printf ' ' | fink --no-use-binary-dist --yes --build-as-nobody rebuild alidot 2>&1 The package 'alidot' will be built without being installed. Reading build dependency for alidot-2.05-1... Reading dependency for alidot-2.05-1... Reading build conflict for alidot-2.05-1... The package 'viennarna' will be installed. Reading dependency for viennarna-1.8.5-205... Reading runtime dependency for viennarna-1.8.5-205... The package 'gcc48-shlibs' will be installed. Reading dependency for gcc48-shlibs-4.8.3-1000... Reading runtime dependency for gcc48-shlibs-4.8.3-1000... The following package will be rebuilt: alidot The following 2 additional packages will be installed: gcc48-shlibs viennarna Do you want to continue? [Y/n] (assuming default) curl --connect-timeout 30 -f -L -A 'fink/0.37.0' -O http://distfiles.master.finkmirrors.net/distfiles/alidot-2.05.tar.gz % Total % Received % Xferd Average Speed Time Time Time Current Dload Upload Total Spent Left Speed 0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0 44 208k 44 93878 0 0 139k 0 0:00:01 --:--:-- 0:00:01 139k 100 208k 100 208k 0 0 264k 0 --:--:-- --:--:-- --:--:-- 264k Reading buildlock packages... All buildlocks accounted for. /sw/bin/dpkg-lockwait -i /sw/fink/dists/stable/main/binary-darwin-x86_64/languages/gcc48-shlibs_4.8.3-1000_darwin-x86_64.deb Selecting previously deselected package gcc48-shlibs. (Reading database ... 4296 files and directories currently installed.) Unpacking gcc48-shlibs (from .../gcc48-shlibs_4.8.3-1000_darwin-x86_64.deb) ... Setting up gcc48-shlibs (4.8.3-1000) ... Clearing dependency_libs of .la files being installed Reading buildlock packages... All buildlocks accounted for. /sw/bin/dpkg-lockwait -i /sw/fink/debs/viennarna_1.8.5-205_darwin-x86_64.deb Selecting previously deselected package viennarna. (Reading database ... 4337 files and directories currently installed.) Unpacking viennarna (from .../viennarna_1.8.5-205_darwin-x86_64.deb) ... Setting up viennarna (1.8.5-205) ... * RNAlib: (RNAlib). The Vienna RNA Package Version 1.8 install-info(/sw/share/info/RNAlib.info): no section specified for new entry, placing at end Setting runtime build-lock... dpkg-deb -b /sw/build.build/root-fink-buildlock-alidot-2.05-1 /sw/build.build dpkg-deb: building package `fink-buildlock-alidot-2.05-1' in `/sw/build.build/fink-buildlock-alidot-2.05-1_2014.07.29-18.24.03_darwin-x86_64.deb'. Installing build-lock package... /sw/bin/dpkg-lockwait -i /sw/build.build/fink-buildlock-alidot-2.05-1_2014.07.29-18.24.03_darwin-x86_64.deb Selecting previously deselected package fink-buildlock-alidot-2.05-1. (Reading database ... 4413 files and directories currently installed.) Unpacking fink-buildlock-alidot-2.05-1 (from .../fink-buildlock-alidot-2.05-1_2014.07.29-18.24.03_darwin-x86_64.deb) ... Setting up fink-buildlock-alidot-2.05-1 (2014.07.29-18.24.03) ... sudo -u fink-bld [ENV] sh -c /tmp/fink.VK8mm env LANG=C LC_ALL=C /sw/bin/tar --no-same-owner --no-same-permissions -xvf /sw/src/alidot-2.05.tar.gz alidot-2.05/ alidot-2.05/README alidot-2.05/ali.h alidot-2.05/compare.h alidot-2.05/pair_mat.h alidot-2.05/pair_stuff.h alidot-2.05/AUTHORS alidot-2.05/COPYING alidot-2.05/ChangeLog alidot-2.05/INSTALL alidot-2.05/Makefile.am alidot-2.05/Makefile.in alidot-2.05/NEWS alidot-2.05/acinclude.m4 alidot-2.05/aclocal.m4 alidot-2.05/alidot.spec.in alidot-2.05/config.guess alidot-2.05/config.h.in alidot-2.05/config.sub alidot-2.05/configure alidot-2.05/configure.in alidot-2.05/depcomp alidot-2.05/getopt.c alidot-2.05/getopt1.c alidot-2.05/install-sh alidot-2.05/missing alidot-2.05/mkinstalldirs alidot-2.05/texinfo.tex alidot-2.05/main.c alidot-2.05/ali.c alidot-2.05/PS_dot.c alidot-2.05/compare.c alidot-2.05/pair_stuff.c alidot-2.05/alidot.texi alidot-2.05/alidot.1 alidot-2.05/AliDot.pl alidot-2.05/cmount.pl alidot-2.05/dprzoom.pl alidot-2.05/split.pl alidot-2.05/anote.pl alidot-2.05/consens.pl alidot-2.05/dpzoom.pl alidot-2.05/xrna.pl alidot-2.05/gnugetopt.h alidot-2.05/Tutorial/ alidot-2.05/Tutorial/Makefile.am alidot-2.05/Tutorial/Makefile.in alidot-2.05/Tutorial/HIV_5prime.seq alidot-2.05/Tutorial/Tutorial alidot-2.05/alidot.info sudo -u fink-bld [ENV] sh -c /tmp/fink.3pOiV ./configure --prefix=/sw --prefix=/sw --mandir=/sw/build.build/root-alidot-2.05-1/sw/share/man --infodir=/sw/build.build/root-alidot-2.05-1/sw/share/info checking for a BSD-compatible install... /usr/bin/install -c checking whether build environment is sane... yes checking for gawk... no checking for mawk... no checking for nawk... no checking for awk... awk checking whether make sets $(MAKE)... yes checking build system type... i386-apple-darwin13.3.0 checking host system type... i386-apple-darwin13.3.0 checking if malloc debugging is wanted... no checking for a BSD-compatible install... /usr/bin/install -c checking for gcc... gcc checking for C compiler default output... 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 gcc accepts -g... yes checking for gcc option to accept ANSI C... none needed checking for style of include used by make... GNU checking dependency style of gcc... gcc3 checking for inline... inline checking how to run the C preprocessor... gcc -E checking for egrep... 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 for unistd.h... (cached) yes checking getopt.h usability... yes checking getopt.h presence... yes checking for getopt.h... yes checking for getopt_long... yes configure: creating ./config.status config.status: creating Makefile config.status: creating Tutorial/Makefile config.status: creating alidot.spec config.status: creating config.h config.status: executing depfiles commands make /Applications/Xcode.app/Contents/Developer/usr/bin/make all-recursive Making all in Tutorial make[2]: Nothing to be done for `all'. source='main.c' object='main.o' libtool=no \ depfile='.deps/main.Po' tmpdepfile='.deps/main.TPo' \ depmode=gcc3 /bin/sh ./depcomp \ gcc -DHAVE_CONFIG_H -I. -I. -I. -I/sw/include -g -O2 -c `test -f 'main.c' || echo './'`main.c source='ali.c' object='ali.o' libtool=no \ depfile='.deps/ali.Po' tmpdepfile='.deps/ali.TPo' \ depmode=gcc3 /bin/sh ./depcomp \ gcc -DHAVE_CONFIG_H -I. -I. -I. -I/sw/include -g -O2 -c `test -f 'ali.c' || echo './'`ali.c source='PS_dot.c' object='PS_dot.o' libtool=no \ depfile='.deps/PS_dot.Po' tmpdepfile='.deps/PS_dot.TPo' \ depmode=gcc3 /bin/sh ./depcomp \ gcc -DHAVE_CONFIG_H -I. -I. -I. -I/sw/include -g -O2 -c `test -f 'PS_dot.c' || echo './'`PS_dot.c source='compare.c' object='compare.o' libtool=no \ depfile='.deps/compare.Po' tmpdepfile='.deps/compare.TPo' \ depmode=gcc3 /bin/sh ./depcomp \ gcc -DHAVE_CONFIG_H -I. -I. -I. -I/sw/include -g -O2 -c `test -f 'compare.c' || echo './'`compare.c source='pair_stuff.c' object='pair_stuff.o' libtool=no \ depfile='.deps/pair_stuff.Po' tmpdepfile='.deps/pair_stuff.TPo' \ depmode=gcc3 /bin/sh ./depcomp \ gcc -DHAVE_CONFIG_H -I. -I. -I. -I/sw/include -g -O2 -c `test -f 'pair_stuff.c' || echo './'`pair_stuff.c main.c:558:42: warning: format specifies type 'float *' but the argument has type 'double *' [-Wformat] if (sscanf(line,"%s (%f) %d", stru, &E, &start)!=3) { ~~ ^~ %lf 1 warning generated. gcc -g -O2 -L/sw/lib -o alidot main.o ali.o PS_dot.o compare.o pair_stuff.o -lm /bin/rm -rf /sw/build.build/root-alidot-2.05-1 /bin/mkdir -p /sw/build.build/root-alidot-2.05-1/sw /bin/mkdir -p /sw/build.build/root-alidot-2.05-1/DEBIAN /usr/sbin/chown -R fink-bld:fink-bld /sw/build.build/root-alidot-2.05-1 sudo -u fink-bld [ENV] sh -c /tmp/fink.mav70 make install prefix=/sw/build.build/root-alidot-2.05-1/sw Making install in Tutorial make[2]: Nothing to be done for `install-exec-am'. make[2]: Nothing to be done for `install-data-am'. /bin/sh ./mkinstalldirs /sw/build.build/root-alidot-2.05-1/sw/bin mkdir -p -- /sw/build.build/root-alidot-2.05-1/sw/bin /usr/bin/install -c alidot /sw/build.build/root-alidot-2.05-1/sw/bin/alidot /bin/sh ./mkinstalldirs /sw/build.build/root-alidot-2.05-1/sw/bin /usr/bin/install -c AliDot.pl /sw/build.build/root-alidot-2.05-1/sw/bin/AliDot.pl /usr/bin/install -c cmount.pl /sw/build.build/root-alidot-2.05-1/sw/bin/cmount.pl /usr/bin/install -c dprzoom.pl /sw/build.build/root-alidot-2.05-1/sw/bin/dprzoom.pl /usr/bin/install -c split.pl /sw/build.build/root-alidot-2.05-1/sw/bin/split.pl /usr/bin/install -c anote.pl /sw/build.build/root-alidot-2.05-1/sw/bin/anote.pl /usr/bin/install -c consens.pl /sw/build.build/root-alidot-2.05-1/sw/bin/consens.pl /usr/bin/install -c dpzoom.pl /sw/build.build/root-alidot-2.05-1/sw/bin/dpzoom.pl /usr/bin/install -c xrna.pl /sw/build.build/root-alidot-2.05-1/sw/bin/xrna.pl /bin/sh ./mkinstalldirs /sw/build.build/root-alidot-2.05-1/sw/share/info mkdir -p -- /sw/build.build/root-alidot-2.05-1/sw/share/info /usr/bin/install -c -m 644 ./alidot.info /sw/build.build/root-alidot-2.05-1/sw/share/info/alidot.info install-info --info-dir=/sw/build.build/root-alidot-2.05-1/sw/share/info /sw/build.build/root-alidot-2.05-1/sw/share/info/alidot.info install-info(/sw/build.build/root-alidot-2.05-1/sw/share/info/alidot.info): no file /sw/build.build/root-alidot-2.05-1/sw/share/info/dir, retrieving backup file /sw/share/info/dir.bak. * Alidot: (alidot). Alidot and related utilities for identifying conserved RNA secondary structure elements from thermodynamic structure predictions and Clustal W sequence alignments. install-info(/sw/build.build/root-alidot-2.05-1/sw/share/info/alidot.info): no section specified for new entry, placing at end cp: /sw/share/info/dir.bak: Permission denied install-info(/sw/build.build/root-alidot-2.05-1/sw/share/info/alidot.info): couldn't backup /sw/build.build/root-alidot-2.05-1/sw/share/info/dir in /sw/share/info/dir.bak: No such file or directory /bin/sh ./mkinstalldirs /sw/build.build/root-alidot-2.05-1/sw/share/man/man1 mkdir -p -- /sw/build.build/root-alidot-2.05-1/sw/share/man/man1 /usr/bin/install -c -m 644 ./alidot.1 /sw/build.build/root-alidot-2.05-1/sw/share/man/man1/alidot.1 mkdir -p /sw/build.build/root-alidot-2.05-1/sw/share/alidot/Tutorial mv Tutorial/Tutorial Tutorial/HIV_5prime.seq /sw/build.build/root-alidot-2.05-1/sw/share/alidot/Tutorial/ sudo -u fink-bld [ENV] sh -c /tmp/fink.PrM0x /usr/bin/install -d -m 700 /sw/build.build/root-alidot-2.05-1/sw/share/doc/alidot /bin/cp -r AUTHORS /sw/build.build/root-alidot-2.05-1/sw/share/doc/alidot/ /bin/cp -r ChangeLog /sw/build.build/root-alidot-2.05-1/sw/share/doc/alidot/ /bin/cp -r COPYING /sw/build.build/root-alidot-2.05-1/sw/share/doc/alidot/ /bin/cp -r INSTALL /sw/build.build/root-alidot-2.05-1/sw/share/doc/alidot/ /bin/cp -r NEWS /sw/build.build/root-alidot-2.05-1/sw/share/doc/alidot/ /bin/cp -r README /sw/build.build/root-alidot-2.05-1/sw/share/doc/alidot/ /bin/chmod -R go=u-w /sw/build.build/root-alidot-2.05-1/sw/share/doc/alidot /bin/rm -f /sw/build.build/root-alidot-2.05-1/sw/info/dir /sw/build.build/root-alidot-2.05-1/sw/info/dir.old /sw/build.build/root-alidot-2.05-1/sw/share/info/dir /sw/build.build/root-alidot-2.05-1/sw/share/info/dir.old Reverting ownership of install dir to root Writing control file... Writing package script postinst... Writing package script prerm... Writing md5sums file... env LANG=C LC_ALL=C dpkg-deb -b root-alidot-2.05-1 /sw/fink/10.9/stable/main/binary-darwin-x86_64/sci dpkg-deb: building package `alidot' in `/sw/fink/10.9/stable/main/binary-darwin-x86_64/sci/alidot_2.05-1_darwin-x86_64.deb'. Removing runtime build-lock... Removing build-lock package... /sw/bin/dpkg-lockwait -r fink-buildlock-alidot-2.05-1 (Reading database ... 4414 files and directories currently installed.) Removing fink-buildlock-alidot-2.05-1 ...