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Gentoo's Bugzilla – Attachment 606858 Details for
Bug 706960
sci-biology/clustalw-mpi-0.13-r2 : fails to build with -fno-common or gcc-10
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sci-biology:clustalw-mpi-0.13-r2:20200128-142727.log
sci-biology:clustalw-mpi-0.13-r2:20200128-142727.log (text/plain), 12.51 KB, created by
Toralf Förster
on 2020-01-28 18:49:32 UTC
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sci-biology:clustalw-mpi-0.13-r2:20200128-142727.log
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Toralf Förster
Created:
2020-01-28 18:49:32 UTC
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12.51 KB
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> * Package: sci-biology/clustalw-mpi-0.13-r2 > * Repository: gentoo > * Maintainer: sci-biology@gentoo.org > * USE: abi_x86_64 amd64 elibc_glibc kernel_linux userland_GNU > * FEATURES: network-sandbox preserve-libs sandbox userpriv usersandbox >>>> Unpacking source... >>>> Unpacking clustalw-mpi-0.13.tar.gz to /var/tmp/portage/sci-biology/clustalw-mpi-0.13-r2/work >>>> Source unpacked in /var/tmp/portage/sci-biology/clustalw-mpi-0.13-r2/work >>>> Preparing source in /var/tmp/portage/sci-biology/clustalw-mpi-0.13-r2/work/clustalw-mpi-0.13 ... > * Applying 0.13-gentoo.patch ... > [ ok ] >>>> Source prepared. >>>> Configuring source in /var/tmp/portage/sci-biology/clustalw-mpi-0.13-r2/work/clustalw-mpi-0.13 ... >>>> Source configured. >>>> Compiling source in /var/tmp/portage/sci-biology/clustalw-mpi-0.13-r2/work/clustalw-mpi-0.13 ... >make -j1 >mpicc -O2 -pipe -march=native -fno-common -c clustalw-mpi.c >mpicc -O2 -pipe -march=native -fno-common -c interface.c >interface.c: In function âcheck_paramâ: >interface.c:207:20: warning: âreturnâ with no value, in function returning non-void > 207 | if(args[0]==NULL) return; > | ^~~~~~ >interface.c:195:13: note: declared here > 195 | static sint check_param(char **args,char *params[], char *param_arg[]) > | ^~~~~~~~~~~ >interface.c: In function âmyexitâ: >interface.c:3976:4: warning: âreturnâ with no value, in function returning non-void > 3976 | return; > | ^~~~~~ >interface.c:3967:12: note: declared here > 3967 | static int myexit(int rval) > | ^~~~~~ >interface.c: In function âopen_output_fileâ: >interface.c:2178:4: warning: ignoring return value of âfgetsâ, declared with attribute warn_unused_result [-Wunused-result] > 2178 | fgets(temp, FILENAMELEN, stdin); > | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ >interface.c:2189:3: warning: ignoring return value of âfgetsâ, declared with attribute warn_unused_result [-Wunused-result] > 2189 | fgets(temp, FILENAMELEN, stdin); > | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ >interface.c: In function âcreate_parameter_outputâ: >interface.c:3871:3: warning: ignoring return value of âfgetsâ, declared with attribute warn_unused_result [-Wunused-result] > 3871 | fgets(temp, FILENAMELEN, stdin); > | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ >interface.c: In function ânew_sequence_alignâ: >interface.c:2431:3: warning: ignoring return value of âfgetsâ, declared with attribute warn_unused_result [-Wunused-result] > 2431 | fgets(temp, MAXLINE, stdin); > | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ >interface.c: In function âget_treeâ: >interface.c:2667:7: warning: ignoring return value of âfgetsâ, declared with attribute warn_unused_result [-Wunused-result] > 2667 | fgets(temp, MAXLINE, stdin); > | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ >interface.c: In function âprofile_alignâ: >interface.c:2811:3: warning: ignoring return value of âfgetsâ, declared with attribute warn_unused_result [-Wunused-result] > 2811 | fgets(temp, MAXLINE, stdin); > | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ >interface.c:2840:3: warning: ignoring return value of âfgetsâ, declared with attribute warn_unused_result [-Wunused-result] > 2840 | fgets(temp, MAXLINE, stdin); > | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ >mpicc -O2 -pipe -march=native -fno-common -c sequence.c >sequence.c: In function âget_clustal_seqâ: >sequence.c:158:2: warning: ignoring return value of âfgetsâ, declared with attribute warn_unused_result [-Wunused-result] > 158 | fgets(line,MAXLINE+1,fin); /* read the title line...ignore it */ > | ^~~~~~~~~~~~~~~~~~~~~~~~~ >sequence.c:163:25: warning: ignoring return value of âfgetsâ, declared with attribute warn_unused_result [-Wunused-result] > 163 | for(i=1;i<seqno;i++) fgets(line,MAXLINE+1,fin); > | ^~~~~~~~~~~~~~~~~~~~~~~~~ >sequence.c: In function âget_msf_seqâ: >sequence.c:97:25: warning: ignoring return value of âfgetsâ, declared with attribute warn_unused_result [-Wunused-result] > 97 | for(i=1;i<seqno;i++) fgets(line,MAXLINE+1,fin); > | ^~~~~~~~~~~~~~~~~~~~~~~~~ >sequence.c: In function âget_seqâ: >sequence.c:724:5: warning: ignoring return value of âfgetsâ, declared with attribute warn_unused_result [-Wunused-result] > 724 | fgets(line,MAXLINE+1,fin); > | ^~~~~~~~~~~~~~~~~~~~~~~~~ >sequence.c:752:5: warning: ignoring return value of âfgetsâ, declared with attribute warn_unused_result [-Wunused-result] > 752 | fgets(line,MAXLINE+1,fin); > | ^~~~~~~~~~~~~~~~~~~~~~~~~ >sequence.c:760:4: warning: ignoring return value of âfgetsâ, declared with attribute warn_unused_result [-Wunused-result] > 760 | fgets(line,MAXLINE+1,fin); > | ^~~~~~~~~~~~~~~~~~~~~~~~~ >sequence.c:786:5: warning: ignoring return value of âfgetsâ, declared with attribute warn_unused_result [-Wunused-result] > 786 | fgets(line,MAXLINE+1,fin); > | ^~~~~~~~~~~~~~~~~~~~~~~~~ >sequence.c:820:6: warning: ignoring return value of âfgetsâ, declared with attribute warn_unused_result [-Wunused-result] > 820 | fgets(line,MAXLINE+1,fin); > | ^~~~~~~~~~~~~~~~~~~~~~~~~ >sequence.c:824:6: warning: ignoring return value of âfgetsâ, declared with attribute warn_unused_result [-Wunused-result] > 824 | fgets(line,MAXLINE+1,fin); > | ^~~~~~~~~~~~~~~~~~~~~~~~~ >sequence.c: In function âget_embl_ssâ: >sequence.c:401:7: warning: ignoring return value of âfgetsâ, declared with attribute warn_unused_result [-Wunused-result] > 401 | fgets(line,MAXLINE+1,fin); > | ^~~~~~~~~~~~~~~~~~~~~~~~~ >sequence.c:406:7: warning: ignoring return value of âfgetsâ, declared with attribute warn_unused_result [-Wunused-result] > 406 | fgets(line,MAXLINE+1,fin); > | ^~~~~~~~~~~~~~~~~~~~~~~~~ >sequence.c:425:7: warning: ignoring return value of âfgetsâ, declared with attribute warn_unused_result [-Wunused-result] > 425 | fgets(line,MAXLINE+1,fin); > | ^~~~~~~~~~~~~~~~~~~~~~~~~ >sequence.c:430:7: warning: ignoring return value of âfgetsâ, declared with attribute warn_unused_result [-Wunused-result] > 430 | fgets(line,MAXLINE+1,fin); > | ^~~~~~~~~~~~~~~~~~~~~~~~~ >sequence.c: In function âget_rsf_ssâ: >sequence.c:496:7: warning: ignoring return value of âfgetsâ, declared with attribute warn_unused_result [-Wunused-result] > 496 | fgets(line,MAXLINE+1,fin); > | ^~~~~~~~~~~~~~~~~~~~~~~~~ >sequence.c:501:7: warning: ignoring return value of âfgetsâ, declared with attribute warn_unused_result [-Wunused-result] > 501 | fgets(line,MAXLINE+1,fin); > | ^~~~~~~~~~~~~~~~~~~~~~~~~ >mpicc -O2 -pipe -march=native -fno-common -c showpair.c >mpicc -O2 -pipe -march=native -fno-common -c malign.c >mpicc -O2 -pipe -march=native -fno-common -c malign_mpi_progressive.c >malign_mpi_progressive.c: In function âkey_compareâ: >malign_mpi_progressive.c:843:11: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast] > 843 | v1 = *(int *) (*((int *) e1)); > | ^ >malign_mpi_progressive.c:844:11: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast] > 844 | v2 = *(int *) (*((int *) e2)); > | ^ >mpicc -O2 -pipe -march=native -fno-common -c malign_mpi_pdiff.c >mpicc -O2 -pipe -march=native -fno-common -c util.c >util.c: In function âgetstrâ: >util.c:179:2: warning: ignoring return value of âfgetsâ, declared with attribute warn_unused_result [-Wunused-result] > 179 | fgets(outstr, MAXLINE, stdin); > | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ >util.c: In function âgetrealâ: >util.c:193:10: warning: ignoring return value of âfgetsâ, declared with attribute warn_unused_result [-Wunused-result] > 193 | fgets(line, MAXLINE, stdin); > | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ >util.c: In function âgetintâ: >util.c:221:10: warning: ignoring return value of âfgetsâ, declared with attribute warn_unused_result [-Wunused-result] > 221 | fgets(line, MAXLINE, stdin); > | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ >util.c: In function âdo_systemâ: >util.c:244:3: warning: ignoring return value of âsystemâ, declared with attribute warn_unused_result [-Wunused-result] > 244 | system(line); > | ^~~~~~~~~~~~ >mpicc -DSERIAL_NJTREE -O2 -pipe -march=native -fno-common -c trees.c >mpicc -O2 -pipe -march=native -fno-common -c gcgcheck.c >mpicc -O2 -pipe -march=native -fno-common -c prfalign_mpi_pdiff.c >mpicc -O2 -pipe -march=native -fno-common -c prfalign_mpi_progressive.c >mpicc -DDYNAMIC_SCHEDULING_PAIRALIGN -O2 -pipe -march=native -fno-common -c pairalign_new.c >mpicc -O2 -pipe -march=native -fno-common -c calcgapcoeff.c >mpicc -O2 -pipe -march=native -fno-common -c calcprf1.c >mpicc -O2 -pipe -march=native -fno-common -c calcprf2.c >mpicc -O2 -pipe -march=native -fno-common -c calctree.c >calctree.c: In function âcreate_treeâ: >calctree.c:362:8: warning: ignoring return value of âfscanfâ, declared with attribute warn_unused_result [-Wunused-result] > 362 | fscanf(fd,"%f",&dist); > | ^~~~~~~~~~~~~~~~~~~~~ >mpicc -O2 -pipe -march=native -fno-common -c readmat.c >mpicc -O2 -pipe -march=native -fno-common -c alnscore.c >mpicc -O2 -pipe -march=native -fno-common -c random.c >mpicc -DDYNAMIC_SCHEDULING_PAIRALIGN -O2 -pipe -march=native -fno-common -c parallel_compare.c >mpicc -O2 -pipe -march=native -fno-common -c prfalign.c >mpicc -O2 -pipe -march=native -fno-common -c stupid.c >stupid.c: In function âmypdiffâ: >stupid.c:347:3: warning: implicit declaration of function âpforward_passâ [-Wimplicit-function-declaration] > 347 | pforward_pass(midi, t, tl, A, B, N, HH, DD); > | ^~~~~~~~~~~~~ >stupid.c:402:3: warning: implicit declaration of function âpreverse_passâ [-Wimplicit-function-declaration] > 402 | preverse_pass(midi, A, B, M, N, go2, RR, SS, gS); > | ^~~~~~~~~~~~~ >mpicc -Wl,-O1 -Wl,--as-needed -o clustalw-mpi clustalw-mpi.o interface.o sequence.o showpair.o malign.o malign_mpi_progressive.o malign_mpi_pdiff.o util.o trees.o gcgcheck.o prfalign_mpi_pdiff.o prfalign_mpi_progressive.o pairalign_new.o calcgapcoeff.o calcprf1.o calcprf2.o calctree.o readmat.o alnscore.o random.o parallel_compare.o prfalign.o stupid.o -lm >/usr/lib/gcc/x86_64-pc-linux-gnu/9.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: parallel_compare.o:(.bss+0x2c): multiple definition of `ktup'; showpair.o:(.bss+0x34): first defined here >/usr/lib/gcc/x86_64-pc-linux-gnu/9.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: parallel_compare.o:(.bss+0x0): multiple definition of `zzd'; showpair.o:(.bss+0x0): first defined here >/usr/lib/gcc/x86_64-pc-linux-gnu/9.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: parallel_compare.o:(.bss+0x8): multiple definition of `zzc'; showpair.o:(.bss+0x8): first defined here >/usr/lib/gcc/x86_64-pc-linux-gnu/9.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: parallel_compare.o:(.bss+0x10): multiple definition of `zzb'; showpair.o:(.bss+0x10): first defined here >/usr/lib/gcc/x86_64-pc-linux-gnu/9.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: parallel_compare.o:(.bss+0x18): multiple definition of `zza'; showpair.o:(.bss+0x18): first defined here >/usr/lib/gcc/x86_64-pc-linux-gnu/9.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: parallel_compare.o:(.bss+0x20): multiple definition of `signif'; showpair.o:(.bss+0x28): first defined here >/usr/lib/gcc/x86_64-pc-linux-gnu/9.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: parallel_compare.o:(.bss+0x28): multiple definition of `window'; showpair.o:(.bss+0x30): first defined here >/usr/lib/gcc/x86_64-pc-linux-gnu/9.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: parallel_compare.o:(.bss+0x24): multiple definition of `wind_gap'; showpair.o:(.bss+0x2c): first defined here >collect2: error: ld returned 1 exit status >make: *** [Makefile:33: clustalw-mpi] Error 1 > * ERROR: sci-biology/clustalw-mpi-0.13-r2::gentoo failed (compile phase): > * emake failed > * > * If you need support, post the output of `emerge --info '=sci-biology/clustalw-mpi-0.13-r2::gentoo'`, > * the complete build log and the output of `emerge -pqv '=sci-biology/clustalw-mpi-0.13-r2::gentoo'`. > * The complete build log is located at '/var/log/portage/sci-biology:clustalw-mpi-0.13-r2:20200128-142727.log'. > * For convenience, a symlink to the build log is located at '/var/tmp/portage/sci-biology/clustalw-mpi-0.13-r2/temp/build.log'. > * The ebuild environment file is located at '/var/tmp/portage/sci-biology/clustalw-mpi-0.13-r2/temp/environment'. > * Working directory: '/var/tmp/portage/sci-biology/clustalw-mpi-0.13-r2/work/clustalw-mpi-0.13' > * S: '/var/tmp/portage/sci-biology/clustalw-mpi-0.13-r2/work/clustalw-mpi-0.13'
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