[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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