printf ' ' | fink --no-use-binary-dist --yes --build-as-nobody rebuild fastlink 2>&1 The package 'fastlink' will be built without being installed. Reading build dependency for fastlink-4.1p-3... Reading dependency for fastlink-4.1p-3... Reading build conflict for fastlink-4.1p-3... The following package will be rebuilt: fastlink curl --connect-timeout 30 -f -L -A 'fink/0.37.0' -o fastlink-4.1p.tar.Z ftp://ftp.ncbi.nih.gov/pub/fastlink/fastlink.tar.Z % Total % Received % Xferd Average Speed Time Time Time Current Dload Upload Total Spent Left Speed 0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0 0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0 0 0 0 0 0 0 0 0 --:--:-- 0:00:01 --:--:-- 0 0 0 0 0 0 0 0 0 --:--:-- 0:00:02 --:--:-- 0 0 1301k 0 1448 0 0 410 0 0:54:11 0:00:03 0:54:08 410 74 1301k 74 967k 0 0 227k 0 0:00:05 0:00:04 0:00:01 227k 100 1301k 100 1301k 0 0 241k 0 0:00:05 0:00:05 --:--:-- 252k 100 1301k 100 1301k 0 0 238k 0 0:00:05 0:00:05 --:--:-- 309k Setting runtime build-lock... dpkg-deb -b /sw/build.build/root-fink-buildlock-fastlink-4.1p-3 /sw/build.build dpkg-deb: building package `fink-buildlock-fastlink-4.1p-3' in `/sw/build.build/fink-buildlock-fastlink-4.1p-3_2014.08.02-13.11.46_darwin-x86_64.deb'. Installing build-lock package... /sw/bin/dpkg-lockwait -i /sw/build.build/fink-buildlock-fastlink-4.1p-3_2014.08.02-13.11.46_darwin-x86_64.deb Selecting previously deselected package fink-buildlock-fastlink-4.1p-3. (Reading database ... 4296 files and directories currently installed.) Unpacking fink-buildlock-fastlink-4.1p-3 (from .../fink-buildlock-fastlink-4.1p-3_2014.08.02-13.11.46_darwin-x86_64.deb) ... Setting up fink-buildlock-fastlink-4.1p-3 (2014.08.02-13.11.46) ... sudo -u fink-bld [ENV] sh -c /tmp/fink.mWdyw env LANG=C LC_ALL=C /sw/bin/tar --no-same-owner --no-same-permissions -xvf /sw/src/fastlink-4.1p.tar.Z fastlink/ fastlink/4.1P/ fastlink/4.1P/alphavms/ fastlink/4.1P/alphavms/NEW.MMS fastlink/4.1P/alphavms/README.ALPHAVMS fastlink/4.1P/alphavms/checkpointdefs.h fastlink/4.1P/alphavms/maketool_vms.c fastlink/4.1P/alphavms/maketool_vms.com fastlink/4.1P/alphavms/setup.com fastlink/4.1P/alphavms/start_pedin.com fastlink/4.1P/irix/ fastlink/4.1P/irix/p4_patchfile.IRIX fastlink/4.1P/src/ fastlink/4.1P/src/.pure fastlink/4.1P/src/Makefile fastlink/4.1P/src/automodified.c fastlink/4.1P/src/check.c fastlink/4.1P/src/checkpointdefs.h fastlink/4.1P/src/ckpt.c fastlink/4.1P/src/comgetvect.c fastlink/4.1P/src/cominputcode.c fastlink/4.1P/src/comlike.c fastlink/4.1P/src/commoncode.c fastlink/4.1P/src/commondefs.h fastlink/4.1P/src/comnuclear.c fastlink/4.1P/src/comoutput.c fastlink/4.1P/src/compar.c fastlink/4.1P/src/compar.h fastlink/4.1P/src/comrec.c fastlink/4.1P/src/gemdefs.h fastlink/4.1P/src/ildefs.h fastlink/4.1P/src/ilgetvect.c fastlink/4.1P/src/ilink.c fastlink/4.1P/src/ilinputcode.c fastlink/4.1P/src/iloldnuclear.c fastlink/4.1P/src/iostuff.c fastlink/4.1P/src/lidefs.h fastlink/4.1P/src/ligetvect.c fastlink/4.1P/src/liinputcode.c fastlink/4.1P/src/linkmap.c fastlink/4.1P/src/lioldnuclear.c fastlink/4.1P/src/lodefs.h fastlink/4.1P/src/lodscore.c fastlink/4.1P/src/logetvect.c fastlink/4.1P/src/loinputcode.c fastlink/4.1P/src/looldnuclear.c fastlink/4.1P/src/loopbrk.c fastlink/4.1P/src/mldefs.h fastlink/4.1P/src/mlgetvect.c fastlink/4.1P/src/mlink.c fastlink/4.1P/src/mlinputcode.c fastlink/4.1P/src/mloldnuclear.c fastlink/4.1P/src/moddefs.h fastlink/4.1P/src/oldsegup.c fastlink/4.1P/src/outbuff.c fastlink/4.1P/src/parmodified.c fastlink/4.1P/src/sexmodified.c fastlink/4.1P/src/slowautomodified.c fastlink/4.1P/src/slowsexmodified.c fastlink/4.1P/src/strbuff.c fastlink/4.1P/src/strbuff.h fastlink/4.1P/src/unknown.c fastlink/4.1P/src/unknown.h fastlink/4.1P/vaxvms/ fastlink/4.1P/vaxvms/FASTLINK_BUILD.VMS fastlink/4.1P/vaxvms/FASTLINK_START.VMS fastlink/4.1P/vaxvms/NEW.MMS fastlink/4.1P/vaxvms/OLD.MMS fastlink/4.1P/vaxvms/README.VAX fastlink/4.1P/vaxvms/decc_checkpointdefs.h fastlink/4.1P/vaxvms/vaxc_checkpointdefs.h fastlink/aix/ fastlink/aix/sachau.ps fastlink/linux/ fastlink/linux/hornik.txt fastlink/README.AIX fastlink/README.ALPHAVMS fastlink/README.Digital fastlink/README.ILINK fastlink/README.IRIX fastlink/README.TreadMarks fastlink/README.VAX fastlink/README.VMS fastlink/README.allele fastlink/README.bugreport fastlink/README.checkpoint fastlink/README.constants fastlink/README.diseq fastlink/README.djgpp fastlink/README.loopfile fastlink/README.lselect fastlink/README.makefile fastlink/README.mapfun fastlink/README.memory fastlink/README.p4 fastlink/README.parallel fastlink/README.scaling fastlink/README.time fastlink/README.trouble fastlink/README.unknown fastlink/loops.ps fastlink/paper1.ps fastlink/paper2.ps fastlink/paper3.ps fastlink/paper4.ps fastlink/paper5.ps fastlink/paper6.ps fastlink/paper7.ps fastlink/traverse.ps fastlink/unknown.ps fastlink/README fastlink/README.DOS fastlink/README.Linux fastlink/README.install fastlink/README.portability fastlink/README.updates sudo -u fink-bld [ENV] sh -c /tmp/fink.vs7Mt [ -r /sw/fink/dists/stable/main/finkinfo/sci/fastlink.patch ] sudo -u fink-bld [ENV] sh -c /tmp/fink.Xpbea patch -p1 < /sw/fink/dists/stable/main/finkinfo/sci/fastlink.patch patching file 4.1P/src/Makefile patching file 4.1P/src/commondefs.h Hunk #1 succeeded at 34 (offset 1 line). patching file 4.1P/src/unknown.h sudo -u fink-bld [ENV] sh -c /tmp/fink.8_cw8 echo "we compile in the install phase" we compile in the install phase /bin/rm -rf /sw/build.build/root-fastlink-4.1p-3 /bin/mkdir -p /sw/build.build/root-fastlink-4.1p-3/sw /bin/mkdir -p /sw/build.build/root-fastlink-4.1p-3/DEBIAN /usr/sbin/chown -R fink-bld:fink-bld /sw/build.build/root-fastlink-4.1p-3 sudo -u fink-bld [ENV] sh -c /tmp/fink.dHV15 /tmp/fink.xAHRs #!/bin/bash -ev cd 4.1p/src install -m755 -d /sw/build.build/root-fastlink-4.1p-3/sw/bin make installfast BINDIR=/sw/build.build/root-fastlink-4.1p-3/sw/bin gcc -O -Dmac -DLODSCORE -c iostuff.c -o loiostuff.o iostuff.c:273:1: warning: control reaches end of non-void function [-Wreturn-type] } ^ 1 warning generated. gcc -O -Dmac -DLODSCORE -c check.c -o locheck.o gcc -O -Dmac -DLODSCORE -c comrec.c -o locomrec.o gcc -O -Dmac -DLODSCORE -c logetvect.c -o logetvect.o gcc -O -Dmac -DLODSCORE -c loinputcode.c -o loinputcode.o gcc -O -Dmac -DLODSCORE -c looldnuclear.c -o looldnuclear.o gcc -O -Dmac -c automodified.c -o automodified.o gcc -O -Dmac -DLODSCORE -c comlike.c -o locomlike.o comlike.c:1522:30: warning: too few arguments in call to 'precollapsedown' precollapsedown(V.proband); ~~~~~~~~~~~~~~~ ^ comlike.c:2186:39: warning: too few arguments in call to 'precollapsedown' precollapsedown(proband[ped - 1]); ~~~~~~~~~~~~~~~ ^ 2 warnings generated. gcc -O -Dmac -c sexmodified.c -o sexmodified.o gcc -O -Dmac -DLODSCORE -c lodscore.c -o lodscore.o gcc -O -Dmac loiostuff.o locheck.o locomrec.o logetvect.o loinputcode.o looldnuclear.o automodified.o locomlike.o sexmodified.o lodscore.o -o /sw/build.build/root-fastlink-4.1p-3/sw/bin/lodscore -lm gcc -O -Dmac -DILINK -c iostuff.c -o iliostuff.o iostuff.c:273:1: warning: control reaches end of non-void function [-Wreturn-type] } ^ 1 warning generated. gcc -O -Dmac -DILINK -c check.c -o ilcheck.o gcc -O -Dmac -DILINK -c cominputcode.c -o ilcominputcode.o cominputcode.c:1547:7: warning: add explicit braces to avoid dangling else [-Wdangling-else] else { /*second violation in this pedigree */ ^ 1 warning generated. gcc -O -Dmac -DILINK -c comrec.c -o ilcomrec.o gcc -O -Dmac -DILINK -c ilgetvect.c -o ilgetvect.o gcc -O -Dmac -DILINK -c ilinputcode.c -o ilinputcode.o gcc -O -Dmac -DILINK -c iloldnuclear.c -o iloldnuclear.o gcc -O -Dmac -c comlike.c -o comlike.o comlike.c:1522:30: warning: too few arguments in call to 'precollapsedown' precollapsedown(V.proband); ~~~~~~~~~~~~~~~ ^ comlike.c:2186:39: warning: too few arguments in call to 'precollapsedown' precollapsedown(proband[ped - 1]); ~~~~~~~~~~~~~~~ ^ 2 warnings generated. gcc -O -Dmac -DILINK -c commoncode.c -o ilcommoncode.o gcc -O -Dmac -DILINK -c ilink.c -o ilink.o gcc -O -Dmac iliostuff.o ilcheck.o ilcominputcode.o ilcomrec.o ilgetvect.o ilinputcode.o iloldnuclear.o automodified.o comlike.o sexmodified.o ilcommoncode.o ilink.o -o /sw/build.build/root-fastlink-4.1p-3/sw/bin/ilink -lm gcc -O -Dmac -DLINKMAP -c iostuff.c -o liiostuff.o iostuff.c:273:1: warning: control reaches end of non-void function [-Wreturn-type] } ^ 1 warning generated. gcc -O -Dmac -DLINKMAP -c check.c -o licheck.o gcc -O -Dmac -DLINKMAP -c cominputcode.c -o licominputcode.o cominputcode.c:1547:7: warning: add explicit braces to avoid dangling else [-Wdangling-else] else { /*second violation in this pedigree */ ^ 1 warning generated. gcc -O -Dmac -DLINKMAP -c comrec.c -o licomrec.o gcc -O -Dmac -DLINKMAP -c ligetvect.c -o ligetvect.o gcc -O -Dmac -DLINKMAP -c liinputcode.c -o liinputcode.o gcc -O -Dmac -DLINKMAP -c lioldnuclear.c -o lioldnuclear.o gcc -O -Dmac -DLINKMAP -c commoncode.c -o licommoncode.o gcc -O -Dmac -DLINKMAP -c linkmap.c -o linkmap.o gcc -O -Dmac liiostuff.o licheck.o licominputcode.o licomrec.o ligetvect.o liinputcode.o lioldnuclear.o automodified.o comlike.o sexmodified.o licommoncode.o linkmap.o -o /sw/build.build/root-fastlink-4.1p-3/sw/bin/linkmap -lm gcc -O -Dmac -DMLINK -c iostuff.c -o mliostuff.o iostuff.c:273:1: warning: control reaches end of non-void function [-Wreturn-type] } ^ 1 warning generated. gcc -O -Dmac -DMLINK -c check.c -o mlcheck.o gcc -O -Dmac -DMLINK -c cominputcode.c -o mlcominputcode.o cominputcode.c:1547:7: warning: add explicit braces to avoid dangling else [-Wdangling-else] else { /*second violation in this pedigree */ ^ 1 warning generated. gcc -O -Dmac -DMLINK -c comrec.c -o mlcomrec.o gcc -O -Dmac -DMLINK -c mlgetvect.c -o mlgetvect.o gcc -O -Dmac -DMLINK -c mlinputcode.c -o mlinputcode.o gcc -O -Dmac -DMLINK -c mloldnuclear.c -o mloldnuclear.o gcc -O -Dmac -DMLINK -c commoncode.c -o mlcommoncode.o gcc -O -Dmac -DMLINK -c mlink.c -o mlink.o mlink.c:287:7: warning: add explicit braces to avoid dangling else [-Wdangling-else] else ^ mlink.c:295:7: warning: add explicit braces to avoid dangling else [-Wdangling-else] else ^ 2 warnings generated. gcc -O -Dmac mliostuff.o mlcheck.o mlcominputcode.o mlcomrec.o mlgetvect.o mlinputcode.o mloldnuclear.o automodified.o comlike.o sexmodified.o mlcommoncode.o mlink.o -o /sw/build.build/root-fastlink-4.1p-3/sw/bin/mlink -lm gcc -O -Dmac unknown.c -c -o unknown.o unknown.c:1819:17: warning: add explicit braces to avoid dangling else [-Wdangling-else] else ^ unknown.c:2030:17: warning: add explicit braces to avoid dangling else [-Wdangling-else] else ^ unknown.c:4362:13: warning: add explicit braces to avoid dangling else [-Wdangling-else] else ^ unknown.c:4367:109: warning: format specifies type 'int' but the argument has type 'long' [-Wformat] fprintf(countfile,"At locus %d person %d has %d homozygous genotypes and\n %d heterozygous genotypes\n",whichsys,i,homoz,heteroz); ~~ ^~~~~~~~ %ld unknown.c:5056:36: warning: for loop has empty body [-Wempty-body] for(ped = 0; ped < MAXPED; ped++); ^ unknown.c:5056:36: note: put the semicolon on a separate line to silence this warning 5 warnings generated. gcc -O -Dmac loopbrk.c -c -o loopbrk.o loopbrk.c:62:25: warning: if statement has empty body [-Wempty-body] if (NULL != countfile); ^ loopbrk.c:62:25: note: put the semicolon on a separate line to silence this warning loopbrk.c:1625:18: warning: using the result of an assignment as a condition without parentheses [-Wparentheses] if (fatherIndex = ped[NodeIndex].paid) { ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ loopbrk.c:1625:18: note: place parentheses around the assignment to silence this warning if (fatherIndex = ped[NodeIndex].paid) { ^ ( ) loopbrk.c:1625:18: note: use '==' to turn this assignment into an equality comparison if (fatherIndex = ped[NodeIndex].paid) { ^ == loopbrk.c:1631:18: warning: using the result of an assignment as a condition without parentheses [-Wparentheses] if (motherIndex = ped[NodeIndex].maid) ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ loopbrk.c:1631:18: note: place parentheses around the assignment to silence this warning if (motherIndex = ped[NodeIndex].maid) ^ ( ) loopbrk.c:1631:18: note: use '==' to turn this assignment into an equality comparison if (motherIndex = ped[NodeIndex].maid) ^ == 3 warnings generated. gcc -O -Dmac loopbrk.o unknown.o -o /sw/build.build/root-fastlink-4.1p-3/sw/bin/unknown -lm sudo -u fink-bld [ENV] sh -c /tmp/fink.R3NlU /usr/bin/install -d -m 700 /sw/build.build/root-fastlink-4.1p-3/sw/share/doc/fastlink /bin/cp -r README /sw/build.build/root-fastlink-4.1p-3/sw/share/doc/fastlink/ /bin/cp -r README.AIX /sw/build.build/root-fastlink-4.1p-3/sw/share/doc/fastlink/ /bin/cp -r README.ALPHAVMS /sw/build.build/root-fastlink-4.1p-3/sw/share/doc/fastlink/ /bin/cp -r README.DOS /sw/build.build/root-fastlink-4.1p-3/sw/share/doc/fastlink/ /bin/cp -r README.Digital /sw/build.build/root-fastlink-4.1p-3/sw/share/doc/fastlink/ /bin/cp -r README.ILINK /sw/build.build/root-fastlink-4.1p-3/sw/share/doc/fastlink/ /bin/cp -r README.IRIX /sw/build.build/root-fastlink-4.1p-3/sw/share/doc/fastlink/ /bin/cp -r README.Linux /sw/build.build/root-fastlink-4.1p-3/sw/share/doc/fastlink/ /bin/cp -r README.TreadMarks /sw/build.build/root-fastlink-4.1p-3/sw/share/doc/fastlink/ /bin/cp -r README.VAX /sw/build.build/root-fastlink-4.1p-3/sw/share/doc/fastlink/ /bin/cp -r README.VMS /sw/build.build/root-fastlink-4.1p-3/sw/share/doc/fastlink/ /bin/cp -r README.allele /sw/build.build/root-fastlink-4.1p-3/sw/share/doc/fastlink/ /bin/cp -r README.bugreport /sw/build.build/root-fastlink-4.1p-3/sw/share/doc/fastlink/ /bin/cp -r README.checkpoint /sw/build.build/root-fastlink-4.1p-3/sw/share/doc/fastlink/ /bin/cp -r README.constants /sw/build.build/root-fastlink-4.1p-3/sw/share/doc/fastlink/ /bin/cp -r README.diseq /sw/build.build/root-fastlink-4.1p-3/sw/share/doc/fastlink/ /bin/cp -r README.djgpp /sw/build.build/root-fastlink-4.1p-3/sw/share/doc/fastlink/ /bin/cp -r README.install /sw/build.build/root-fastlink-4.1p-3/sw/share/doc/fastlink/ /bin/cp -r README.loopfile /sw/build.build/root-fastlink-4.1p-3/sw/share/doc/fastlink/ /bin/cp -r README.lselect /sw/build.build/root-fastlink-4.1p-3/sw/share/doc/fastlink/ /bin/cp -r README.makefile /sw/build.build/root-fastlink-4.1p-3/sw/share/doc/fastlink/ /bin/cp -r README.mapfun /sw/build.build/root-fastlink-4.1p-3/sw/share/doc/fastlink/ /bin/cp -r README.memory /sw/build.build/root-fastlink-4.1p-3/sw/share/doc/fastlink/ /bin/cp -r README.p4 /sw/build.build/root-fastlink-4.1p-3/sw/share/doc/fastlink/ /bin/cp -r README.parallel /sw/build.build/root-fastlink-4.1p-3/sw/share/doc/fastlink/ /bin/cp -r README.portability /sw/build.build/root-fastlink-4.1p-3/sw/share/doc/fastlink/ /bin/cp -r README.scaling /sw/build.build/root-fastlink-4.1p-3/sw/share/doc/fastlink/ /bin/cp -r README.time /sw/build.build/root-fastlink-4.1p-3/sw/share/doc/fastlink/ /bin/cp -r README.trouble /sw/build.build/root-fastlink-4.1p-3/sw/share/doc/fastlink/ /bin/cp -r README.unknown /sw/build.build/root-fastlink-4.1p-3/sw/share/doc/fastlink/ /bin/cp -r README.updates /sw/build.build/root-fastlink-4.1p-3/sw/share/doc/fastlink/ /bin/cp -r loops.ps /sw/build.build/root-fastlink-4.1p-3/sw/share/doc/fastlink/ /bin/cp -r paper1.ps /sw/build.build/root-fastlink-4.1p-3/sw/share/doc/fastlink/ /bin/cp -r paper2.ps /sw/build.build/root-fastlink-4.1p-3/sw/share/doc/fastlink/ /bin/cp -r paper3.ps /sw/build.build/root-fastlink-4.1p-3/sw/share/doc/fastlink/ /bin/cp -r paper4.ps /sw/build.build/root-fastlink-4.1p-3/sw/share/doc/fastlink/ /bin/cp -r paper5.ps /sw/build.build/root-fastlink-4.1p-3/sw/share/doc/fastlink/ /bin/cp -r paper6.ps /sw/build.build/root-fastlink-4.1p-3/sw/share/doc/fastlink/ /bin/cp -r paper7.ps /sw/build.build/root-fastlink-4.1p-3/sw/share/doc/fastlink/ /bin/cp -r traverse.ps /sw/build.build/root-fastlink-4.1p-3/sw/share/doc/fastlink/ /bin/cp -r unknown.ps /sw/build.build/root-fastlink-4.1p-3/sw/share/doc/fastlink/ /bin/chmod -R go=u-w /sw/build.build/root-fastlink-4.1p-3/sw/share/doc/fastlink /bin/rm -f /sw/build.build/root-fastlink-4.1p-3/sw/info/dir /sw/build.build/root-fastlink-4.1p-3/sw/info/dir.old /sw/build.build/root-fastlink-4.1p-3/sw/share/info/dir /sw/build.build/root-fastlink-4.1p-3/sw/share/info/dir.old Reverting ownership of install dir to root Writing control file... Writing md5sums file... env LANG=C LC_ALL=C dpkg-deb -b root-fastlink-4.1p-3 /sw/fink/10.9/stable/main/binary-darwin-x86_64/sci dpkg-deb: building package `fastlink' in `/sw/fink/10.9/stable/main/binary-darwin-x86_64/sci/fastlink_4.1p-3_darwin-x86_64.deb'. Removing runtime build-lock... Removing build-lock package... /sw/bin/dpkg-lockwait -r fink-buildlock-fastlink-4.1p-3 (Reading database ... 4297 files and directories currently installed.) Removing fink-buildlock-fastlink-4.1p-3 ...