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Gentoo's Bugzilla – Attachment 838353 Details for
Bug 883663
sci-biology/clustalw-mpi-0.13-r3 - stupid.c: error: implicit declaration of function pforward_pass [-Werror=implicit-function-decl
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sci-biology:clustalw-mpi-0.13-r3:20221129-185501.log
sci-biology:clustalw-mpi-0.13-r3:20221129-185501.log (text/plain), 8.32 KB, created by
Toralf Förster
on 2022-11-29 19:16:19 UTC
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sci-biology:clustalw-mpi-0.13-r3:20221129-185501.log
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Toralf Förster
Created:
2022-11-29 19:16:19 UTC
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8.32 KB
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> * Package: sci-biology/clustalw-mpi-0.13-r3:0 > * 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-r3/work >>>> Source unpacked in /var/tmp/portage/sci-biology/clustalw-mpi-0.13-r3/work >>>> Preparing source in /var/tmp/portage/sci-biology/clustalw-mpi-0.13-r3/work/clustalw-mpi-0.13 ... > * Applying clustalw-mpi-0.13-makefile.patch ... > [ ok ] > * Applying clustalw-mpi-0.13-fno-common.patch ... > [ ok ] >>>> Source prepared. > * Clang 16 testing: this build is using a /etc/portage/bashrc hook (2022-11-24T21:47)! > * Clang 16 testing: see https://wiki.gentoo.org/wiki/Modern_C_porting for more info. >>>> Configuring source in /var/tmp/portage/sci-biology/clustalw-mpi-0.13-r3/work/clustalw-mpi-0.13 ... >>>> Source configured. >>>> Compiling source in /var/tmp/portage/sci-biology/clustalw-mpi-0.13-r3/work/clustalw-mpi-0.13 ... >make -j4 >mpicc -pipe -march=native -fno-diagnostics-color -O2 -D_GLIBCXX_ASSERTIONS -Werror=implicit-function-declaration -Werror=implicit-int -c prfalign_mpi_pdiff.c >mpicc -pipe -march=native -fno-diagnostics-color -O2 -D_GLIBCXX_ASSERTIONS -Werror=implicit-function-declaration -Werror=implicit-int -c malign_mpi_progressive.c >mpicc -pipe -march=native -fno-diagnostics-color -O2 -D_GLIBCXX_ASSERTIONS -Werror=implicit-function-declaration -Werror=implicit-int -c sequence.c >mpicc -pipe -march=native -fno-diagnostics-color -O2 -D_GLIBCXX_ASSERTIONS -Werror=implicit-function-declaration -Werror=implicit-int -c clustalw-mpi.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)); > | ^ >sequence.c: In function âget_clustal_seqâ: >sequence.c:158:9: warning: ignoring return value of âfgetsâ declared with attribute âwarn_unused_resultâ [-Wunused-result] > 158 | fgets(line,MAXLINE+1,fin); /* read the title line...ignore it */ > | ^~~~~~~~~~~~~~~~~~~~~~~~~ >sequence.c:163:46: warning: ignoring return value of âfgetsâ declared with attribute âwarn_unused_resultâ [-Wunused-result] > 163 | for(i=1;i<seqno;i++) fgets(line,MAXLINE+1,fin); > | ^~~~~~~~~~~~~~~~~~~~~~~~~ >sequence.c: In function âget_msf_seqâ: >sequence.c:97:46: warning: ignoring return value of âfgetsâ declared with attribute âwarn_unused_resultâ [-Wunused-result] > 97 | for(i=1;i<seqno;i++) fgets(line,MAXLINE+1,fin); > | ^~~~~~~~~~~~~~~~~~~~~~~~~ >sequence.c: In function âget_seqâ: >sequence.c:724:33: warning: ignoring return value of âfgetsâ declared with attribute âwarn_unused_resultâ [-Wunused-result] > 724 | fgets(line,MAXLINE+1,fin); > | ^~~~~~~~~~~~~~~~~~~~~~~~~ >sequence.c:752:33: warning: ignoring return value of âfgetsâ declared with attribute âwarn_unused_resultâ [-Wunused-result] > 752 | fgets(line,MAXLINE+1,fin); > | ^~~~~~~~~~~~~~~~~~~~~~~~~ >sequence.c:760:25: warning: ignoring return value of âfgetsâ declared with attribute âwarn_unused_resultâ [-Wunused-result] > 760 | fgets(line,MAXLINE+1,fin); > | ^~~~~~~~~~~~~~~~~~~~~~~~~ >sequence.c:786:33: warning: ignoring return value of âfgetsâ declared with attribute âwarn_unused_resultâ [-Wunused-result] > 786 | fgets(line,MAXLINE+1,fin); > | ^~~~~~~~~~~~~~~~~~~~~~~~~ >sequence.c:820:41: warning: ignoring return value of âfgetsâ declared with attribute âwarn_unused_resultâ [-Wunused-result] > 820 | fgets(line,MAXLINE+1,fin); > | ^~~~~~~~~~~~~~~~~~~~~~~~~ >sequence.c:824:41: warning: ignoring return value of âfgetsâ declared with attribute âwarn_unused_resultâ [-Wunused-result] > 824 | fgets(line,MAXLINE+1,fin); > | ^~~~~~~~~~~~~~~~~~~~~~~~~ >sequence.c: In function âget_embl_ssâ: >sequence.c:401:49: warning: ignoring return value of âfgetsâ declared with attribute âwarn_unused_resultâ [-Wunused-result] > 401 | fgets(line,MAXLINE+1,fin); > | ^~~~~~~~~~~~~~~~~~~~~~~~~ >sequence.c:406:49: warning: ignoring return value of âfgetsâ declared with attribute âwarn_unused_resultâ [-Wunused-result] > 406 | fgets(line,MAXLINE+1,fin); > | ^~~~~~~~~~~~~~~~~~~~~~~~~ >sequence.c:425:49: warning: ignoring return value of âfgetsâ declared with attribute âwarn_unused_resultâ [-Wunused-result] > 425 | fgets(line,MAXLINE+1,fin); > | ^~~~~~~~~~~~~~~~~~~~~~~~~ >sequence.c:430:49: warning: ignoring return value of âfgetsâ declared with attribute âwarn_unused_resultâ [-Wunused-result] > 430 | fgets(line,MAXLINE+1,fin); > | ^~~~~~~~~~~~~~~~~~~~~~~~~ >sequence.c: In function âget_rsf_ssâ: >sequence.c:496:49: warning: ignoring return value of âfgetsâ declared with attribute âwarn_unused_resultâ [-Wunused-result] > 496 | fgets(line,MAXLINE+1,fin); > | ^~~~~~~~~~~~~~~~~~~~~~~~~ >sequence.c:501:49: warning: ignoring return value of âfgetsâ declared with attribute âwarn_unused_resultâ [-Wunused-result] > 501 | fgets(line,MAXLINE+1,fin); > | ^~~~~~~~~~~~~~~~~~~~~~~~~ >mpicc -pipe -march=native -fno-diagnostics-color -O2 -D_GLIBCXX_ASSERTIONS -Werror=implicit-function-declaration -Werror=implicit-int -c stupid.c >stupid.c: In function âmypdiffâ: >stupid.c:347:17: error: implicit declaration of function âpforward_passâ [-Werror=implicit-function-declaration] > 347 | pforward_pass(midi, t, tl, A, B, N, HH, DD); > | ^~~~~~~~~~~~~ >stupid.c:402:17: error: implicit declaration of function âpreverse_passâ [-Werror=implicit-function-declaration] > 402 | preverse_pass(midi, A, B, M, N, go2, RR, SS, gS); > | ^~~~~~~~~~~~~ >cc1: some warnings being treated as errors >make: *** [Makefile:52: stupid.o] Error 1 shuffle=2408644963 >make: *** Waiting for unfinished jobs.... >In function âget_seqâ, > inlined from âreadseqsâ at sequence.c:988:9: >sequence.c:846:62: warning: writing 1 byte into a region of size 0 [-Wstringop-overflow=] > 846 | for (i=0;i<offset;i++) seq[++(*len)] = '-'; > | ~~~~~~~~~~~~~~^~~~~ > * ERROR: sci-biology/clustalw-mpi-0.13-r3::gentoo failed (compile phase): > * emake failed > * > * If you need support, post the output of `emerge --info '=sci-biology/clustalw-mpi-0.13-r3::gentoo'`, > * the complete build log and the output of `emerge -pqv '=sci-biology/clustalw-mpi-0.13-r3::gentoo'`. > * The complete build log is located at '/var/log/portage/sci-biology:clustalw-mpi-0.13-r3:20221129-185501.log'. > * For convenience, a symlink to the build log is located at '/var/tmp/portage/sci-biology/clustalw-mpi-0.13-r3/temp/build.log'. > * The ebuild environment file is located at '/var/tmp/portage/sci-biology/clustalw-mpi-0.13-r3/temp/environment'. > * Working directory: '/var/tmp/portage/sci-biology/clustalw-mpi-0.13-r3/work/clustalw-mpi-0.13' > * S: '/var/tmp/portage/sci-biology/clustalw-mpi-0.13-r3/work/clustalw-mpi-0.13' >
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