sci-chemistry:theseus-3.3.0:20200405-051111.log

sci-chemistry:theseus-3.3.0:20200405-051111.log (text/plain), 14.79 KB, created by Toralf Förster on 2020-04-05 09:10:50 UTC

 * Package:    sci-chemistry/theseus-3.3.0
 * Repository: gentoo
 * Maintainer: [e-mail]
 * 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/'