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Gentoo's Bugzilla – Attachment 819520 Details for
Bug 875041
sci-biology/unafold-3.8-r1 - energy.c: error: implicit declaration of function readOrDie [-Werror=implicit-function-declaration]
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sci-biology:unafold-3.8-r1:20221004-070604.log
sci-biology:unafold-3.8-r1:20221004-070604.log (text/plain), 11.30 KB, created by
Toralf Förster
on 2022-10-04 16:39:16 UTC
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Description:
sci-biology:unafold-3.8-r1:20221004-070604.log
Filename:
MIME Type:
Creator:
Toralf Förster
Created:
2022-10-04 16:39:16 UTC
Size:
11.30 KB
patch
obsolete
> * 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 âloadStackâ: >energy.c:118:15: error: implicit declaration of function âreadOrDieâ [-Werror=implicit-function-declaration] > 118 | readOrDie(1, "stack", gFile, "%lf", &stackEnergies[i][j][ii][jj]); > | ^~~~~~~~~ >energy.c: In function âloadStackâ: >energy.c:118:15: error: implicit declaration of function âreadOrDieâ [-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' >
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