... a.out
 checking whether the C compiler works... yes
 checking whether we are cross compiling... no
 checking for suffix of executables... 
 checking for suffix of object files... o
 checking whether we are using the GNU C compiler... yes
 checking whether gcc accepts -g... yes
 checking for gcc option to accept ANSI C... none needed
 checking for style of include used by make... GNU
 checking dependency style of gcc... gcc3
 checking for a BSD-compatible install... /usr/bin/install -c
 checking whether make sets $(MAKE)... (cached) yes
 checking for ranlib... ranlib
 configure: using OMEIS root... /OME/OMEIS
 configure: using OMEIS JPEG quality default... 80
 checking for special C compiler options needed for large files... no
 checking for _FILE_OFFSET_BITS value needed for large files... 64
 checking for _LARGE_FILES value needed for large files... no
 checking for BZ2_bzDecompress in -lbz2... yes
 checking how to run the C preprocessor... gcc -E
 checking for egrep... grep -E
 checking for ANSI C header files... yes
 checking for sys/types.h... yes
 checking for sys/stat.h... yes
 checking for stdlib.h... yes
 checking for string.h... yes
 checking for memory.h... yes
 checking for strings.h... yes
 checking for inttypes.h... yes
 checking for stdint.h... yes
 checking for unistd.h... yes
 checking bzlib.h usability... yes
 checking bzlib.h presence... yes
 checking for bzlib.h... yes
 checking for png_init_io in -lpng... yes
 checking png.h usability... yes
 checking png.h presence... yes
 checking for png.h... yes
 checking for jpeg_start_compress in -ljpeg... yes
 checking jpeglib.h usability... yes
 checking jpeglib.h presence... yes
 checking for jpeglib.h... yes
 checking for TIFFReadScanline in -ltiff... yes
 checking tiffio.h usability... yes
 checking tiffio.h presence... yes
 checking for tiffio.h... yes
 checking if ssl is wanted... yes
 OpenSSL found in /usr
 checking if zlib is wanted... yes
 checking for inflateEnd in -lz... yes
 checking zlib.h usability... yes
 checking zlib.h presence... yes
 checking for zlib.h... yes
 checking for inflateEnd in -lz... (cached) yes
 checking zlib in /usr... ok
 checking for compat version of Berkeley DB... /usr/include/db_185.h
 checking for Berkeley DB usability... yes
 checking for LZW encoder in -ltiff... yes
 checking for ANSI C header files... (cached) yes
 checking fcntl.h usability... yes
 checking fcntl.h presence... yes
 checking for fcntl.h... yes
 checking limits.h usability... yes
 checking limits.h presence... yes
 checking for limits.h... yes
 checking sys/time.h usability... yes
 checking sys/time.h presence... yes
 checking for sys/time.h... yes
 checking for unistd.h... (cached) yes
 checking for an ANSI C-conforming const... yes
 checking for off_t... yes
 checking for size_t... yes
 checking for stdlib.h... (cached) yes
 checking for unistd.h... (cached) yes
 checking for getpagesize... yes
 checking for working mmap... yes
 checking for vprintf... yes
 checking for _doprnt... no
 checking for mkdir... yes
 checking for socket... yes
 checking for strdup... yes
 checking for strerror... yes
 checking for strstr... yes
 configure: creating ./config.status
 config.status: creating Makefile
 config.status: creating zoom/Makefile
 config.status: creating zoom/lib/Makefile
 config.status: creating config.h
 config.status: config.h is unchanged
 config.status: executing depfiles commands
"

COMPILING MODULE -- 'make'
FAILURE -- OUTPUT: "make  all-recursive
 make[1]: Entering directory `/home/ome/OME/src/C/omeis'
 Making all in zoom
 make[2]: Entering directory `/home/ome/OME/src/C/omeis/zoom'
 Making all in lib
 make[3]: Entering directory `/home/ome/OME/src/C/omeis/zoom/lib'
 source='window.c' object='window.o' libtool=no \
 depfile='.deps/window.Po' tmpdepfile='.deps/window.TPo' \
 depmode=gcc3 /bin/sh ../../depcomp \
 gcc -DHAVE_CONFIG_H -I. -I. -I../..  -DOMEIS_ROOT=\"/OME/OMEIS\" -I../include -I/usr/include/libxml2 -I/usr/include  -g -O2 -I/usr/include/openssl -DHAVE_SSL -I/usr/include -c `test -f 'window.c' || echo './'`window.c
 source='pic.c' object='pic.o' libtool=no \
 depfile='.deps/pic.Po' tmpdepfile='.deps/pic.TPo' \
 depmode=gcc3 /bin/sh ../../depcomp \
 gcc -DHAVE_CONFIG_H -I. -I. -I../..  -DOMEIS_ROOT=\"/OME/OMEIS\" -I../include -I/usr/include/libxml2 -I/usr/include  -g -O2 -I/usr/include/openssl -DHAVE_SSL -I/usr/include -c `test -f 'pic.c' || echo './'`pic.c
 source='pic_file.c' object='pic_file.o' libtool=no \
 depfile='.deps/pic_file.Po' tmpdepfile='.deps/pic_file.TPo' \
 depmode=gcc3 /bin/sh ../../depcomp \
 gcc -DHAVE_CONFIG_H -I. -I. -I../..  -DOMEIS_ROOT=\"/OME/OMEIS\" -I../include -I/usr/include/libxml2 -I/usr/include  -g -O2 -I/usr/include/openssl -DHAVE_SSL -I/usr/include -c `test -f 'pic_file.c' || echo './'`pic_file.c
 source='pic_all.c' object='pic_all.o' libtool=no \
 depfile='.deps/pic_all.Po' tmpdepfile='.deps/pic_all.TPo' \
 depmode=gcc3 /bin/sh ../../depcomp \
 gcc -DHAVE_CONFIG_H -I. -I. -I../..  -DOMEIS_ROOT=\"/OME/OMEIS\" -I../include -I/usr/include/libxml2 -I/usr/include  -g -O2 -I/usr/include/openssl -DHAVE_SSL -I/usr/include -c `test -f 'pic_all.c' || echo './'`pic_all.c
 source='swap.c' object='swap.o' libtool=no \
 depfile='.deps/swap.Po' tmpdepfile='.deps/swap.TPo' \
 depmode=gcc3 /bin/sh ../../depcomp \
 gcc -DHAVE_CONFIG_H -I. -I. -I../..  -DOMEIS_ROOT=\"/OME/OMEIS\" -I../include -I/usr/include/libxml2 -I/usr/include  -g -O2 -I/usr/include/openssl -DHAVE_SSL -I/usr/include -c `test -f 'swap.c' || echo './'`swap.c
 source='tiff.c' object='tiff.o' libtool=no \
 depfile='.deps/tiff.Po' tmpdepfile='.deps/tiff.TPo' \
 depmode=gcc3 /bin/sh ../../depcomp \
 gcc -DHAVE_CONFIG_H -I. -I. -I../..  -DOMEIS_ROOT=\"/OME/OMEIS\" -I../include -I/usr/include/libxml2 -I/usr/include  -g -O2 -I/usr/include/openssl -DHAVE_SSL -I/usr/include -c `test -f 'tiff.c' || echo './'`tiff.c
 source='jpeg.c' object='jpeg.o' libtool=no \
 depfile='.deps/jpeg.Po' tmpdepfile='.deps/jpeg.TPo' \
 depmode=gcc3 /bin/sh ../../depcomp \
 gcc -DHAVE_CONFIG_H -I. -I. -I../..  -DOMEIS_ROOT=\"/OME/OMEIS\" -I../include -I/usr/include/libxml2 -I/usr/include  -g -O2 -I/usr/include/openssl -DHAVE_SSL -I/usr/include -c `test -f 'jpeg.c' || echo './'`jpeg.c
 source='png.c' object='png.o' libtool=no \
 depfile='.deps/png.Po' tmpdepfile='.deps/png.TPo' \
 depmode=gcc3 /bin/sh ../../depcomp \
 gcc -DHAVE_CONFIG_H -I. -I. -I../..  -DOMEIS_ROOT=\"/OME/OMEIS\" -I../include -I/usr/include/libxml2 -I/usr/include  -g -O2 -I/usr/include/openssl -DHAVE_SSL -I/usr/include -c `test -f 'png.c' || echo './'`png.c
 source='omeis.c' object='omeis.o' libtool=no \
 depfile='.deps/omeis.Po' tmpdepfile='.deps/omeis.TPo' \
 depmode=gcc3 /bin/sh ../../depcomp \
 gcc -DHAVE_CONFIG_H -I. -I. -I../..  -DOMEIS_ROOT=\"/OME/OMEIS\" -I../include -I/usr/include/libxml2 -I/usr/include  -g -O2 -I/usr/include/openssl -DHAVE_SSL -I/usr/include -c `test -f 'omeis.c' || echo './'`omeis.c
 rm -f libpic.a
 ar cru libpic.a window.o pic.o pic_file.o pic_all.o swap.o tiff.o jpeg.o png.o omeis.o 
 ranlib libpic.a
 source='zoom.c' object='zoom.o' libtool=no \
 depfile='.deps/zoom.Po' tmpdepfile='.deps/zoom.TPo' \
 depmode=gcc3 /bin/sh ../../depcomp \
 gcc -DHAVE_CONFIG_H -I. -I. -I../..  -DOMEIS_ROOT=\"/OME/OMEIS\" -I../include -I/usr/include/libxml2 -I/usr/include  -g -O2 -I/usr/include/openssl -DHAVE_SSL -I/usr/include -c `test -f 'zoom.c' || echo './'`zoom.c
 source='scanline.c' object='scanline.o' libtool=no \
 depfile='.deps/scanline.Po' tmpdepfile='.deps/scanline.TPo' \
 depmode=gcc3 /bin/sh ../../depcomp \
 gcc -DHAVE_CONFIG_H -I. -I. -I../..  -DOMEIS_ROOT=\"/OME/OMEIS\" -I../include -I/usr/include/libxml2 -I/usr/include  -g -O2 -I/usr/include/openssl -DHAVE_SSL -I/usr/include -c `test -f 'scanline.c' || echo './'`scanline.c
 scanline.c: In function ‘scanline_zero’:
 scanline.c:98: warning: incompatible implicit declaration of built-in function ‘bzero’
 source='filt.c' object='filt.o' libtool=no \
 depfile='.deps/filt.Po' tmpdepfile='.deps/filt.TPo' \
 depmode=gcc3 /bin/sh ../../depcomp \
 gcc -DHAVE_CONFIG_H -I. -I. -I../..  -DOMEIS_ROOT=\"/OME/OMEIS\" -I../include -I/usr/include/libxml2 -I/usr/include  -g -O2 -I/usr/include/openssl -DHAVE_SSL -I/usr/include -c `test -f 'filt.c' || echo './'`filt.c
 rm -f libzoom.a
 ar cru libzoom.a zoom.o scanline.o filt.o 
 ranlib libzoom.a
 make[3]: Leaving directory `/home/ome/OME/src/C/omeis/zoom/lib'
 make[3]: Entering directory `/home/ome/OME/src/C/omeis/zoom'
 make[3]: Nothing to be done for `all-am'.
 make[3]: Leaving directory `/home/ome/OME/src/C/omeis/zoom'
 make[2]: Leaving directory `/home/ome/OME/src/C/omeis/zoom'
 make[2]: Entering directory `/home/ome/OME/src/C/omeis'
 source='File.c' object='File.o' libtool=no \
 depfile='.deps/File.Po' tmpdepfile='.deps/File.TPo' \
 depmode=gcc3 /bin/sh ./depcomp \
 gcc -DHAVE_CONFIG_H -I. -I. -I.  -DOMEIS_ROOT=\"/OME/OMEIS\" -Izoom/include -I/usr/include/libxml2 -I/usr/include  -g -O2 -I/usr/include/openssl -DHAVE_SSL -I/usr/include -c `test -f 'File.c' || echo './'`File.c
 File.c: In function ‘ExpungeFile’:
 File.c:214: warning: pointer targets in passing argument 2 of ‘sha1DB_get’ differ in signedness
 File.c:215: warning: pointer targets in passing argument 2 of ‘sha1DB_del’ differ in signedness
 File.c:370: warning: pointer targets in passing argument 2 of ‘sha1DB_get’ differ in signedness
 File.c:371: warning: pointer targets in passing argument 2 of ‘sha1DB_del’ differ in signedness
 File.c:372: warning: pointer targets in passing argument 2 of ‘sha1DB_put’ differ in signedness
 File.c: In function ‘get_rel_path’:
 File.c:913: warning: assignment discards qualifiers from pointer target type
 File.c:916: warning: assignment discards qualifiers from pointer target type
 File.c: In function ‘FinishFile’:
 File.c:957: warning: pointer targets in passing argument 3 of ‘get_md_from_buffer’ differ in signedness
 File.c:970: warning: pointer targets in passing argument 2 of ‘sha1DB_get’ differ in signedness
 File.c:1035: warning: pointer targets in passing argument 2 of ‘sha1DB_put’ differ in signedness
 source='Pixels.c' object='Pixels.o' libtool=no \
 depfile='.deps/Pixels.Po' tmpdepfile='.deps/Pixels.TPo' \
 depmode=gcc3 /bin/sh ./depcomp \
 gcc -DHAVE_CONFIG_H -I. -I. -I.  -DOMEIS_ROOT=\"/OME/OMEIS\" -Izoom/include -I/usr/include/libxml2 -I/usr/include  -g -O2 -I/usr/include/openssl -DHAVE_SSL -I/usr/include -c `test -f 'Pixels.c' || echo './'`Pixels.c
 Pixels.c: In function ‘ScalePixels’:
 Pixels.c:1194: warning: pointer targets in assignment differ in signedness
 source='OMEIS_Error.c' object='OMEIS_Error.o' libtool=no \
 depfile='.deps/OMEIS_Error.Po' tmpdepfile='.deps/OMEIS_Error.TPo' \
 depmode=gcc3 /bin/sh ./depcomp \
 gcc -DHAVE_CONFIG_H -I. -I. -I.  -DOMEIS_ROOT=\"/OME/OMEIS\" -Izoom/include -I/usr/include/libxml2 -I/usr/include  -g -O2 -I/usr/include/openssl -DHAVE_SSL -I/usr/include -c `test -f 'OMEIS_Error.c' || echo './'`OMEIS_Error.c
 OMEIS_Error.c:51: error: static declaration of ‘OMEIS_ERROR_STR’ follows non-static declaration
 OMEIS_Error.h:69: error: previous declaration of ‘OMEIS_ERROR_STR’ was here
 make[2]: *** [OMEIS_Error.o] Error 1
 make[2]: Leaving directory `/home/ome/OME/src/C/omeis'
 make[1]: *** [all-recursive] Error 1
 make[1]: Leaving directory `/home/ome/OME/src/C/omeis'
 make: *** [all] Error 2
"



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