* Package: sci-biology/unafold-3.8-r1:0 * 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 unafold-3.8.tar.bz2 to /var/tmp/portage/sci-biology/unafold-3.8-r1/work >>> Source unpacked in /var/tmp/portage/sci-biology/unafold-3.8-r1/work >>> Preparing source in /var/tmp/portage/sci-biology/unafold-3.8-r1/work/unafold-3.8 ... * Applying unafold-3.8-doc-version.patch ... [ ok ] >>> Source prepared. >>> Configuring source in /var/tmp/portage/sci-biology/unafold-3.8-r1/work/unafold-3.8 ... * econf: updating unafold-3.8/config/config.guess with /usr/share/gnuconfig/config.guess * econf: updating unafold-3.8/config/config.sub with /usr/share/gnuconfig/config.sub ./configure --prefix=/usr --build=x86_64-pc-linux-gnu --host=x86_64-pc-linux-gnu --mandir=/usr/share/man --infodir=/usr/share/info --datadir=/usr/share --sysconfdir=/etc --localstatedir=/var/lib --disable-dependency-tracking --docdir=/usr/share/doc/unafold-3.8-r1 --htmldir=/usr/share/doc/unafold-3.8-r1/html --libdir=/usr/lib64 checking for a BSD-compatible install... /usr/lib/portage/python3.10/ebuild-helpers/xattr/install -c checking whether build environment is sane... yes checking for a thread-safe mkdir -p... /bin/mkdir -p checking for gawk... gawk checking whether make sets $(MAKE)... yes checking build system type... x86_64-pc-linux-gnu checking for x86_64-pc-linux-gnu-gcc... x86_64-pc-linux-gnu-gcc checking for C compiler default output file name... a.out checking whether the C compiler works... yes checking whether we are cross compiling... no checking for suffix of executables... checking for suffix of object files... o checking whether we are using the GNU C compiler... yes checking whether x86_64-pc-linux-gnu-gcc accepts -g... yes checking for x86_64-pc-linux-gnu-gcc option to accept ISO C89... none needed checking for style of include used by make... GNU checking dependency style of x86_64-pc-linux-gnu-gcc... none checking for a BSD-compatible install... /usr/lib/portage/python3.10/ebuild-helpers/xattr/install -c checking whether ln -s works... yes checking for perl... /usr/bin/perl checking for perl version greater than or equal to 5.6.1... ok checking for gnuplot... system('gnuplot', "$prefix.gp") == 0 or die ; checking whether compiler needs -mieee... no checking how to run the C preprocessor... x86_64-pc-linux-gnu-gcc -E checking for X... libraries /usr/lib64, headers checking host system type... x86_64-pc-linux-gnu checking for the pthreads library -lpthreads... no checking whether pthreads work without any flags... yes checking for joinable pthread attribute... PTHREAD_CREATE_JOINABLE checking if more special flags are required for pthreads... no checking for cc_r... x86_64-pc-linux-gnu-gcc checking for grep that handles long lines and -e... /bin/grep checking for egrep... /bin/grep -E checking for ANSI C header files... yes checking for sys/types.h... yes checking for sys/stat.h... yes checking for stdlib.h... yes checking for string.h... yes checking for memory.h... yes checking for strings.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for unistd.h... yes checking windows.h usability... no checking windows.h presence... no checking for windows.h... no checking for OpenGL library... -lGL checking for x86_64-pc-linux-gnu-g++... x86_64-pc-linux-gnu-g++ checking whether we are using the GNU C++ compiler... yes checking whether x86_64-pc-linux-gnu-g++ accepts -g... yes checking dependency style of x86_64-pc-linux-gnu-g++... none checking for OpenGL Utility library... -lGLU checking whether -R must be followed by a space... no checking for gethostbyname... yes checking for connect... yes checking for remove... yes checking for shmat... yes checking for IceConnectionNumber in -lICE... yes checking for GLUT library... -lglut checking for gdlib-config... no checking for inflateReset in -lz... yes checking for png_check_sig in -lpng... no checking for gdImageCreate in -lgd... yes checking for gdImageGif in -lgd... yes checking for gdImageJpeg in -lgd... yes checking for gdImagePng in -lgd... yes checking for dirent.h that defines DIR... yes checking for library containing opendir... none required checking for ANSI C header files... (cached) yes checking fcntl.h usability... yes checking fcntl.h presence... yes checking for fcntl.h... yes checking ieeefp.h usability... no checking ieeefp.h presence... no checking for ieeefp.h... no checking libintl.h usability... yes checking libintl.h presence... yes checking for libintl.h... yes checking limits.h usability... yes checking limits.h presence... yes checking for limits.h... yes checking for stdlib.h... (cached) yes checking for string.h... (cached) yes checking for an ANSI C-conforming const... yes checking whether scanf() understands "inf"... no configure: creating ./config.status config.status: creating Makefile config.status: creating src/Makefile config.status: creating scripts/Makefile config.status: creating data/Makefile config.status: creating doc/Makefile config.status: creating tests/Makefile config.status: creating scripts/concentrations.pl config.status: creating scripts/concentrations-same.pl config.status: creating scripts/hybrid2.pl config.status: creating scripts/hybrid-2s.pl config.status: creating scripts/hybrid-ss-2s.pl config.status: creating scripts/hybrid-select.pl config.status: creating scripts/melt.pl config.status: creating scripts/plot2ann.pl config.status: creating scripts/h-num.pl config.status: creating scripts/ss-count.pl config.status: creating scripts/ct-energy-det.pl config.status: creating scripts/UNAFold.pl config.status: creating scripts/ITC-plot.pl config.status: creating scripts/vantHoff-plot.pl config.status: creating doc/hybrid.1 config.status: creating doc/hybrid-min.1 config.status: creating doc/hybrid-ss.1 config.status: creating doc/hybrid-ss-min.1 config.status: creating doc/hybrid-ss-noml.1 config.status: creating doc/hybrid-ss-simple.1 config.status: creating doc/hybrid-plot.1 config.status: creating doc/hybrid-plot-ng.1 config.status: creating doc/concentration.1 config.status: creating doc/concentration-same.1 config.status: creating doc/concentrations.pl.1 config.status: creating doc/concentrations-same.pl.1 config.status: creating doc/ensemble-dg.1 config.status: creating doc/ensemble-dg-same.1 config.status: creating doc/ensemble-ext.1 config.status: creating doc/ensemble-ext-same.1 config.status: creating doc/dG2dH.1 config.status: creating doc/dG2dS.1 config.status: creating doc/dG2Cp.1 config.status: creating doc/ct-energy.1 config.status: creating doc/hybrid2.pl.1 config.status: creating doc/hybrid2-x.pl.1 config.status: creating doc/hybrid2-min.pl.1 config.status: creating doc/hybrid2-min-x.pl.1 config.status: creating doc/hybrid2-2s.pl.1 config.status: creating doc/hybrid2-2s-x.pl.1 config.status: creating doc/ct-ext.1 config.status: creating doc/ct-uniq.1 config.status: creating doc/hybrid-2s.pl.1 config.status: creating doc/hybrid-ss-2s.pl.1 config.status: creating doc/ct-prob.1 config.status: creating doc/melt.pl.1 config.status: creating doc/plot2ann.pl.1 config.status: creating doc/h-num.pl.1 config.status: creating doc/ss-count.pl.1 config.status: creating doc/hybrid-select.pl.1 config.status: creating doc/ct2rnaml.1 config.status: creating doc/ct-energy-det.pl.1 config.status: creating doc/UNAFold.pl.1 config.status: creating doc/ITC-plot.pl.1 config.status: creating doc/vantHoff-plot.pl.1 config.status: creating config.h config.status: executing depfiles commands >>> Source configured. >>> Compiling source in /var/tmp/portage/sci-biology/unafold-3.8-r1/work/unafold-3.8 ... make -j4 make all-recursive make[1]: Entering directory '/var/tmp/portage/sci-biology/unafold-3.8-r1/work/unafold-3.8' Making all in src make[2]: Entering directory '/var/tmp/portage/sci-biology/unafold-3.8-r1/work/unafold-3.8/src' x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -DPKGDATADIR=\"/usr/share/unafold/\" -pipe -march=native -fno-diagnostics-color -O2 -Werror=implicit-function-declaration -Werror=implicit-int -O3 -c getopt.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -DPKGDATADIR=\"/usr/share/unafold/\" -pipe -march=native -fno-diagnostics-color -O2 -Werror=implicit-function-declaration -Werror=implicit-int -O3 -c getopt1.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -DPKGDATADIR=\"/usr/share/unafold/\" -pipe -march=native -fno-diagnostics-color -O2 -Werror=implicit-function-declaration -Werror=implicit-int -O3 -c energy.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -DPKGDATADIR=\"/usr/share/unafold/\" -pipe -march=native -fno-diagnostics-color -O2 -Werror=implicit-function-declaration -Werror=implicit-int -O3 -c xmalloc.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -DPKGDATADIR=\"/usr/share/unafold/\" -pipe -march=native -fno-diagnostics-color -O2 -Werror=implicit-function-declaration -Werror=implicit-int -O3 -c hybrid.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -DENERGY=int -DINTEGER -DPRECISION=1000 -DPKGDATADIR=\"/usr/share/unafold/\" -pipe -march=native -fno-diagnostics-color -O2 -Werror=implicit-function-declaration -Werror=implicit-int -O3 -c -o hybrid_min-energy.o `test -f 'energy.c' || echo './'`energy.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -DENERGY=int -DINTEGER -DPRECISION=1000 -DPKGDATADIR=\"/usr/share/unafold/\" -pipe -march=native -fno-diagnostics-color -O2 -Werror=implicit-function-declaration -Werror=implicit-int -O3 -c -o hybrid_min-hybrid-min.o `test -f 'hybrid-min.c' || echo './'`hybrid-min.c energy.c: In function ‘loadStack’: energy.c:118:15: error: implicit declaration of function ‘readOrDie’ [-Werror=implicit-function-declaration] 118 | readOrDie(1, "stack", gFile, "%lf", &stackEnergies[i][j][ii][jj]); | ^~~~~~~~~ energy.c: In function ‘loadStack’: energy.c:118:15: error: implicit declaration of function ‘readOrDie’ [-Werror=implicit-function-declaration] 118 | readOrDie(1, "stack", gFile, "%lf", &stackEnergies[i][j][ii][jj]); | ^~~~~~~~~ cc1: some warnings being treated as errors make[2]: *** [Makefile:521: energy.o] Error 1 make[2]: *** Waiting for unfinished jobs.... cc1: some warnings being treated as errors make[2]: *** [Makefile:549: hybrid_min-energy.o] Error 1 make[2]: Leaving directory '/var/tmp/portage/sci-biology/unafold-3.8-r1/work/unafold-3.8/src' make[1]: *** [Makefile:259: all-recursive] Error 1 make[1]: Leaving directory '/var/tmp/portage/sci-biology/unafold-3.8-r1/work/unafold-3.8' make: *** [Makefile:198: all] Error 2 * ERROR: sci-biology/unafold-3.8-r1::gentoo failed (compile phase): * emake failed * * If you need support, post the output of `emerge --info '=sci-biology/unafold-3.8-r1::gentoo'`, * the complete build log and the output of `emerge -pqv '=sci-biology/unafold-3.8-r1::gentoo'`. * The complete build log is located at '/var/log/portage/sci-biology:unafold-3.8-r1:20221004-070604.log'. * For convenience, a symlink to the build log is located at '/var/tmp/portage/sci-biology/unafold-3.8-r1/temp/build.log'. * The ebuild environment file is located at '/var/tmp/portage/sci-biology/unafold-3.8-r1/temp/environment'. * Working directory: '/var/tmp/portage/sci-biology/unafold-3.8-r1/work/unafold-3.8' * S: '/var/tmp/portage/sci-biology/unafold-3.8-r1/work/unafold-3.8'