218233 2008-04-18 09:05 0000 sci-biology/ncbi-tools-20060507: cannot compile against openmotif-2.3.0-r1 2008-04-22 00:23:35 0000 1 1 1 Unclassified Gentoo Linux Applications unspecified All Linux RESOLVED FIXED P2 normal --- 1 mmokrejs@ribosome.natur.cuni.cz ribosome@gentoo.org amd64@gentoo.org sci-biology@gentoo.org ulm@gentoo.org mmokrejs@ribosome.natur.cuni.cz 2008-04-18 09:05:52 0000 The compilation step on amd64 fails with: x86_64-pc-linux-gnu-gcc -pipe -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -o Psequin -I. -O2 -march=nocona -fomit-frame-pointer -pipe -I../include -L../lib -I/usr/X11R6/include -L/usr/X11R6/lib -DWIN_MOTIF -UINTERNAL_NCBI_SEQUIN sequin1.c sequin2.c sequin3.c sequin4.c sequin5.c sequin6.c sequin7.c sequin8.c sequin9.c sequin10.c sequinx.c -lncbicn3d -lddvlib -lvibnet -lncbidesk -lblastapi -lblast -lncbimmdb -lncbitxc2 -lncbiid1 -lnetblast -lncbitool -lblastcompadj -lncbimla -lncbiNacc -lnetentr -lnetcli -lncbicdr -lvibrant -lncbiobj -lncbi -L/usr/X11R6/lib -lXmu -Wl,-Bstatic -lXm -Wl,-Bdynamic -lXt -lSM -lICE -lXext -lXp -lX11 -ldl -lm sequin3.c: In function 'AddBlastTag': sequin3.c:14805: warning: cast from pointer to integer of different size sequin3.c: In function 'CommonAddBlastToSeqAnnot': sequin3.c:14830: warning: cast to pointer from integer of different size sequin9.c: In function 'UpdatePairToUpdateTitlesDialog': sequin9.c:13974: warning: large integer implicitly truncated to unsigned type sequin9.c:13995: warning: large integer implicitly truncated to unsigned type sequin9.c:14015: warning: large integer implicitly truncated to unsigned type sequin9.c:14030: warning: large integer implicitly truncated to unsigned type ../lib/libncbi.a(ncbifile.o): In function `Nlm_TmpNam': ncbifile.c:(.text+0x153): warning: the use of `tempnam' is dangerous, better use `mkstemp' /usr/lib/gcc/x86_64-pc-linux-gnu/4.1.2/../../../../lib64/libXm.a(Jpeg.o): In function `load_jpeg': (.text+0x1a8): undefined reference to `jpeg_std_error' /usr/lib/gcc/x86_64-pc-linux-gnu/4.1.2/../../../../lib64/libXm.a(Jpeg.o): In function `load_jpeg': (.text+0x1d6): undefined reference to `jpeg_destroy_decompress' /usr/lib/gcc/x86_64-pc-linux-gnu/4.1.2/../../../../lib64/libXm.a(Jpeg.o): In function `load_jpeg': (.text+0x1fc): undefined reference to `jpeg_CreateDecompress' /usr/lib/gcc/x86_64-pc-linux-gnu/4.1.2/../../../../lib64/libXm.a(Jpeg.o): In function `load_jpeg': (.text+0x209): undefined reference to `jpeg_stdio_src' /usr/lib/gcc/x86_64-pc-linux-gnu/4.1.2/../../../../lib64/libXm.a(Jpeg.o): In function `load_jpeg': (.text+0x216): undefined reference to `jpeg_read_header' /usr/lib/gcc/x86_64-pc-linux-gnu/4.1.2/../../../../lib64/libXm.a(Jpeg.o): In function `load_jpeg': (.text+0x21e): undefined reference to `jpeg_calc_output_dimensions' /usr/lib/gcc/x86_64-pc-linux-gnu/4.1.2/../../../../lib64/libXm.a(Jpeg.o): In function `load_jpeg': (.text+0x226): undefined reference to `jpeg_start_decompress' /usr/lib/gcc/x86_64-pc-linux-gnu/4.1.2/../../../../lib64/libXm.a(Jpeg.o): In function `load_jpeg': (.text+0x28b): undefined reference to `jpeg_read_scanlines' /usr/lib/gcc/x86_64-pc-linux-gnu/4.1.2/../../../../lib64/libXm.a(Jpeg.o): In function `load_jpeg': (.text+0x2c2): undefined reference to `jpeg_finish_decompress' /usr/lib/gcc/x86_64-pc-linux-gnu/4.1.2/../../../../lib64/libXm.a(Jpeg.o): In function `load_jpeg': (.text+0x2ca): undefined reference to `jpeg_destroy_decompress' /usr/lib/gcc/x86_64-pc-linux-gnu/4.1.2/../../../../lib64/libXm.a(Png.o): In function `png_load_file': (.text+0x7d): undefined reference to `png_check_sig' /usr/lib/gcc/x86_64-pc-linux-gnu/4.1.2/../../../../lib64/libXm.a(Png.o): In function `png_load_file': (.text+0x95): undefined reference to `png_create_read_struct' /usr/lib/gcc/x86_64-pc-linux-gnu/4.1.2/../../../../lib64/libXm.a(Png.o): In function `png_load_file': (.text+0xaa): undefined reference to `png_create_info_struct' /usr/lib/gcc/x86_64-pc-linux-gnu/4.1.2/../../../../lib64/libXm.a(Png.o): In function `png_load_file': (.text+0xc8): undefined reference to `png_destroy_read_struct' /usr/lib/gcc/x86_64-pc-linux-gnu/4.1.2/../../../../lib64/libXm.a(Png.o): In function `png_load_file': (.text+0x10b): undefined reference to `png_destroy_read_struct' /usr/lib/gcc/x86_64-pc-linux-gnu/4.1.2/../../../../lib64/libXm.a(Png.o): In function `png_load_file': (.text+0x130): undefined reference to `png_init_io' /usr/lib/gcc/x86_64-pc-linux-gnu/4.1.2/../../../../lib64/libXm.a(Png.o): In function `png_load_file': (.text+0x142): undefined reference to `png_set_sig_bytes' /usr/lib/gcc/x86_64-pc-linux-gnu/4.1.2/../../../../lib64/libXm.a(Png.o): In function `png_load_file': (.text+0x157): undefined reference to `png_read_info' /usr/lib/gcc/x86_64-pc-linux-gnu/4.1.2/../../../../lib64/libXm.a(Png.o): In function `png_load_file': (.text+0x1a3): undefined reference to `png_get_IHDR' /usr/lib/gcc/x86_64-pc-linux-gnu/4.1.2/../../../../lib64/libXm.a(Png.o): In function `png_load_file': (.text+0x202): undefined reference to `png_get_valid' /usr/lib/gcc/x86_64-pc-linux-gnu/4.1.2/../../../../lib64/libXm.a(Png.o): In function `png_load_file': (.text+0x24c): undefined reference to `png_get_valid' /usr/lib/gcc/x86_64-pc-linux-gnu/4.1.2/../../../../lib64/libXm.a(Png.o): In function `png_load_file': (.text+0x295): undefined reference to `png_get_gAMA' /usr/lib/gcc/x86_64-pc-linux-gnu/4.1.2/../../../../lib64/libXm.a(Png.o): In function `png_load_file': (.text+0x2b3): undefined reference to `png_read_update_info' /usr/lib/gcc/x86_64-pc-linux-gnu/4.1.2/../../../../lib64/libXm.a(Png.o): In function `png_load_file': (.text+0x2c8): undefined reference to `png_get_rowbytes' /usr/lib/gcc/x86_64-pc-linux-gnu/4.1.2/../../../../lib64/libXm.a(Png.o): In function `png_load_file': (.text+0x2eb): undefined reference to `png_get_channels' /usr/lib/gcc/x86_64-pc-linux-gnu/4.1.2/../../../../lib64/libXm.a(Png.o): In function `png_load_file': (.text+0x331): undefined reference to `png_destroy_read_struct' /usr/lib/gcc/x86_64-pc-linux-gnu/4.1.2/../../../../lib64/libXm.a(Png.o): In function `png_load_file': (.text+0x348): undefined reference to `png_set_gray_to_rgb' /usr/lib/gcc/x86_64-pc-linux-gnu/4.1.2/../../../../lib64/libXm.a(Png.o): In function `png_load_file': (.text+0x35a): undefined reference to `png_set_expand' /usr/lib/gcc/x86_64-pc-linux-gnu/4.1.2/../../../../lib64/libXm.a(Png.o): In function `png_load_file': (.text+0x3b9): undefined reference to `png_set_gamma' /usr/lib/gcc/x86_64-pc-linux-gnu/4.1.2/../../../../lib64/libXm.a(Png.o): In function `png_load_file': (.text+0x3ec): undefined reference to `png_destroy_read_struct' /usr/lib/gcc/x86_64-pc-linux-gnu/4.1.2/../../../../lib64/libXm.a(Png.o): In function `png_load_file': (.text+0x422): undefined reference to `png_set_strip_16' /usr/lib/gcc/x86_64-pc-linux-gnu/4.1.2/../../../../lib64/libXm.a(Png.o): In function `png_load_file': (.text+0x441): undefined reference to `png_get_bKGD' /usr/lib/gcc/x86_64-pc-linux-gnu/4.1.2/../../../../lib64/libXm.a(Png.o): In function `png_load_file': (.text+0x4aa): undefined reference to `png_set_expand' /usr/lib/gcc/x86_64-pc-linux-gnu/4.1.2/../../../../lib64/libXm.a(Png.o): In function `png_load_file': (.text+0x4bc): undefined reference to `png_set_expand' /usr/lib/gcc/x86_64-pc-linux-gnu/4.1.2/../../../../lib64/libXm.a(Png.o): In function `png_load_file': (.text+0x530): undefined reference to `png_read_image' /usr/lib/gcc/x86_64-pc-linux-gnu/4.1.2/../../../../lib64/libXm.a(Png.o): In function `png_load_file': (.text+0x547): undefined reference to `png_read_end' /usr/lib/gcc/x86_64-pc-linux-gnu/4.1.2/../../../../lib64/libXm.a(Png.o): In function `png_load_file': (.text+0x574): undefined reference to `png_destroy_read_struct' collect2: ld returned 1 exit status *** Error code 1 Stop. pmake: stopped in /var/tmp/portage/sci-biology/ncbi-tools-20060507/work/ncbi/build This problem does not happen with sci-biology/ncbi-tools-20080302. Please stabilize this version for amd64. jer@gentoo.org 2008-04-18 13:12:43 0000 Please provide your emerge --info as well. ribosome@gentoo.org 2008-04-22 00:23:35 0000 20080302 stable on x86 and amd64. Thanks for reporting, and sorry for the delay.