* Package: sci-chemistry/theseus-3.3.0 * Repository: gentoo * Maintainer: sci-chemistry@gentoo.org * USE: abi_x86_64 amd64 elibc_musl kernel_linux userland_GNU * FEATURES: network-sandbox preserve-libs sandbox userpriv usersandbox >>> Unpacking source... >>> Unpacking theseus_3.3.0.tar.gz to /var/tmp/portage/sci-chemistry/theseus-3.3.0/work >>> Source unpacked in /var/tmp/portage/sci-chemistry/theseus-3.3.0/work >>> Preparing source in /var/tmp/portage/sci-chemistry/theseus-3.3.0/work/theseus_src ... >>> Source prepared. >>> Configuring source in /var/tmp/portage/sci-chemistry/theseus-3.3.0/work/theseus_src ... >>> Source configured. >>> Compiling source in /var/tmp/portage/sci-chemistry/theseus-3.3.0/work/theseus_src ... make -j1 ltheseus ( cd libdistfit; make && cp libdistfit.a ../lib ) make[1]: Entering directory '/var/tmp/portage/sci-chemistry/theseus-3.3.0/work/theseus_src/libdistfit' x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=native -std=c11 -c statistics.c x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=native -std=c11 -c beta_dist.c x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=native -std=c11 -c betaprime_dist.c x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=native -std=c11 -c betasym_dist.c x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=native -std=c11 -c binomial_dist.c x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=native -std=c11 -c cauchy_dist.c x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=native -std=c11 -c chi_dist.c x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=native -std=c11 -c chisqr_dist.c x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=native -std=c11 -c chisqrgen_dist.c x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=native -std=c11 -c EVD_dist.c x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=native -std=c11 -c exp_dist.c x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=native -std=c11 -c gamma_dist.c x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=native -std=c11 -c invchisqr_dist.c x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=native -std=c11 -c invgamma_dist.c x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=native -std=c11 -c invgauss_dist.c x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=native -std=c11 -c laplace_dist.c x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=native -std=c11 -c logistic_dist.c x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=native -std=c11 -c lognormal_dist.c x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=native -std=c11 -c maxwell_dist.c x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=native -std=c11 -c negbinom_dist.c x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=native -std=c11 -c normal_dist.c x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=native -std=c11 -c pareto_dist.c x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=native -std=c11 -c rayleigh_dist.c x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=native -std=c11 -c recinvgauss_dist.c x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=native -std=c11 -c rice_dist.c x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=native -std=c11 -c uniform_dist.c x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=native -std=c11 -c vonmises_dist.c x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=native -std=c11 -c weibull_dist.c x86_64-gentoo-linux-musl-ar -rvs libdistfit.a statistics.o beta_dist.o betaprime_dist.o betasym_dist.o binomial_dist.o cauchy_dist.o chi_dist.o chisqr_dist.o chisqrgen_dist.o EVD_dist.o exp_dist.o gamma_dist.o invchisqr_dist.o invgamma_dist.o invgauss_dist.o laplace_dist.o logistic_dist.o lognormal_dist.o maxwell_dist.o negbinom_dist.o normal_dist.o pareto_dist.o rayleigh_dist.o recinvgauss_dist.o rice_dist.o uniform_dist.o vonmises_dist.o weibull_dist.o x86_64-gentoo-linux-musl-ar: creating libdistfit.a a - statistics.o a - beta_dist.o a - betaprime_dist.o a - betasym_dist.o a - binomial_dist.o a - cauchy_dist.o a - chi_dist.o a - chisqr_dist.o a - chisqrgen_dist.o a - EVD_dist.o a - exp_dist.o a - gamma_dist.o a - invchisqr_dist.o a - invgamma_dist.o a - invgauss_dist.o a - laplace_dist.o a - logistic_dist.o a - lognormal_dist.o a - maxwell_dist.o a - negbinom_dist.o a - normal_dist.o a - pareto_dist.o a - rayleigh_dist.o a - recinvgauss_dist.o a - rice_dist.o a - uniform_dist.o a - vonmises_dist.o a - weibull_dist.o x86_64-gentoo-linux-musl-ranlib libdistfit.a make[1]: Leaving directory '/var/tmp/portage/sci-chemistry/theseus-3.3.0/work/theseus_src/libdistfit' ( cd libDLTutils; make && cp libDLTutils.a ../lib ) make[1]: Entering directory '/var/tmp/portage/sci-chemistry/theseus-3.3.0/work/theseus_src/libDLTutils' x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=native -std=c11 -c DLTutils.c DLTutils.c: In function ‘mystrncpy’: DLTutils.c:159:5: warning: ‘strncpy’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 159 | strncpy(s1, s2, len); | ^~~~~~~~~~~~~~~~~~~~ DLTutils.c:156:26: note: length computed here 156 | size_t len = strlen(s2); /* minimum allocated length of s2 */ | ^~~~~~~~~~ DLTutils.c: In function ‘mystrcpy’: DLTutils.c:173:5: warning: ‘strncpy’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 173 | strncpy(s1, s2, len); | ^~~~~~~~~~~~~~~~~~~~ DLTutils.c:171:27: note: length computed here 171 | size_t len = strlen(s2); | ^~~~~~~~~~ x86_64-gentoo-linux-musl-ar -rvs libDLTutils.a DLTutils.o x86_64-gentoo-linux-musl-ar: creating libDLTutils.a a - DLTutils.o x86_64-gentoo-linux-musl-ranlib libDLTutils.a make[1]: Leaving directory '/var/tmp/portage/sci-chemistry/theseus-3.3.0/work/theseus_src/libDLTutils' ( cd libmsa; make && cp libmsa.a ../lib ) make[1]: Entering directory '/var/tmp/portage/sci-chemistry/theseus-3.3.0/work/theseus_src/libmsa' x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=native -std=c11 -c msa.c msa.c: In function ‘MSAcombine2’: msa.c:956:9: warning: ‘strncpy’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 956 | strncpy(msao->name[m], msa1->name[m], strlen(msa1->name[m])+1); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ msa.c:956:47: note: length computed here 956 | strncpy(msao->name[m], msa1->name[m], strlen(msa1->name[m])+1); | ^~~~~~~~~~~~~~~~~~~~~ msa.c:959:9: warning: ‘strncpy’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 959 | strncpy(msao->name[m + num1], msa2->name[m], strlen(msa2->name[m])+1); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ msa.c:959:54: note: length computed here 959 | strncpy(msao->name[m + num1], msa2->name[m], strlen(msa2->name[m])+1); | ^~~~~~~~~~~~~~~~~~~~~ msa.c: In function ‘reada2m’: msa.c:1110:5: warning: ‘strncpy’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 1110 | strncpy(msa->filename, msafile_name, strlen(msafile_name)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ msa.c: In function ‘readaln’: msa.c:1297:5: warning: ‘strncpy’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 1297 | strncpy(msa->filename, msafile_name, strlen(msafile_name)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ x86_64-gentoo-linux-musl-ar -rvs libmsa.a msa.o x86_64-gentoo-linux-musl-ar: creating libmsa.a a - msa.o x86_64-gentoo-linux-musl-ranlib libmsa.a make[1]: Leaving directory '/var/tmp/portage/sci-chemistry/theseus-3.3.0/work/theseus_src/libmsa' ( cd libdltmath; make && cp libdltmath.a ../lib ) make[1]: Entering directory '/var/tmp/portage/sci-chemistry/theseus-3.3.0/work/theseus_src/libdltmath' x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=native -std=c11 -c ludcmp.c x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=native -std=c11 -c MatUtils.c x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=native -std=c11 -c Mat3Utils.c x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=native -std=c11 -c Mat4Utils.c x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=native -std=c11 -c VecUtils.c x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=native -std=c11 -c quicksort.c x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=native -std=c11 -c integrate.c x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=native -std=c11 -c eigen_gsl.c x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=native -std=c11 -c MultivarGamma.c x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=native -std=c11 -c specfunc.c x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=native -std=c11 -c RegGamma.c x86_64-gentoo-linux-musl-ar -rvs libdltmath.a ludcmp.o MatUtils.o Mat3Utils.o Mat4Utils.o VecUtils.o quicksort.o integrate.o eigen_gsl.o MultivarGamma.o specfunc.o RegGamma.o x86_64-gentoo-linux-musl-ar: creating libdltmath.a a - ludcmp.o a - MatUtils.o a - Mat3Utils.o a - Mat4Utils.o a - VecUtils.o a - quicksort.o a - integrate.o a - eigen_gsl.o a - MultivarGamma.o a - specfunc.o a - RegGamma.o x86_64-gentoo-linux-musl-ranlib libdltmath.a make[1]: Leaving directory '/var/tmp/portage/sci-chemistry/theseus-3.3.0/work/theseus_src/libdltmath' ( cd libdssplite; make && cp libdssplite.a ../lib ) make[1]: Entering directory '/var/tmp/portage/sci-chemistry/theseus-3.3.0/work/theseus_src/libdssplite' x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=native -std=c11 -c dssplite.c x86_64-gentoo-linux-musl-ar -rvs libdssplite.a dssplite.o x86_64-gentoo-linux-musl-ar: creating libdssplite.a a - dssplite.o x86_64-gentoo-linux-musl-ranlib libdssplite.a make[1]: Leaving directory '/var/tmp/portage/sci-chemistry/theseus-3.3.0/work/theseus_src/libdssplite' x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=native -std=c11 -c CovMat.c x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=native -std=c11 -c DistMat.c x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=native -std=c11 -c Embed.c x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=native -std=c11 -c Error.c x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=native -std=c11 -c FragCds.c x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=native -std=c11 -c FragDist.c x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=native -std=c11 -c HierarchVars.c x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=native -std=c11 -c lodmats.c x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=native -std=c11 -c MultiPose.c x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=native -std=c11 -c MultiPose2MSA.c MultiPose2MSA.c: In function ‘pdb2fst’: MultiPose2MSA.c:1111:9: warning: ‘strncat’ specified bound 4 equals source length [-Wstringop-overflow=] 1111 | strncat(outfile, ".fst", 4); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ MultiPose2MSA.c:1110:9: warning: ‘strncpy’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 1110 | strncpy(outfile, pdbi->filename, strlen(pdbi->filename)+1); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ MultiPose2MSA.c:1110:42: note: length computed here 1110 | strncpy(outfile, pdbi->filename, strlen(pdbi->filename)+1); | ^~~~~~~~~~~~~~~~~~~~~~ x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=native -std=c11 -c MultiPosePth.c x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=native -std=c11 -c PCAstats.c x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=native -std=c11 -c pdbIO.c pdbIO.c: In function ‘WriteFileMap’: pdbIO.c:1422:9: warning: ‘strncpy’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 1422 | strncpy(tmpStr, myPDBs->cds[ii]->filename, (tmpLen + 1) * sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pdbIO.c:1421:18: note: length computed here 1421 | tmpLen = strlen(myPDBs->cds[ii]->filename); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pdbIO.c: In function ‘WriteTheseusPDBFiles’: pdbIO.c:1718:9: warning: ‘strncpy’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 1718 | strncpy(outfile_name, fname, strlen(fname)+1); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pdbIO.c:1718:38: note: length computed here 1718 | strncpy(outfile_name, fname, strlen(fname)+1); | ^~~~~~~~~~~~~ pdbIO.c:1720:9: warning: ‘strncat’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 1720 | strncat(outfile_name, pdbA->cds[i]->filename, strlen(pdbA->cds[i]->filename)+1); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pdbIO.c:1720:55: note: length computed here 1720 | strncat(outfile_name, pdbA->cds[i]->filename, strlen(pdbA->cds[i]->filename)+1); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=native -std=c11 -c pdbMalloc.c x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=native -std=c11 -c pdbStats.c x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=native -std=c11 -c pdbUtils.c x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=native -std=c11 -c QuarticHornFrag.c x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=native -std=c11 -c RandCds.c x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=native -std=c11 -c pdbSSM.c x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=native -std=c11 -c ProcGSLSVD.c x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=native -std=c11 -c ProcGSLSVDNu.c x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=native -std=c11 -c ProcJacobiSVD.c x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=native -std=c11 -c GibbsMet.c x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=native -std=c11 -c qcprot.c x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=native -std=c11 -c StructAlign.c x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=native -std=c11 -c NWfill.c NWfill.c:39:10: fatal error: error.h: No such file or directory 39 | #include "error.h" | ^~~~~~~~~ compilation terminated. make: *** [Makefile:55: NWfill.o] Error 1 * ERROR: sci-chemistry/theseus-3.3.0::gentoo failed (compile phase): * emake failed * * If you need support, post the output of `emerge --info '=sci-chemistry/theseus-3.3.0::gentoo'`, * the complete build log and the output of `emerge -pqv '=sci-chemistry/theseus-3.3.0::gentoo'`. * The complete build log is located at '/var/log/portage/sci-chemistry:theseus-3.3.0:20200405-051111.log'. * For convenience, a symlink to the build log is located at '/var/tmp/portage/sci-chemistry/theseus-3.3.0/temp/build.log'. * The ebuild environment file is located at '/var/tmp/portage/sci-chemistry/theseus-3.3.0/temp/environment'. * Working directory: '/var/tmp/portage/sci-chemistry/theseus-3.3.0/work/theseus_src' * S: '/var/tmp/portage/sci-chemistry/theseus-3.3.0/work/theseus_src/'