[Debian-med-packaging] Bug#655806: mafft: FTBFS: test failed

[Lucas Nussbaum]

Source: mafft
Version: 6.864-1
Severity: serious
Tags: wheezy sid
User: debian-qa at lists.debian.org
Usertags: qa-ftbfs-20120112 qa-ftbfs
Justification: FTBFS on amd64

Hi,

During a rebuild of all packages in sid, your package failed to build on
amd64.

Relevant part:
> make[2]: Entering directory `/build/mafft-bZ9hLD/mafft-6.864/core'
> cp mafft mafft-homologs.rb ../scripts
> chmod 755 ../scripts/*
> cp dvtditr dndfast7 dndblast sextet5 mafft-distance pairlocalalign pair2hat3s multi2hat3s rnatest pairash splittbfast disttbfast tbfast mafft-profile f2cl mccaskillwrap contrafoldwrap countlen seq2regtable regtable2seq score getlag dndpre dndpre2 setcore replaceu restoreu version ../binaries
> chmod 755 ../binaries/*
> cp mafft.1 mafft-homologs.1 ../binaries
> done.
> mkdir -p /build/mafft-bZ9hLD/mafft-6.864/debian/mafft/usr/lib/mafft/lib/mafft
> chmod 755 /build/mafft-bZ9hLD/mafft-6.864/debian/mafft/usr/lib/mafft/lib/mafft
> mkdir -p /build/mafft-bZ9hLD/mafft-6.864/debian/mafft/usr/lib/mafft/bin
> chmod 755 /build/mafft-bZ9hLD/mafft-6.864/debian/mafft/usr/lib/mafft/bin
> chmod 755 mafft mafft-homologs.rb
> install mafft mafft-homologs.rb  /build/mafft-bZ9hLD/mafft-6.864/debian/mafft/usr/lib/mafft/bin
> chmod 755 dvtditr dndfast7 dndblast sextet5 mafft-distance pairlocalalign pair2hat3s multi2hat3s rnatest pairash splittbfast disttbfast tbfast mafft-profile f2cl mccaskillwrap contrafoldwrap countlen seq2regtable regtable2seq score getlag dndpre dndpre2 setcore replaceu restoreu version
> install dvtditr dndfast7 dndblast sextet5 mafft-distance pairlocalalign pair2hat3s multi2hat3s rnatest pairash splittbfast disttbfast tbfast mafft-profile f2cl mccaskillwrap contrafoldwrap countlen seq2regtable regtable2seq score getlag dndpre dndpre2 setcore replaceu restoreu version /build/mafft-bZ9hLD/mafft-6.864/debian/mafft/usr/lib/mafft/lib/mafft
> install -m 644 mafft.1 mafft-homologs.1 /build/mafft-bZ9hLD/mafft-6.864/debian/mafft/usr/lib/mafft/lib/mafft
> ( cd /build/mafft-bZ9hLD/mafft-6.864/debian/mafft/usr/lib/mafft/bin; \
> rm -f linsi ginsi einsi fftns fftnsi nwns nwnsi xinsi qinsi; \
> rm -f mafft-linsi mafft-ginsi mafft-einsi mafft-fftns mafft-fftnsi mafft-nwns mafft-nwnsi mafft-xinsi mafft-qinsi; \
> ln -s mafft linsi; ln -s mafft ginsi; ln -s mafft fftns; \
> ln -s mafft fftnsi; ln -s mafft nwns; ln -s mafft nwnsi; \
> ln -s mafft einsi; \
> ln -s mafft mafft-linsi; ln -s mafft mafft-ginsi; ln -s mafft mafft-fftns; \
> ln -s mafft mafft-fftnsi; ln -s mafft mafft-nwns; ln -s mafft mafft-nwnsi; \
> ln -s mafft mafft-einsi; ln -s mafft mafft-xinsi; ln -s mafft mafft-qinsi;\
> rm -f mafft-profile mafft-profile.exe; ln -s /build/mafft-bZ9hLD/mafft-6.864/debian/mafft/usr/lib/mafft/lib/mafft/mafft-profile .; \
> rm -f mafft-distance mafft-distance.exe; ln -s /build/mafft-bZ9hLD/mafft-6.864/debian/mafft/usr/lib/mafft/lib/mafft/mafft-distance . )
> mkdir -p /build/mafft-bZ9hLD/mafft-6.864/debian/mafft/usr/share/man/man1
> chmod 755 /build/mafft-bZ9hLD/mafft-6.864/debian/mafft/usr/share/man/man1
> install -m 644 mafft.1 mafft-homologs.1 /build/mafft-bZ9hLD/mafft-6.864/debian/mafft/usr/share/man/man1
> make[2]: Leaving directory `/build/mafft-bZ9hLD/mafft-6.864/core'
> rm /build/mafft-bZ9hLD/mafft-6.864/debian/mafft/usr/lib/mafft/lib/mafft/*.1
> # Testing Mafft…
> MAFFT_BINARIES=/build/mafft-bZ9hLD/mafft-6.864/binaries scripts/mafft 				test/sample | diff test/sample.fftns2 -
> scripts/mafft: 1185: scripts/mafft: cannot create /dev/stderr: Permission denied
> scripts/mafft: 1186: scripts/mafft: cannot create /dev/stderr: Permission denied
> scripts/mafft: 1187: scripts/mafft: cannot create /dev/stderr: Permission denied
> scripts/mafft: 1188: scripts/mafft: cannot create /dev/stderr: Permission denied
> scripts/mafft: 1189: scripts/mafft: cannot create /dev/stderr: Permission denied
> scripts/mafft: 1190: scripts/mafft: cannot create /dev/stderr: Permission denied
> scripts/mafft: 1309: scripts/mafft: cannot create /dev/stderr: Permission denied
> 1,468d0
> < >     1== M63632   1 Lampetra japonica rhodopsin <>[BBRC174,1125-1132'91]
> < ------------------------------------------------------------
> < ---------MNGTE--GDNFYVP----FSNKTGLARSPYEYPQY-YLAEPWK--------
> < -YSALAAYMFFLILVGFPVNFLTLFVTVQHKKLRTPLNYILLNLAMANLFMVLFG-FTVT
> < MYTSMN-GYFV--FGPTMCSIEGFFATLGGEVALWSLVVLAIERYIVICKPMGN-FRFGN
> < THAIMGVAFTWIMALAC-AAPPLVG-W-----SRYIPEGMQCSCGPDYYTLNPNFNNESY
> < VVYMFVVHFLVPFVIIFFCYGRLLCTV---------------------------------
> < ------------------------------------------------------------
> < ------------------------------KEAAAAQQ----------ESASTQKA----
> < -------------------------EKEVTRMVVLMVIGFLVCWVPYASVAFYIFTHQGS
> < D---FGATFMTLPAFFAKSSALYNPVIYILMNKQFRNCMITTLCCGKN------PLGDDE
> < --SGASTSKTEVSSVS-TSPVSPA------------------------------------
> < ---------------------------------------------------
> < >     2== U22180   1 rat opsin <rod>[J.Mol.Neurosci.5(3),207-209'94]
> < ------------------------------------------------------------
> < ---------MNGTE--GPNFYVP----FSNITGVVRSPFEQPQY-YLAEPWQ--------
> < -FSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVFGG-FTTT
> < LYTSLH-GYFV--FGPTGCNLEGFFATLGGEIGLWSLVVLAIERYVVVCKPMSN-FRFGE
> < NHAIMGVAFTWVMALAC-AAPPLVG-W-----SRYIPEGMQCSCGIDYYTLKPEVNNESF
> < VIYMFVVHFTIPMIVIFFCYGQLVFTV---------------------------------
> < ------------------------------------------------------------
> < ------------------------------KEAAAQQQ----------ESATTQKA----
> < -------------------------EKEVTRMVIIMVIFFLICWLPYASVAMYIFTHQGS
> < N---FGPIFMTLPAFFAKTASIYNPIIYIMMNKQFRNCMLTSLCCGKN------PLGDDE
> < --ASATASKTE------TSQVAPA------------------------------------
> < ---------------------------------------------------
> < >     3== M92038   1 chicken green sensitive cone opsin <retina>[PNAS89,5932-5936'9
> < ------------------------------------------------------------
> < ---------MNGTE--GINFYVP----MSNKTGVVRSPFEYPQY-YLAEPWK--------
> < -YRLVCCYIFFLISTGLPINLLTLLVTFKHKKLRQPLNYILVNLAVADLFMACFG-FTVT
> < FYTAWN-GYFV--FGPVGCAVEGFFATLGGQVALWSLVVLAIERYIVVCKPMGN-FRFSA
> < THAMMGIAFTWVMAFSC-AAPPLFG-W-----SRYMPEGMQCSCGPDYYTHNPDYHNESY
> < VLYMFVIHFIIPVVVIFFSYGRLICKV---------------------------------
> < ------------------------------------------------------------
> < ------------------------------REAAAQQQ----------ESATTQKA----
> < -------------------------EKEVTRMVILMVLGFMLAWTPYAVVAFWIFTNKGA
> < D---FTATLMAVPAFFSKSSSLYNPIIYVLMNKQFRNCMITTICCGKN------PFGDED
> < VSSTVSQSKTEVSSVS-SSQVSPA------------------------------------
> < ---------------------------------------------------
> < >     4=p A45229 opsin, green-sensitive (clone GFgr-1) - goldfish
> < ------------------------------------------------------------
> < ---------MNGTE--GKNFYVP----MSNRTGLVRSPFEYPQY-YLAEPWQ--------
> < -FKILALYLFFLMSMGLPINGLTLVVTAQHKKLRQPLNFILVNLAVAGTIMVCFG-FTVT
> < FYTAIN-GYFV--LGPTGCAVEGFMATLGGEVALWSLVVLAIERYIVVCKPMGS-FKFSS
> < SHAFAGIAFTWVMALAC-AAPPLFG-W-----SRYIPEGMQCSCGPDYYTLNPDYNNESY
> < VIYMFVCHFILPVAVIFFTYGRLVCTV---------------------------------
> < ------------------------------------------------------------
> < ------------------------------KAAAAQQQ----------DSASTQKA----
> < -------------------------EREVTKMVILMVFGFLIAWTPYATVAAWIFFNKGA
> < D---FSAKFMAIPAFFSKSSALYNPVIYVLLNKQFRNCMLTTIFCGKN------PLGDDE
> < -SSTVSTSKTEVSS------VSPA------------------------------------
> < ---------------------------------------------------
> < >     5=p B45229 opsin, green-sensitive (clone GFgr-2) - goldfish
> < ------------------------------------------------------------
> < ---------MNGTE--GNNFYVP----LSNRTGLVRSPFEYPQY-YLAEPWQ--------
> < -FKLLAVYMFFLICLGLPINGLTLICTAQHKKLRQPLNFILVNLAVAGAIMVCFG-FTVT
> < FYTAIN-GYFA--LGPTGCAVEGFMATLGGEVALWSLVVLAIERYIVVCKPMGS-FKFSS
> < THASAGIAFTWVMAMAC-AAPPLVG-W-----SRYIPEGIQCSCGPDYYTLNPEYNNESY
> < VLYMFICHFILPVTIIFFTYGRLVCTV---------------------------------
> < ------------------------------------------------------------
> < ------------------------------KAAAAQQQ----------DSASTQKA----
> < -------------------------EREVTKMVILMVLGFLVAWTPYATVAAWIFFNKGA
> make[1]: *** [override_dh_install] Error 1

The full build log is available from:
   http://people.debian.org/~lucas/logs/2012/01/12/mafft_6.864-1_lsid64.buildlog

A list of current common problems and possible solutions is available at 
http://wiki.debian.org/qa.debian.org/FTBFS . You're welcome to contribute!

About the archive rebuild: The rebuild was done on about 50 AMD64 nodes
of the Grid'5000 platform, using a clean chroot.  Internet was not
accessible from the build systems.