* 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 ‘IdenticalSeqs’: treesub.c:1310:33: error: passing argument 3 of ‘printSeqs’ 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 ‘unsigned char **’ but argument is of type ‘char **’ 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 ‘ReadSeq’: treesub.c:858:31: error: passing argument 2 of ‘printsma’ 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 ‘char **’ but argument is of type ‘unsigned char **’ 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 ‘printsma’ 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 ‘char **’ but argument is of type ‘unsigned char **’ 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 ‘IdenticalSeqs’: treesub.c: In function ‘printPatterns’: treesub.c:1310:33: error: passing argument 3 of ‘printSeqs’ 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 ‘unsigned char **’ but argument is of type ‘char **’ 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 ‘printsma’ 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 ‘char **’ but argument is of type ‘unsigned char **’ 153 | int printsma (FILE*fout, char*spname[], unsigned char*z[], int ns, int l, int lline, int gap, int seqtype, | ~~~~~^~~~~~~~ treesub.c: In function ‘AllPatterns’: treesub.c:1361:25: error: passing argument 2 of ‘printsma’ 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 ‘char **’ but argument is of type ‘unsigned char **’ 153 | int printsma (FILE*fout, char*spname[], unsigned char*z[], int ns, int l, int lline, int gap, int seqtype, | ~~~~~^~~~~~~~ make: *** [: basemlg] Error 1 make: *** Waiting for unfinished jobs.... make: *** [: baseml] Error 1 make: *** [: 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'