[Debian-med-packaging] Bug#833515: alter-sequence-alignment: FTBFS: failed to create task or type foreach

Chris Lamb lamby at debian.org
Fri Aug 5 10:46:20 UTC 2016 

Source: alter-sequence-alignment
Version: 1.3.3+dfsg-1
Severity: serious
Justification: fails to build from source
User: reproducible-builds at lists.alioth.debian.org
Usertags: ftbfs
X-Debbugs-Cc: reproducible-builds at lists.alioth.debian.org

Dear Maintainer,

alter-sequence-alignment fails to build from source in unstable/amd64:

  [..]

  update-alternatives: using /usr/lib/jvm/java-8-openjdk-amd64/bin/jstack to provide /usr/bin/jstack (jstack) in auto mode
  update-alternatives: using /usr/lib/jvm/java-8-openjdk-amd64/bin/jrunscript to provide /usr/bin/jrunscript (jrunscript) in auto mode
  update-alternatives: using /usr/lib/jvm/java-8-openjdk-amd64/bin/javadoc to provide /usr/bin/javadoc (javadoc) in auto mode
  update-alternatives: using /usr/lib/jvm/java-8-openjdk-amd64/bin/jhat to provide /usr/bin/jhat (jhat) in auto mode
  update-alternatives: using /usr/lib/jvm/java-8-openjdk-amd64/bin/javap to provide /usr/bin/javap (javap) in auto mode
  update-alternatives: using /usr/lib/jvm/java-8-openjdk-amd64/bin/jar to provide /usr/bin/jar (jar) in auto mode
  update-alternatives: using /usr/lib/jvm/java-8-openjdk-amd64/bin/xjc to provide /usr/bin/xjc (xjc) in auto mode
  update-alternatives: using /usr/lib/jvm/java-8-openjdk-amd64/bin/schemagen to provide /usr/bin/schemagen (schemagen) in auto mode
  update-alternatives: using /usr/lib/jvm/java-8-openjdk-amd64/bin/jps to provide /usr/bin/jps (jps) in auto mode
  update-alternatives: using /usr/lib/jvm/java-8-openjdk-amd64/bin/extcheck to provide /usr/bin/extcheck (extcheck) in auto mode
  update-alternatives: using /usr/lib/jvm/java-8-openjdk-amd64/bin/jmap to provide /usr/bin/jmap (jmap) in auto mode
  update-alternatives: using /usr/lib/jvm/java-8-openjdk-amd64/bin/jstatd to provide /usr/bin/jstatd (jstatd) in auto mode
  update-alternatives: using /usr/lib/jvm/java-8-openjdk-amd64/bin/jdb to provide /usr/bin/jdb (jdb) in auto mode
  update-alternatives: using /usr/lib/jvm/java-8-openjdk-amd64/bin/serialver to provide /usr/bin/serialver (serialver) in auto mode
  update-alternatives: using /usr/lib/jvm/java-8-openjdk-amd64/bin/wsgen to provide /usr/bin/wsgen (wsgen) in auto mode
  update-alternatives: using /usr/lib/jvm/java-8-openjdk-amd64/bin/jcmd to provide /usr/bin/jcmd (jcmd) in auto mode
  update-alternatives: using /usr/lib/jvm/java-8-openjdk-amd64/bin/jarsigner to provide /usr/bin/jarsigner (jarsigner) in auto mode
  Setting up openjdk-8-jre:amd64 (8u102-b14.1-1) ...
  update-alternatives: using /usr/lib/jvm/java-8-openjdk-amd64/jre/bin/policytool to provide /usr/bin/policytool (policytool) in auto mode
  Setting up ant (1.9.7-3) ...
  Setting up javacc (5.0-5) ...
  Setting up default-jre-headless (2:1.8-57) ...
  Setting up default-jdk-headless (2:1.8-57) ...
  Setting up openjdk-8-jdk:amd64 (8u102-b14.1-1) ...
  update-alternatives: using /usr/lib/jvm/java-8-openjdk-amd64/bin/appletviewer to provide /usr/bin/appletviewer (appletviewer) in auto mode
  update-alternatives: using /usr/lib/jvm/java-8-openjdk-amd64/bin/jconsole to provide /usr/bin/jconsole (jconsole) in auto mode
  Setting up default-jre (2:1.8-57) ...
  Setting up ant-contrib (1.0~b3+svn177-8) ...
  Setting up default-jdk (2:1.8-57) ...
  Setting up alter-sequence-alignment-build-deps (1.3.3+dfsg-1) ...
  Processing triggers for libc-bin (2.23-4) ...
  Processing triggers for systemd (231-1) ...
  Processing triggers for ca-certificates (20160104) ...
  Updating certificates in /etc/ssl/certs...
  173 added, 0 removed; done.
  Running hooks in /etc/ca-certificates/update.d...
  
  Adding debian:ACCVRAIZ1.pem
  Adding debian:ACEDICOM_Root.pem
  Adding debian:AC_Raíz_Certicámara_S.A..pem
  Adding debian:Actalis_Authentication_Root_CA.pem
  Adding debian:AddTrust_External_Root.pem
  Adding debian:AddTrust_Low-Value_Services_Root.pem
  Adding debian:AddTrust_Public_Services_Root.pem
  Adding debian:AddTrust_Qualified_Certificates_Root.pem
  Adding debian:AffirmTrust_Commercial.pem
  Adding debian:AffirmTrust_Networking.pem
  Adding debian:AffirmTrust_Premium.pem
  Adding debian:AffirmTrust_Premium_ECC.pem
  Adding debian:ApplicationCA_-_Japanese_Government.pem
  Adding debian:Atos_TrustedRoot_2011.pem
  Adding debian:Autoridad_de_Certificacion_Firmaprofesional_CIF_A62634068.pem
  Adding debian:Baltimore_CyberTrust_Root.pem
  Adding debian:Buypass_Class_2_CA_1.pem
  Adding debian:Buypass_Class_2_Root_CA.pem
  Adding debian:Buypass_Class_3_Root_CA.pem
  Adding debian:CA_Disig.pem
  Adding debian:CA_Disig_Root_R1.pem
  Adding debian:CA_Disig_Root_R2.pem
  Adding debian:CA_WoSign_ECC_Root.pem
  Adding debian:CFCA_EV_ROOT.pem
  Adding debian:CNNIC_ROOT.pem
  Adding debian:COMODO_Certification_Authority.pem
  Adding debian:COMODO_ECC_Certification_Authority.pem
  Adding debian:COMODO_RSA_Certification_Authority.pem
  Adding debian:Camerfirma_Chambers_of_Commerce_Root.pem
  Adding debian:Camerfirma_Global_Chambersign_Root.pem
  Adding debian:Certification_Authority_of_WoSign_G2.pem
  Adding debian:Certigna.pem
  Adding debian:Certinomis_-_Autorité_Racine.pem
  Adding debian:Certinomis_-_Root_CA.pem
  Adding debian:Certplus_Class_2_Primary_CA.pem
  Adding debian:Certum_Root_CA.pem
  Adding debian:Certum_Trusted_Network_CA.pem
  Adding debian:Chambers_of_Commerce_Root_-_2008.pem
  Adding debian:China_Internet_Network_Information_Center_EV_Certificates_Root.pem
  Adding debian:ComSign_CA.pem
  Adding debian:Comodo_AAA_Services_root.pem
  Adding debian:Comodo_Secure_Services_root.pem
  Adding debian:Comodo_Trusted_Services_root.pem
  Adding debian:Cybertrust_Global_Root.pem
  Adding debian:D-TRUST_Root_Class_3_CA_2_2009.pem
  Adding debian:D-TRUST_Root_Class_3_CA_2_EV_2009.pem
  Adding debian:DST_ACES_CA_X6.pem
  Adding debian:DST_Root_CA_X3.pem
  Adding debian:Deutsche_Telekom_Root_CA_2.pem
  Adding debian:DigiCert_Assured_ID_Root_CA.pem
  Adding debian:DigiCert_Assured_ID_Root_G2.pem
  Adding debian:DigiCert_Assured_ID_Root_G3.pem
  Adding debian:DigiCert_Global_Root_CA.pem
  Adding debian:DigiCert_Global_Root_G2.pem
  Adding debian:DigiCert_Global_Root_G3.pem
  Adding debian:DigiCert_High_Assurance_EV_Root_CA.pem
  Adding debian:DigiCert_Trusted_Root_G4.pem
  Adding debian:E-Tugra_Certification_Authority.pem
  Adding debian:EBG_Elektronik_Sertifika_Hizmet_Sağlayıcısı.pem
  Adding debian:EC-ACC.pem
  Adding debian:EE_Certification_Centre_Root_CA.pem
  Adding debian:Entrust.net_Premium_2048_Secure_Server_CA.pem
  Adding debian:Entrust_Root_Certification_Authority.pem
  Adding debian:Entrust_Root_Certification_Authority_-_EC1.pem
  Adding debian:Entrust_Root_Certification_Authority_-_G2.pem
  Adding debian:Equifax_Secure_CA.pem
  Adding debian:Equifax_Secure_Global_eBusiness_CA.pem
  Adding debian:Equifax_Secure_eBusiness_CA_1.pem
  Adding debian:GeoTrust_Global_CA.pem
  Adding debian:GeoTrust_Global_CA_2.pem
  Adding debian:GeoTrust_Primary_Certification_Authority.pem
  Adding debian:GeoTrust_Primary_Certification_Authority_-_G2.pem
  Adding debian:GeoTrust_Primary_Certification_Authority_-_G3.pem
  Adding debian:GeoTrust_Universal_CA.pem
  Adding debian:GeoTrust_Universal_CA_2.pem
  Adding debian:GlobalSign_ECC_Root_CA_-_R4.pem
  Adding debian:GlobalSign_ECC_Root_CA_-_R5.pem
  Adding debian:GlobalSign_Root_CA.pem
  Adding debian:GlobalSign_Root_CA_-_R2.pem
  Adding debian:GlobalSign_Root_CA_-_R3.pem
  Adding debian:Global_Chambersign_Root_-_2008.pem
  Adding debian:Go_Daddy_Class_2_CA.pem
  Adding debian:Go_Daddy_Root_Certificate_Authority_-_G2.pem
  Adding debian:Hellenic_Academic_and_Research_Institutions_RootCA_2011.pem
  Adding debian:Hongkong_Post_Root_CA_1.pem
  Adding debian:IGC_A.pem
  Adding debian:IdenTrust_Commercial_Root_CA_1.pem
  Adding debian:IdenTrust_Public_Sector_Root_CA_1.pem
  Adding debian:Izenpe.com.pem
  Adding debian:Juur-SK.pem
  Adding debian:Microsec_e-Szigno_Root_CA.pem
  Adding debian:Microsec_e-Szigno_Root_CA_2009.pem
  Adding debian:NetLock_Arany_=Class_Gold=_Főtanúsítvány.pem
  Adding debian:NetLock_Business_=Class_B=_Root.pem
  Adding debian:NetLock_Express_=Class_C=_Root.pem
  Adding debian:NetLock_Notary_=Class_A=_Root.pem
  Adding debian:NetLock_Qualified_=Class_QA=_Root.pem
  Adding debian:Network_Solutions_Certificate_Authority.pem
  Adding debian:OISTE_WISeKey_Global_Root_GA_CA.pem
  Adding debian:OISTE_WISeKey_Global_Root_GB_CA.pem
  Adding debian:PSCProcert.pem
  Adding debian:QuoVadis_Root_CA.pem
  Adding debian:QuoVadis_Root_CA_1_G3.pem
  Adding debian:QuoVadis_Root_CA_2.pem
  Adding debian:QuoVadis_Root_CA_2_G3.pem
  Adding debian:QuoVadis_Root_CA_3.pem
  Adding debian:QuoVadis_Root_CA_3_G3.pem
  Adding debian:RSA_Security_2048_v3.pem
  Adding debian:Root_CA_Generalitat_Valenciana.pem
  Adding debian:S-TRUST_Authentication_and_Encryption_Root_CA_2005_PN.pem
  Adding debian:S-TRUST_Universal_Root_CA.pem
  Adding debian:SecureSign_RootCA11.pem
  Adding debian:SecureTrust_CA.pem
  Adding debian:Secure_Global_CA.pem
  Adding debian:Security_Communication_EV_RootCA1.pem
  Adding debian:Security_Communication_RootCA2.pem
  Adding debian:Security_Communication_Root_CA.pem
  Adding debian:Sonera_Class_1_Root_CA.pem
  Adding debian:Sonera_Class_2_Root_CA.pem
  Adding debian:Staat_der_Nederlanden_EV_Root_CA.pem
  Adding debian:Staat_der_Nederlanden_Root_CA.pem
  Adding debian:Staat_der_Nederlanden_Root_CA_-_G2.pem
  Adding debian:Staat_der_Nederlanden_Root_CA_-_G3.pem
  Adding debian:Starfield_Class_2_CA.pem
  Adding debian:Starfield_Root_Certificate_Authority_-_G2.pem
  Adding debian:Starfield_Services_Root_Certificate_Authority_-_G2.pem
  Adding debian:StartCom_Certification_Authority.pem
  Adding debian:StartCom_Certification_Authority_2.pem
  Adding debian:StartCom_Certification_Authority_G2.pem
  Adding debian:SwissSign_Gold_CA_-_G2.pem
  Adding debian:SwissSign_Platinum_CA_-_G2.pem
  Adding debian:SwissSign_Silver_CA_-_G2.pem
  Adding debian:Swisscom_Root_CA_1.pem
  Adding debian:Swisscom_Root_CA_2.pem
  Adding debian:Swisscom_Root_EV_CA_2.pem
  Adding debian:T-TeleSec_GlobalRoot_Class_2.pem
  Adding debian:T-TeleSec_GlobalRoot_Class_3.pem
  Adding debian:TC_TrustCenter_Class_3_CA_II.pem
  Adding debian:TURKTRUST_Certificate_Services_Provider_Root_2007.pem
  Adding debian:TWCA_Global_Root_CA.pem
  Adding debian:TWCA_Root_Certification_Authority.pem
  Adding debian:Taiwan_GRCA.pem
  Adding debian:TeliaSonera_Root_CA_v1.pem
  Adding debian:Trustis_FPS_Root_CA.pem
  Adding debian:TÜBİTAK_UEKAE_Kök_Sertifika_Hizmet_Sağlayıcısı_-_Sürüm_3.pem
  Adding debian:TÜRKTRUST_Elektronik_Sertifika_Hizmet_Sağlayıcısı_H5.pem
  Adding debian:TÜRKTRUST_Elektronik_Sertifika_Hizmet_Sağlayıcısı_H6.pem
  Adding debian:USERTrust_ECC_Certification_Authority.pem
  Adding debian:USERTrust_RSA_Certification_Authority.pem
  Adding debian:UTN_USERFirst_Email_Root_CA.pem
  Adding debian:UTN_USERFirst_Hardware_Root_CA.pem
  Adding debian:VeriSign_Class_3_Public_Primary_Certification_Authority_-_G4.pem
  Adding debian:VeriSign_Class_3_Public_Primary_Certification_Authority_-_G5.pem
  Adding debian:VeriSign_Universal_Root_Certification_Authority.pem
  Adding debian:Verisign_Class_1_Public_Primary_Certification_Authority.pem
  Adding debian:Verisign_Class_1_Public_Primary_Certification_Authority_-_G2.pem
  Adding debian:Verisign_Class_1_Public_Primary_Certification_Authority_-_G3.pem
  Adding debian:Verisign_Class_2_Public_Primary_Certification_Authority_-_G2.pem
  Adding debian:Verisign_Class_2_Public_Primary_Certification_Authority_-_G3.pem
  Adding debian:Verisign_Class_3_Public_Primary_Certification_Authority.pem
  Adding debian:Verisign_Class_3_Public_Primary_Certification_Authority_-_G2.pem
  Adding debian:Verisign_Class_3_Public_Primary_Certification_Authority_-_G3.pem
  Adding debian:Verisign_Class_3_Public_Primary_Certification_Authority_2.pem
  Adding debian:Visa_eCommerce_Root.pem
  Adding debian:WellsSecure_Public_Root_Certificate_Authority.pem
  Adding debian:WoSign.pem
  Adding debian:WoSign_China.pem
  Adding debian:XRamp_Global_CA_Root.pem
  Adding debian:certSIGN_ROOT_CA.pem
  Adding debian:ePKI_Root_Certification_Authority.pem
  Adding debian:thawte_Primary_Root_CA.pem
  Adding debian:thawte_Primary_Root_CA_-_G2.pem
  Adding debian:thawte_Primary_Root_CA_-_G3.pem
  done.
  done.
  Processing triggers for libgdk-pixbuf2.0-0:amd64 (2.34.0-1) ...
  
  **************************************************************************************
  ** Environment                                                                      **
  **************************************************************************************
  
  PATH=/home/lamby/git/projects/dotfiles/dotfiles/..//bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin
  HOSTNAME=6380be5ce088
  TERM=xterm
  PAGER=more
  DISPLAY=:0
  DOCKER_IMAGE=lamby-debian-sid
  DEB_BUILD_OPTIONS=parallel=9
  PIP_DOWNLOAD_CACHE=/home/lamby/.cache/pip
  HOME=/home/lamby
  LOGNAME=lamby
  SHLVL=1
  PWD=/home/lamby/temp/cdt.20160805114201.z3HVWv8yoY.alter-sequence-alignment/alter-sequence-alignment-1.3.3+dfsg
  OLDPWD=/home/lamby/temp/cdt.20160805114201.z3HVWv8yoY.alter-sequence-alignment
  GPG_TTY=/dev/console
  QUILT_PATCHES=debian/patches
  QUILT_NO_DIFF_INDEX=1
  QUILT_REFRESH_ARGS=-p ab --no-timestamps --no-index
  DEBEMAIL=lamby at debian.org
  DEBFULLNAME=Chris Lamb
  EDITOR=vim
  LESS=-cgiFx4M
  GPG_KEY=1E953E27D4311E58
  BLASTER=A220 I5 D1 H5 P330 T6
  _=/usr/bin/env
  
  **************************************************************************************
  ** Building alter-sequence-alignment 1.3.3+dfsg-1 on amd64                          **
  **************************************************************************************
  
   dpkg-buildpackage -rfakeroot -D -us -uc -b
  dpkg-buildpackage: info: source package alter-sequence-alignment
  dpkg-buildpackage: info: source version 1.3.3+dfsg-1
  dpkg-buildpackage: info: source distribution unstable
  dpkg-buildpackage: info: source changed by Andreas Tille <tille at debian.org>
   dpkg-source --before-build alter-sequence-alignment-1.3.3+dfsg
  dpkg-buildpackage: info: host architecture amd64
   fakeroot debian/rules clean
  dh clean --with javahelper
     dh_testdir
     dh_auto_clean
  	ant clean
  Buildfile: /home/lamby/temp/cdt.20160805114201.z3HVWv8yoY.alter-sequence-alignment/alter-sequence-alignment-1.3.3+dfsg/build.xml
  
  clean:
    [taskdef] Could not load definitions from resource net/sf/antcontrib/antcontrib.properties. It could not be found.
  
  clean:
  
  BUILD SUCCESSFUL
  Total time: 0 seconds
     jh_clean
     dh_clean
   debian/rules build
  dh build --with javahelper
     dh_testdir
     dh_update_autotools_config
     dh_auto_configure
     jh_linkjars
     dh_auto_build
  	ant -Duser.name debian
  Buildfile: /home/lamby/temp/cdt.20160805114201.z3HVWv8yoY.alter-sequence-alignment/alter-sequence-alignment-1.3.3+dfsg/build.xml
  
  buildlib:
    [taskdef] Could not load definitions from resource net/sf/antcontrib/antcontrib.properties. It could not be found.
  
  clean:
  
  javacc:
  
  BUILD FAILED
  /home/lamby/temp/cdt.20160805114201.z3HVWv8yoY.alter-sequence-alignment/alter-sequence-alignment-1.3.3+dfsg/build.xml:5: The following error occurred while executing this line:
  /home/lamby/temp/cdt.20160805114201.z3HVWv8yoY.alter-sequence-alignment/alter-sequence-alignment-1.3.3+dfsg/alter-lib/build.xml:32: Problem: failed to create task or type foreach
  Cause: The name is undefined.
  Action: Check the spelling.
  Action: Check that any custom tasks/types have been declared.
  Action: Check that any <presetdef>/<macrodef> declarations have taken place.
  
  
  Total time: 0 seconds
  dh_auto_build: ant -Duser.name debian returned exit code 1
  debian/rules:6: recipe for target 'build' failed
  make: *** [build] Error 2

  [..]

The full build log is attached.


Regards,

-- 
      ,''`.
     : :'  :     Chris Lamb
     `. `'`      lamby at debian.org / chris-lamb.co.uk
       `-
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