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Gentoo's Bugzilla – Attachment 879407 Details for
Bug 919885
sci-biology/paml-4.9j - treesub.c: error: passing argument 3 of printSeqs from incompatible pointer type [-Wincompatible-pointer-types]
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sci-biology:paml-4.9j:20231214-144044.log
sci-biology:paml-4.9j:20231214-144044.log (text/plain), 7.04 KB, created by
Toralf Förster
on 2023-12-14 14:48:56 UTC
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Description:
sci-biology:paml-4.9j:20231214-144044.log
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Creator:
Toralf Förster
Created:
2023-12-14 14:48:56 UTC
Size:
7.04 KB
patch
obsolete
> * Package: sci-biology/paml-4.9j:0 > * Repository: gentoo > * Maintainer: sci-biology@gentoo.org > * USE: abi_x86_64 amd64 elibc_glibc kernel_linux > * FEATURES: network-sandbox preserve-libs sandbox userpriv usersandbox > >>>> Unpacking source... >>>> Unpacking paml4.9j.tgz to /var/tmp/portage/sci-biology/paml-4.9j/work >>>> Source unpacked in /var/tmp/portage/sci-biology/paml-4.9j/work >>>> Preparing source in /var/tmp/portage/sci-biology/paml-4.9j/work/paml4.9j ... > * Applying paml-4.9j-makefile.patch ... > [ ok ] > * Applying paml-4.9j-fno-common.patch ... > [ ok ] >>>> Source prepared. >>>> Configuring source in /var/tmp/portage/sci-biology/paml-4.9j/work/paml4.9j ... >>>> Source configured. >>>> Compiling source in /var/tmp/portage/sci-biology/paml-4.9j/work/paml4.9j ... >make -j4 -C src >make: Entering directory '/var/tmp/portage/sci-biology/paml-4.9j/work/paml4.9j/src' >x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -fno-diagnostics-color -Wno-unused-result -c -o tools.o tools.c >x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -fno-diagnostics-color -Wno-unused-result -Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0 chi2.c -lm -o chi2 >x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -fno-diagnostics-color -Wno-unused-result -Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0 baseml.c tools.o paml.h -lm -o baseml >x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -fno-diagnostics-color -Wno-unused-result -Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0 basemlg.c tools.o paml.h -lm -o basemlg >x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -fno-diagnostics-color -Wno-unused-result -Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0 codeml.c tools.o paml.h -lm -o codeml >x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -fno-diagnostics-color -Wno-unused-result -Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0 evolver.c tools.o paml.h -lm -o evolver >In file included from baseml.c:131: >treesub.c: In function âIdenticalSeqsâ: >treesub.c:1310:33: error: passing argument 3 of âprintSeqsâ from incompatible pointer type [-Wincompatible-pointer-types] > 1310 | printSeqs(ftmp, com.z, com.spname, com.ns, com.ls, com.npatt, com.fpatt, NULL, keep, 1); > | ~~~^~~~~~~ > | | > | char ** >In file included from baseml.c:11: >paml.h:150:63: note: expected âunsigned char **â but argument is of type âchar **â > 150 | id printSeqs(FILE *fout, unsigned char *z[], unsigned char *spnames[], int ns, int ls, int npatt, double fpatt[], int *pose, char keep[], int format); > | ~~~~~~~~~~~~~~~^~~~~~~~~ > >In file included from basemlg.c:80: >treesub.c: In function âReadSeqâ: >treesub.c:858:31: error: passing argument 2 of âprintsmaâ from incompatible pointer type [-Wincompatible-pointer-types] > 858 | printsma(fout, com.spname, com.z, com.ns, com.ls, com.ls, gap, com.seqtype, 0, 0, NULL); > | ~~~^~~~~~~ > | | > | unsigned char ** >In file included from basemlg.c:11: >paml.h:153:31: note: expected âchar **â but argument is of type âunsigned char **â > 153 | int printsma (FILE*fout, char*spname[], unsigned char*z[], int ns, int l, int lline, int gap, int seqtype, > | ~~~~~^~~~~~~~ >treesub.c:866:28: error: passing argument 2 of âprintsmaâ from incompatible pointer type [-Wincompatible-pointer-types] > 866 | printsma(fout, com.spname, com.z, com.ns, com.ls, com.ls, gap, com.seqtype, 0, 0, NULL); > | ~~~^~~~~~~ > | | > | unsigned char ** >paml.h:153:31: note: expected âchar **â but argument is of type âunsigned char **â > 153 | int printsma (FILE*fout, char*spname[], unsigned char*z[], int ns, int l, int lline, int gap, int seqtype, > | ~~~~~^~~~~~~~ >In file included from codeml.c:238: >treesub.c: In function âIdenticalSeqsâ: >treesub.c: In function âprintPatternsâ: >treesub.c:1310:33: error: passing argument 3 of âprintSeqsâ from incompatible pointer type [-Wincompatible-pointer-types] > 1310 | printSeqs(ftmp, com.z, com.spname, com.ns, com.ls, com.npatt, com.fpatt, NULL, keep, 1); > | ~~~^~~~~~~ > | | > | char ** >In file included from codeml.c:17: >paml.h:150:63: note: expected âunsigned char **â but argument is of type âchar **â > 150 | id printSeqs(FILE *fout, unsigned char *z[], unsigned char *spnames[], int ns, int ls, int npatt, double fpatt[], int *pose, char keep[], int format); > | ~~~~~~~~~~~~~~~^~~~~~~~~ > >treesub.c:1093:25: error: passing argument 2 of âprintsmaâ from incompatible pointer type [-Wincompatible-pointer-types] > 1093 | printsma(fout, com.spname, com.z, com.ns, com.npatt, com.npatt, gap, com.seqtype, 1, 0, NULL); > | ~~~^~~~~~~ > | | > | unsigned char ** >paml.h:153:31: note: expected âchar **â but argument is of type âunsigned char **â > 153 | int printsma (FILE*fout, char*spname[], unsigned char*z[], int ns, int l, int lline, int gap, int seqtype, > | ~~~~~^~~~~~~~ >treesub.c: In function âAllPatternsâ: >treesub.c:1361:25: error: passing argument 2 of âprintsmaâ from incompatible pointer type [-Wincompatible-pointer-types] > 1361 | printsma(fout, com.spname, com.z, com.ns, com.ls, com.ls, gap, com.seqtype, 1, 0, NULL); > | ~~~^~~~~~~ > | | > | unsigned char ** >paml.h:153:31: note: expected âchar **â but argument is of type âunsigned char **â > 153 | int printsma (FILE*fout, char*spname[], unsigned char*z[], int ns, int l, int lline, int gap, int seqtype, > | ~~~~~^~~~~~~~ >make: *** [<builtin>: basemlg] Error 1 >make: *** Waiting for unfinished jobs.... >make: *** [<builtin>: baseml] Error 1 >make: *** [<builtin>: codeml] Error 1 >make: Leaving directory '/var/tmp/portage/sci-biology/paml-4.9j/work/paml4.9j/src' > * ERROR: sci-biology/paml-4.9j::gentoo failed (compile phase): > * emake failed > * > * If you need support, post the output of `emerge --info '=sci-biology/paml-4.9j::gentoo'`, > * the complete build log and the output of `emerge -pqv '=sci-biology/paml-4.9j::gentoo'`. > * The complete build log is located at '/var/log/portage/sci-biology:paml-4.9j:20231214-144044.log'. > * For convenience, a symlink to the build log is located at '/var/tmp/portage/sci-biology/paml-4.9j/temp/build.log'. > * The ebuild environment file is located at '/var/tmp/portage/sci-biology/paml-4.9j/temp/environment'. > * Working directory: '/var/tmp/portage/sci-biology/paml-4.9j/work/paml4.9j' > * S: '/var/tmp/portage/sci-biology/paml-4.9j/work/paml4.9j' >
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