[Debian-med-packaging] Further questions for megan-ce (Was: Gradle help for libcontrolsfx-java seeked)

Mon May 22 11:20:37 UTC 2017

Hi,

thanks to Tony I was able to reduce the number of build errors in megan-ce
since these vanished when adding [1] to the Build-Depends.

There are some remaining issues I keep on searching help for:

  1. malt[2] does not build without megan-ce.jar and megan[3]
     does not build without malt.jar.

Errors are like:

    [javac] /build/megan-ce-0.0+20170515/antbuild/src/megan/assembly/ReadAssembler.java:24: error: package malt.align does not exist
    [javac] import malt.align.SimpleAligner4DNA;
    [javac]                  ^
    [javac] /build/megan-ce-0.0+20170515/antbuild/src/megan/classification/data/String2IntegerFileBasedABinMap.java:23: error: package malt.util does not exist
    [javac] import malt.util.MurmurHash3;
    [javac]                 ^

  2. Upstream includes contrasts.jar containing *.java + *.class
     but no explicite license statement.  The e-mail address of the
     author mentioned inside metainformation
        Max Schubach <max.schubach at informatik.uni-tuebingen.de>
     bounces and I opened an issue at megan-ce upstream[4] to
     clarify this.  Any better idea to get contrasts.jar?
     Error in log is:

    [javac] /build/megan-ce-0.0+20170515/antbuild/src/megan/groups/commands/ComputeContrastsCommand.java:21: error: package contrasts does not exist
    [javac] import contrasts.Contrasts;
    [javac]                 ^
    ...
    [javac] /build/megan-ce-0.0+20170515/antbuild/src/megan/groups/commands/ComputeContrastsCommand.java:114: error: cannot find symbol
    [javac]                     final Contrasts contrasts = new Contrasts();
    [javac]                           ^
    [javac]   symbol:   class Contrasts

  3. Different errors I'm seeking help for:

    [javac] /build/megan-ce-0.0+20170515/antbuild/src/rusch/megan5client/connector/Megan5ServerConnector.java:72: error: cannot access MultiValueMap
    [javac]         headers.add("Authorization", "Basic " + base64Creds);
    [javac]                ^
    [javac]   class file for org.springframework.util.MultiValueMap not found
    [javac] /build/megan-ce-0.0+20170515/antbuild/src/rusch/megan5client/connector/Megan5ServerConnector.java:73: error: incompatible types: HttpEntity<HttpHeaders> cannot be converted to HttpEntity<String>
    [javac]         request = new HttpEntity<>(headers);
    [javac]                   ^
    [javac] /build/megan-ce-0.0+20170515/antbuild/src/rusch/megan5client/connector/Megan5ServerConnector.java:85: error: cannot access ParameterizedTypeReference
    [javac]             url2response.put(requestURL, restTemplate.exchange(requestURL, HttpMethod.GET, request, RMADataset[].class).getBody());
    [javac]                                                      ^
    [javac]   class file for org.springframework.core.ParameterizedTypeReference not found

I'd also like to read comments on my decision to not package
com.install4j.api (see quilt patch[5]) which is just checking for new
upstream version which I think is expendable since there is no point
in having a different upgrade mechanism than apt.

I'v attached the full build log.

Kind regards

      Andreas.

[1] https://anonscm.debian.org/git/pkg-java/controlsfx.git
[2] https://anonscm.debian.org/git/debian-med/malt.git
[3] https://anonscm.debian.org/git/debian-med/megan-ce.git
[4] https://github.com/danielhuson/megan-ce/issues/5
[5] https://anonscm.debian.org/cgit/debian-med/megan-ce.git/tree/debian/patches/do_not_check_for_update.patch

-- 
http://fam-tille.de
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Setting up libarchive-zip-perl (1.59-1) ...
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Setting up libwavpack1:amd64 (5.0.0-2) ...
Setting up liblcms2-2:amd64 (2.8-4) ...
Setting up libjbig0:amd64 (2.1-3.1+b2) ...
Setting up libpcsclite1:amd64 (1.8.21-1) ...
Setting up libsigsegv2:amd64 (2.10-5) ...
Setting up fonts-dejavu-core (2.37-1) ...
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Setting up libasound2-data (1.1.3-5) ...
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Setting up libcontrolsfx-java (8.40.12-1) ...
Setting up libcap2:amd64 (1:2.25-1) ...
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Setting up libproxy1v5:amd64 (0.4.14-2) ...
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Setting up libbsd0:amd64 (0.8.3-1) ...
Setting up libnspr4:amd64 (2:4.12-6) ...
Setting up ucf (3.0036) ...
Setting up libvpx4:amd64 (1.6.1-3) ...
Setting up libxml2:amd64 (2.9.4+dfsg1-2.2) ...
Setting up libopus0:amd64 (1.2~alpha2-1) ...
Setting up libfreetype6:amd64 (2.6.3-3.2) ...
Setting up libtasn1-6:amd64 (4.10-1) ...
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Setting up libatk1.0-data (2.22.0-1) ...
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Setting up libcrystalhd3:amd64 (1:0.0~git20110715.fdd2f19-12) ...
Processing triggers for libc-bin (2.24-10) ...
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Setting up libatinject-jsr330-api-java (1.0+ds1-2) ...
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Setting up libva-drm1:amd64 (1.7.3-2) ...
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Setting up libkeyutils1:amd64 (1.5.9-9) ...
Setting up bsdmainutils (9.0.12+nmu1) ...
update-alternatives: using /usr/bin/bsd-write to provide /usr/bin/write (write) in auto mode
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Setting up x11-common (1:7.7+19) ...
update-rc.d: warning: start and stop actions are no longer supported; falling back to defaults
invoke-rc.d: could not determine current runlevel
[....] Setting up X socket directories... /tmp/.X11-unix /tmp/.ICE-unix[?25l7[1G[[32m ok [39;49m8[?12l[?25h.
Setting up ca-certificates (20161130) ...
Updating certificates in /etc/ssl/certs...
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Setting up libgsm1:amd64 (1.0.13-4+b2) ...
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Setting up autopoint (0.19.8.1-2) ...
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Setting up libdbus-1-3:amd64 (1.10.18-1) ...
Setting up libwrap0:amd64 (7.6.q-26) ...
Setting up libavahi-common-data:amd64 (0.6.32-2) ...
Setting up libwayland-server0:amd64 (1.12.0-1) ...
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Setting up libfile-stripnondeterminism-perl (0.033-2) ...
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Setting up libopenmpt0:amd64 (0.2.7386~beta20.3-3) ...
Setting up libglib2.0-0:amd64 (2.50.3-2) ...
Setting up libpython3.5-stdlib:amd64 (3.5.3-1) ...
Setting up libwayland-client0:amd64 (1.12.0-1) ...
Setting up libgbm1:amd64 (13.0.6-1+b2) ...
Setting up libflac8:amd64 (1.3.2-1) ...
Setting up libwebpmux2:amd64 (0.5.2-1) ...
Setting up libnss3:amd64 (2:3.26.2-1) ...
Setting up libharfbuzz0b:amd64 (1.4.2-1) ...
Setting up glib-networking-services (2.50.0-1+b1) ...
Setting up autoconf (2.69-10) ...
Setting up libthai0:amd64 (0.1.26-1) ...
Setting up file (1:5.30-1) ...
Setting up libkrb5support0:amd64 (1.15-1) ...
Setting up libjson-glib-1.0-0:amd64 (1.2.6-1) ...
Setting up libcroco3:amd64 (0.6.11-3) ...
Setting up libcommons-parent-java (39-3) ...
Setting up libatk1.0-0:amd64 (2.22.0-1) ...
Setting up libp11-kit0:amd64 (0.23.3-5) ...
Setting up automake (1:1.15-6) ...
update-alternatives: using /usr/bin/automake-1.15 to provide /usr/bin/automake (automake) in auto mode
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Setting up man-db (2.7.6.1-2) ...
Not building database; man-db/auto-update is not 'true'.
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Setting up libcolord2:amd64 (1.3.3-2) ...
Setting up libvorbisenc2:amd64 (1.3.5-4) ...
Setting up libxcb1:amd64 (1.12-1) ...
Setting up libwayland-cursor0:amd64 (1.12.0-1) ...
Setting up libtool (2.4.6-2) ...
Setting up python3.5 (3.5.3-1) ...
Setting up libpython3-stdlib:amd64 (3.5.3-1) ...
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Setting up libfontconfig1:amd64 (2.11.0-6.7+b1) ...
Setting up libxcb-dri2-0:amd64 (1.12-1) ...
Setting up libsm6:amd64 (2:1.2.2-1+b3) ...
Setting up libxcb-dri3-0:amd64 (1.12-1) ...
Setting up libk5crypto3:amd64 (1.15-1) ...
Setting up libxcb-glx0:amd64 (1.12-1) ...
Setting up libxcb-xfixes0:amd64 (1.12-1) ...
Setting up libxcb-render0:amd64 (1.12-1) ...
Setting up dconf-service (0.26.0-2+b1) ...
Setting up gettext (0.19.8.1-2) ...
Setting up libgnutls30:amd64 (3.5.8-5) ...
Setting up libx11-6:amd64 (2:1.6.4-3) ...
Setting up libcommons-logging-java (1.2-1) ...
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Setting up libxcb-sync1:amd64 (1.12-1) ...
Setting up libsndfile1:amd64 (1.0.27-2) ...
Setting up intltool-debian (0.35.0+20060710.4) ...
Setting up libbluray1:amd64 (1:0.9.3-3) ...
Setting up libxcomposite1:amd64 (1:0.4.4-2) ...
Setting up libxcb-shm0:amd64 (1.12-1) ...
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Setting up libkrb5-3:amd64 (1.15-1) ...
Setting up libxft2:amd64 (2.3.2-1+b2) ...
Setting up libspring-core-java (4.3.5-1) ...
Setting up dconf-gsettings-backend:amd64 (0.26.0-2+b1) ...
Setting up libspring-beans-java (4.3.5-1) ...
Setting up fontconfig (2.11.0-6.7+b1) ...
Regenerating fonts cache... done.
Setting up libegl1-mesa:amd64 (13.0.6-1+b2) ...
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Setting up po-debconf (1.0.20) ...
Setting up gsettings-desktop-schemas (3.22.0-1) ...
Setting up libgtk-3-common (3.22.12-1) ...
Setting up libatspi2.0-0:amd64 (2.22.0-6) ...
Setting up libgdk-pixbuf2.0-0:amd64 (2.36.5-2) ...
Setting up libvdpau1:amd64 (1.1.1-6) ...
Setting up libspring-expression-java (4.3.5-1) ...
Setting up libspring-aop-java (4.3.5-1) ...
Setting up libxmu6:amd64 (2:1.1.2-2) ...
Setting up libgssapi-krb5-2:amd64 (1.15-1) ...
Setting up gtk-update-icon-cache (3.22.12-1) ...
Setting up libxcursor1:amd64 (1:1.1.14-1+b4) ...
Setting up libxxf86dga1:amd64 (2:1.1.4-1+b3) ...
Setting up glib-networking:amd64 (2.50.0-1+b1) ...
Setting up libpango-1.0-0:amd64 (1.40.5-1) ...
Setting up libwayland-egl1-mesa:amd64 (13.0.6-1+b2) ...
Setting up libatk-bridge2.0-0:amd64 (2.22.0-2) ...
Setting up libxv1:amd64 (2:1.0.11-1) ...
Setting up libxxf86vm1:amd64 (1:1.1.4-1+b2) ...
Setting up libxrandr2:amd64 (2:1.5.1-1) ...
Setting up libva-x11-1:amd64 (1.7.3-2) ...
Setting up libcups2:amd64 (2.2.1-8) ...
Setting up libxi6:amd64 (2:1.7.9-1) ...
Setting up libxaw7:amd64 (2:1.0.13-1+b2) ...
Setting up libcairo2:amd64 (1.14.8-1) ...
Setting up libxinerama1:amd64 (2:1.1.3-1+b3) ...
Setting up libspring-context-java (4.3.5-1) ...
Setting up libxdamage1:amd64 (1:1.1.4-2+b3) ...
Setting up libavutil55:amd64 (7:3.2.4-1) ...
Setting up libssh-gcrypt-4:amd64 (0.7.3-2) ...
Setting up libcairo-gobject2:amd64 (1.14.8-1) ...
Setting up libsoup2.4-1:amd64 (2.56.0-2) ...
Setting up libsoup-gnome2.4-1:amd64 (2.56.0-2) ...
Setting up libswresample2:amd64 (7:3.2.4-1) ...
Setting up libspring-web-java (4.3.5-1) ...
Setting up libxtst6:amd64 (2:1.2.3-1) ...
Setting up libpangoft2-1.0-0:amd64 (1.40.5-1) ...
Setting up libgl1-mesa-glx:amd64 (13.0.6-1+b2) ...
Setting up librest-0.7-0:amd64 (0.8.0-2) ...
Setting up libtheora0:amd64 (1.1.1+dfsg.1-14+b1) ...
Setting up libavcodec57:amd64 (7:3.2.4-1) ...
Setting up x11-utils (7.7+3+b1) ...
Setting up libpangocairo-1.0-0:amd64 (1.40.5-1) ...
Setting up libpulse0:amd64 (10.0-1) ...
Setting up libatk-wrapper-java (0.33.3-13) ...
Setting up libchromaprint1:amd64 (1.4.2-1) ...
Setting up librsvg2-2:amd64 (2.40.16-1+b1) ...
Setting up librsvg2-common:amd64 (2.40.16-1+b1) ...
Setting up libavformat57:amd64 (7:3.2.4-1) ...
Setting up adwaita-icon-theme (3.22.0-1) ...
update-alternatives: using /usr/share/icons/Adwaita/cursor.theme to provide /usr/share/icons/default/index.theme (x-cursor-theme) in auto mode
Setting up libgtk2.0-0:amd64 (2.24.31-2) ...
Setting up libopenjfx-jni (8u131-b11-2) ...
Setting up gnome-icon-theme (3.12.0-2) ...
update-alternatives: using /usr/share/icons/gnome/scalable/places/debian-swirl.svg to provide /usr/share/icons/gnome/scalable/places/start-here.svg (start-here.svg) in auto mode
Setting up libgtk-3-0:amd64 (3.22.12-1) ...
Setting up libatk-wrapper-java-jni:amd64 (0.33.3-13) ...
Setting up libopenjfx-java (8u131-b11-2) ...
Setting up openjdk-8-jre-headless:amd64 (8u131-b11-2) ...
update-alternatives: using /usr/lib/jvm/java-8-openjdk-amd64/jre/bin/rmid to provide /usr/bin/rmid (rmid) in auto mode
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update-alternatives: using /usr/lib/jvm/java-8-openjdk-amd64/jre/bin/keytool to provide /usr/bin/keytool (keytool) in auto mode
update-alternatives: using /usr/lib/jvm/java-8-openjdk-amd64/jre/bin/jjs to provide /usr/bin/jjs (jjs) in auto mode
update-alternatives: using /usr/lib/jvm/java-8-openjdk-amd64/jre/bin/pack200 to provide /usr/bin/pack200 (pack200) in auto mode
update-alternatives: using /usr/lib/jvm/java-8-openjdk-amd64/jre/bin/rmiregistry to provide /usr/bin/rmiregistry (rmiregistry) in auto mode
update-alternatives: using /usr/lib/jvm/java-8-openjdk-amd64/jre/bin/unpack200 to provide /usr/bin/unpack200 (unpack200) in auto mode
update-alternatives: using /usr/lib/jvm/java-8-openjdk-amd64/jre/bin/orbd to provide /usr/bin/orbd (orbd) in auto mode
update-alternatives: using /usr/lib/jvm/java-8-openjdk-amd64/jre/bin/servertool to provide /usr/bin/servertool (servertool) in auto mode
update-alternatives: using /usr/lib/jvm/java-8-openjdk-amd64/jre/bin/tnameserv to provide /usr/bin/tnameserv (tnameserv) in auto mode
update-alternatives: using /usr/lib/jvm/java-8-openjdk-amd64/jre/lib/jexec to provide /usr/bin/jexec (jexec) in auto mode
Setting up libconcurrent-java (1.3.4-4) ...
Setting up ca-certificates-java (20161107) ...
Adding debian:Security_Communication_Root_CA.pem
Adding debian:IdenTrust_Commercial_Root_CA_1.pem
Adding debian:GeoTrust_Primary_Certification_Authority.pem
Adding debian:Starfield_Class_2_CA.pem
Adding debian:thawte_Primary_Root_CA.pem
Adding debian:TWCA_Global_Root_CA.pem
Adding debian:UTN_USERFirst_Hardware_Root_CA.pem
Adding debian:Hellenic_Academic_and_Research_Institutions_RootCA_2011.pem
Adding debian:SwissSign_Silver_CA_-_G2.pem
Adding debian:Hellenic_Academic_and_Research_Institutions_ECC_RootCA_2015.pem
Adding debian:QuoVadis_Root_CA_1_G3.pem
Adding debian:Security_Communication_EV_RootCA1.pem
Adding debian:AffirmTrust_Premium_ECC.pem
Adding debian:Starfield_Services_Root_Certificate_Authority_-_G2.pem
Adding debian:EE_Certification_Centre_Root_CA.pem
Adding debian:StartCom_Certification_Authority.pem
Adding debian:Izenpe.com.pem
Adding debian:E-Tugra_Certification_Authority.pem
Adding debian:Verisign_Class_1_Public_Primary_Certification_Authority.pem
Adding debian:Baltimore_CyberTrust_Root.pem
Adding debian:EC-ACC.pem
Adding debian:OpenTrust_Root_CA_G2.pem
Adding debian:VeriSign_Class_3_Public_Primary_Certification_Authority_-_G5.pem
Adding debian:Microsec_e-Szigno_Root_CA_2009.pem
Adding debian:Buypass_Class_3_Root_CA.pem
Adding debian:DigiCert_Assured_ID_Root_G3.pem
Adding debian:CNNIC_ROOT.pem
Adding debian:GlobalSign_Root_CA_-_R3.pem
Adding debian:China_Internet_Network_Information_Center_EV_Certificates_Root.pem
Adding debian:Certification_Authority_of_WoSign_G2.pem
Adding debian:ePKI_Root_Certification_Authority.pem
Adding debian:ApplicationCA_-_Japanese_Government.pem
Adding debian:AddTrust_External_Root.pem
Adding debian:Swisscom_Root_CA_2.pem
Adding debian:Staat_der_Nederlanden_Root_CA_-_G2.pem
Adding debian:CFCA_EV_ROOT.pem
Adding debian:Hongkong_Post_Root_CA_1.pem
Adding debian:Certum_Trusted_Network_CA.pem
Adding debian:QuoVadis_Root_CA_3.pem
Adding debian:S-TRUST_Authentication_and_Encryption_Root_CA_2005_PN.pem
Adding debian:Entrust_Root_Certification_Authority_-_EC1.pem
Adding debian:Certigna.pem
Adding debian:Microsec_e-Szigno_Root_CA.pem
Adding debian:DigiCert_Assured_ID_Root_CA.pem
Adding debian:GeoTrust_Universal_CA_2.pem
Adding debian:AddTrust_Qualified_Certificates_Root.pem
Adding debian:Certum_Trusted_Network_CA_2.pem
Adding debian:D-TRUST_Root_Class_3_CA_2_2009.pem
Adding debian:DigiCert_Global_Root_CA.pem
Adding debian:GlobalSign_ECC_Root_CA_-_R4.pem
Adding debian:SwissSign_Gold_CA_-_G2.pem
Adding debian:S-TRUST_Universal_Root_CA.pem
Adding debian:T-TeleSec_GlobalRoot_Class_2.pem
Adding debian:QuoVadis_Root_CA_3_G3.pem
Adding debian:thawte_Primary_Root_CA_-_G2.pem
Adding debian:Certplus_Class_2_Primary_CA.pem
Adding debian:Starfield_Root_Certificate_Authority_-_G2.pem
Adding debian:T?B?TAK_UEKAE_K?k_Sertifika_Hizmet_Sa?lay?c?s?_-_S?r?m_3.pem
Adding debian:DigiCert_Global_Root_G3.pem
Adding debian:GlobalSign_ECC_Root_CA_-_R5.pem
Adding debian:VeriSign_Class_3_Public_Primary_Certification_Authority_-_G4.pem
Adding debian:Verisign_Class_2_Public_Primary_Certification_Authority_-_G3.pem
Adding debian:Entrust.net_Premium_2048_Secure_Server_CA.pem
Adding debian:Equifax_Secure_CA.pem
Adding debian:Security_Communication_RootCA2.pem
Adding debian:ISRG_Root_X1.pem
Adding debian:COMODO_ECC_Certification_Authority.pem
Adding debian:GeoTrust_Universal_CA.pem
Adding debian:ACEDICOM_Root.pem
Adding debian:Certplus_Root_CA_G1.pem
Adding debian:DigiCert_Global_Root_G2.pem
Adding debian:GeoTrust_Global_CA.pem
Adding debian:USERTrust_ECC_Certification_Authority.pem
Adding debian:TeliaSonera_Root_CA_v1.pem
Adding debian:DigiCert_Assured_ID_Root_G2.pem
Adding debian:Buypass_Class_2_Root_CA.pem
Adding debian:Verisign_Class_3_Public_Primary_Certification_Authority_-_G3.pem
Adding debian:Go_Daddy_Class_2_CA.pem
Adding debian:Hellenic_Academic_and_Research_Institutions_RootCA_2015.pem
Adding debian:DigiCert_High_Assurance_EV_Root_CA.pem
Adding debian:Sonera_Class_2_Root_CA.pem
Adding debian:AffirmTrust_Commercial.pem
Adding debian:GeoTrust_Primary_Certification_Authority_-_G3.pem
Adding debian:QuoVadis_Root_CA.pem
Adding debian:Certum_Root_CA.pem
Adding debian:Equifax_Secure_eBusiness_CA_1.pem
Adding debian:IGC_A.pem
Adding debian:Swisscom_Root_EV_CA_2.pem
Adding debian:ACCVRAIZ1.pem
Adding debian:Deutsche_Telekom_Root_CA_2.pem
Adding debian:OpenTrust_Root_CA_G1.pem
Adding debian:Comodo_Trusted_Services_root.pem
Adding debian:D-TRUST_Root_Class_3_CA_2_EV_2009.pem
Adding debian:Verisign_Class_3_Public_Primary_Certification_Authority.pem
Adding debian:AddTrust_Low-Value_Services_Root.pem
Adding debian:SecureSign_RootCA11.pem
Adding debian:Entrust_Root_Certification_Authority_-_G2.pem
Adding debian:WoSign.pem
Adding debian:NetLock_Arany_=Class_Gold=_F?tan?s?tv?ny.pem
Adding debian:Staat_der_Nederlanden_EV_Root_CA.pem
Adding debian:Buypass_Class_2_CA_1.pem
Adding debian:StartCom_Certification_Authority_2.pem
Adding debian:Camerfirma_Global_Chambersign_Root.pem
Adding debian:Verisign_Class_1_Public_Primary_Certification_Authority_-_G3.pem
Adding debian:GlobalSign_Root_CA.pem
Adding debian:Certplus_Root_CA_G2.pem
Adding debian:UTN_USERFirst_Email_Root_CA.pem
Adding debian:AffirmTrust_Networking.pem
Adding debian:GeoTrust_Primary_Certification_Authority_-_G2.pem
Adding debian:SwissSign_Platinum_CA_-_G2.pem
Adding debian:Chambers_of_Commerce_Root_-_2008.pem
Adding debian:Cybertrust_Global_Root.pem
Adding debian:T?RKTRUST_Elektronik_Sertifika_Hizmet_Sa?lay?c?s?_H6.pem
Adding debian:WellsSecure_Public_Root_Certificate_Authority.pem
Adding debian:T?RKTRUST_Elektronik_Sertifika_Hizmet_Sa?lay?c?s?_H5.pem
Adding debian:PSCProcert.pem
Adding debian:COMODO_RSA_Certification_Authority.pem
Adding debian:CA_Disig_Root_R1.pem
Adding debian:Swisscom_Root_CA_1.pem
Adding debian:DigiCert_Trusted_Root_G4.pem
Adding debian:XRamp_Global_CA_Root.pem
Adding debian:DST_ACES_CA_X6.pem
Adding debian:AC_Ra?z_Certic?mara_S.A..pem
Adding debian:StartCom_Certification_Authority_G2.pem
Adding debian:CA_Disig_Root_R2.pem
Adding debian:TURKTRUST_Certificate_Services_Provider_Root_2007.pem
Adding debian:AddTrust_Public_Services_Root.pem
Adding debian:Comodo_AAA_Services_root.pem
Adding debian:AffirmTrust_Premium.pem
Adding debian:ComSign_CA.pem
Adding debian:Secure_Global_CA.pem
Adding debian:VeriSign_Universal_Root_Certification_Authority.pem
Adding debian:Atos_TrustedRoot_2011.pem
Adding debian:Juur-SK.pem
Adding debian:TWCA_Root_Certification_Authority.pem
Adding debian:OpenTrust_Root_CA_G3.pem
Adding debian:COMODO_Certification_Authority.pem
Adding debian:Autoridad_de_Certificacion_Firmaprofesional_CIF_A62634068.pem
Adding debian:OISTE_WISeKey_Global_Root_GA_CA.pem
Adding debian:T-TeleSec_GlobalRoot_Class_3.pem
Adding debian:EBG_Elektronik_Sertifika_Hizmet_Sa?lay?c?s?.pem
Adding debian:Go_Daddy_Root_Certificate_Authority_-_G2.pem
Adding debian:Comodo_Secure_Services_root.pem
Adding debian:CA_WoSign_ECC_Root.pem
Adding debian:thawte_Primary_Root_CA_-_G3.pem
Adding debian:Equifax_Secure_Global_eBusiness_CA.pem
Adding debian:Global_Chambersign_Root_-_2008.pem
Adding debian:Actalis_Authentication_Root_CA.pem
Adding debian:Trustis_FPS_Root_CA.pem
Adding debian:TC_TrustCenter_Class_3_CA_II.pem
Adding debian:WoSign_China.pem
Adding debian:Verisign_Class_2_Public_Primary_Certification_Authority_-_G2.pem
Adding debian:Camerfirma_Chambers_of_Commerce_Root.pem
Adding debian:QuoVadis_Root_CA_2_G3.pem
Adding debian:QuoVadis_Root_CA_2.pem
Adding debian:GlobalSign_Root_CA_-_R2.pem
Adding debian:certSIGN_ROOT_CA.pem
Adding debian:Certinomis_-_Root_CA.pem
Adding debian:IdenTrust_Public_Sector_Root_CA_1.pem
Adding debian:SecureTrust_CA.pem
Adding debian:Visa_eCommerce_Root.pem
Adding debian:RSA_Security_2048_v3.pem
Adding debian:Taiwan_GRCA.pem
Adding debian:Root_CA_Generalitat_Valenciana.pem
Adding debian:USERTrust_RSA_Certification_Authority.pem
Adding debian:OISTE_WISeKey_Global_Root_GB_CA.pem
Adding debian:Certinomis_-_Autorit?_Racine.pem
Adding debian:Network_Solutions_Certificate_Authority.pem
Adding debian:SZAFIR_ROOT_CA2.pem
Adding debian:Staat_der_Nederlanden_Root_CA_-_G3.pem
Adding debian:Entrust_Root_Certification_Authority.pem
Adding debian:GeoTrust_Global_CA_2.pem
Adding debian:DST_Root_CA_X3.pem
done.
Setting up dh-autoreconf (14) ...
Setting up python3 (3.5.3-1) ...
Setting up openjdk-8-jdk-headless:amd64 (8u131-b11-2) ...
update-alternatives: using /usr/lib/jvm/java-8-openjdk-amd64/bin/idlj to provide /usr/bin/idlj (idlj) in auto mode
update-alternatives: using /usr/lib/jvm/java-8-openjdk-amd64/bin/jdeps to provide /usr/bin/jdeps (jdeps) in auto mode
update-alternatives: using /usr/lib/jvm/java-8-openjdk-amd64/bin/wsimport to provide /usr/bin/wsimport (wsimport) in auto mode
update-alternatives: using /usr/lib/jvm/java-8-openjdk-amd64/bin/rmic to provide /usr/bin/rmic (rmic) in auto mode
update-alternatives: using /usr/lib/jvm/java-8-openjdk-amd64/bin/jinfo to provide /usr/bin/jinfo (jinfo) in auto mode
update-alternatives: using /usr/lib/jvm/java-8-openjdk-amd64/bin/jsadebugd to provide /usr/bin/jsadebugd (jsadebugd) in auto mode
update-alternatives: using /usr/lib/jvm/java-8-openjdk-amd64/bin/native2ascii to provide /usr/bin/native2ascii (native2ascii) in auto mode
update-alternatives: using /usr/lib/jvm/java-8-openjdk-amd64/bin/jstat to provide /usr/bin/jstat (jstat) in auto mode
update-alternatives: using /usr/lib/jvm/java-8-openjdk-amd64/bin/javac to provide /usr/bin/javac (javac) in auto mode
update-alternatives: using /usr/lib/jvm/java-8-openjdk-amd64/bin/javah to provide /usr/bin/javah (javah) in auto mode
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 devscripts (2.17.5) ...
Setting up openjdk-8-jre:amd64 (8u131-b11-2) ...
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 (1.9.9-1) ...
Setting up dh-python (2.20170125) ...
Setting up libcolt-free-java (1.2.0+dfsg-4) ...
Setting up default-jre-headless (2:1.8-58) ...
Setting up default-jdk-headless (2:1.8-58) ...
Setting up debhelper (10.2.5) ...
Setting up openjdk-8-jdk:amd64 (8u131-b11-2) ...
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 (2:1.8-58) ...
Setting up dh-strip-nondeterminism (0.033-2) ...
Setting up javahelper (0.59) ...
Setting up default-jdk (2:1.8-58) ...
Processing triggers for libc-bin (2.24-10) ...
Processing triggers for ca-certificates (20161130) ...
Updating certificates in /etc/ssl/certs...
0 added, 0 removed; done.
Running hooks in /etc/ca-certificates/update.d...

done.
done.
Processing triggers for libgdk-pixbuf2.0-0:amd64 (2.36.5-2) ...
Reading package lists...
Building dependency tree...
Reading state information...
Reading extended state information...
Initializing package states...
Writing extended state information...
Building tag database...
 -> Finished parsing the build-deps
Reading package lists...
Building dependency tree...
Reading state information...
apt-utils is already the newest version (1.4.4).
The following NEW packages will be installed:
  fakeroot libfakeroot
0 upgraded, 2 newly installed, 0 to remove and 2 not upgraded.
Need to get 0 B/131 kB of archives.
After this operation, 374 kB of additional disk space will be used.
Selecting previously unselected package libfakeroot:amd64.
(Reading database ... 
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(Reading database ... 31716 files and directories currently installed.)
Preparing to unpack .../libfakeroot_1.21-3.1_amd64.deb ...
Unpacking libfakeroot:amd64 (1.21-3.1) ...
Selecting previously unselected package fakeroot.
Preparing to unpack .../fakeroot_1.21-3.1_amd64.deb ...
Unpacking fakeroot (1.21-3.1) ...
Processing triggers for libc-bin (2.24-10) ...
Setting up libfakeroot:amd64 (1.21-3.1) ...
Processing triggers for man-db (2.7.6.1-2) ...
Not building database; man-db/auto-update is not 'true'.
Setting up fakeroot (1.21-3.1) ...
update-alternatives: using /usr/bin/fakeroot-sysv to provide /usr/bin/fakeroot (fakeroot) in auto mode
Processing triggers for libc-bin (2.24-10) ...
[0mI: Copying back the cached apt archive contents[0m
[0mI: Building the package[0m
[0mI: Running cd /build/megan-ce-0.0+20170515/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin" HOME="/nonexistent" dpkg-buildpackage -us -uc  -i\.git -I.git  -rfakeroot[0m
dpkg-buildpackage: info: source package megan-ce
dpkg-buildpackage: info: source version 0.0+20170515-1
dpkg-buildpackage: info: source distribution UNRELEASED
dpkg-buildpackage: info: source changed by Andreas Tille <tille at debian.org>
 dpkg-source -i.git -I.git --before-build megan-ce-0.0+20170515
dpkg-buildpackage: info: host architecture amd64
 fakeroot debian/rules clean
dh clean --with javahelper
   dh_testdir
   dh_auto_clean
   dh_autoreconf_clean
   jh_clean
   debian/rules override_dh_clean
make[1]: Entering directory '/build/megan-ce-0.0+20170515'
dh_clean
rm -rf antbuild/classes antbuild/src
make[1]: Leaving directory '/build/megan-ce-0.0+20170515'
 dpkg-source -i.git -I.git -b megan-ce-0.0+20170515
dpkg-source: info: using source format '3.0 (quilt)'
dpkg-source: info: building megan-ce using existing ./megan-ce_0.0+20170515.orig.tar.xz
dpkg-source: info: building megan-ce in megan-ce_0.0+20170515-1.debian.tar.xz
dpkg-source: info: building megan-ce in megan-ce_0.0+20170515-1.dsc
 debian/rules build
dh build --with javahelper
   dh_testdir
   dh_update_autotools_config
   dh_autoreconf
   dh_auto_configure
   jh_linkjars
   debian/rules override_dh_auto_build
make[1]: Entering directory '/build/megan-ce-0.0+20170515'
ant -buildfile antbuild/build.xml jar
Buildfile: /build/megan-ce-0.0+20170515/antbuild/build.xml

init:
    [mkdir] Created dir: /build/megan-ce-0.0+20170515/antbuild/src
    [mkdir] Created dir: /build/megan-ce-0.0+20170515/antbuild/classes
    [mkdir] Created dir: /build/megan-ce-0.0+20170515/antbuild/classes/resources

copy_resources:
    [mkdir] Created dir: /build/megan-ce-0.0+20170515/antbuild/classes/resources/css
    [mkdir] Created dir: /build/megan-ce-0.0+20170515/antbuild/classes/resources/files
     [copy] Copying 1 file to /build/megan-ce-0.0+20170515/antbuild/classes

copy_sources:
     [copy] Copying 1133 files to /build/megan-ce-0.0+20170515/antbuild/src

compile:
    [javac] Compiling 1130 source files to /build/megan-ce-0.0+20170515/antbuild/classes
    [javac] warning: [options] bootstrap class path not set in conjunction with -source 1.7
    [javac] /build/megan-ce-0.0+20170515/antbuild/src/megan/assembly/ReadAssembler.java:24: error: package malt.align does not exist
    [javac] import malt.align.SimpleAligner4DNA;
    [javac]                  ^
    [javac] /build/megan-ce-0.0+20170515/antbuild/src/megan/classification/data/String2IntegerFileBasedABinMap.java:23: error: package malt.util does not exist
    [javac] import malt.util.MurmurHash3;
    [javac]                 ^
    [javac] /build/megan-ce-0.0+20170515/antbuild/src/megan/groups/commands/ComputeContrastsCommand.java:21: error: package contrasts does not exist
    [javac] import contrasts.Contrasts;
    [javac]                 ^
    [javac] /build/megan-ce-0.0+20170515/antbuild/src/megan/assembly/ReadAssembler.java:251: error: cannot find symbol
    [javac]                             final SimpleAligner4DNA simpleAlignerDNA = new SimpleAligner4DNA();
    [javac]                                   ^
    [javac]   symbol: class SimpleAligner4DNA
    [javac] /build/megan-ce-0.0+20170515/antbuild/src/megan/assembly/ReadAssembler.java:251: error: cannot find symbol
    [javac]                             final SimpleAligner4DNA simpleAlignerDNA = new SimpleAligner4DNA();
    [javac]                                                                            ^
    [javac]   symbol: class SimpleAligner4DNA
    [javac] /build/megan-ce-0.0+20170515/antbuild/src/megan/assembly/ReadAssembler.java:264: error: package SimpleAligner4DNA does not exist
    [javac]                                     final SimpleAligner4DNA.OverlapType overlapType = simpleAlignerDNA.getOverlap(iBytes, jBytes, overlap);
    [javac]                                                            ^
    [javac] /build/megan-ce-0.0+20170515/antbuild/src/megan/assembly/ReadAssembler.java:267: error: package SimpleAligner4DNA does not exist
    [javac]                                     if (overlapType == SimpleAligner4DNA.OverlapType.QueryContainedInRef) {
    [javac]                                                                         ^
    [javac] /build/megan-ce-0.0+20170515/antbuild/src/megan/assembly/ReadAssembler.java:277: error: package SimpleAligner4DNA does not exist
    [javac]                                     } else if (overlapType == SimpleAligner4DNA.OverlapType.QuerySuffix2RefPrefix && overlap.get() >= minOverlap) {
    [javac]                                                                                ^
    [javac] /build/megan-ce-0.0+20170515/antbuild/src/megan/assembly/ReadAssembler.java:283: error: package SimpleAligner4DNA does not exist
    [javac]                                     } else if (overlapType == SimpleAligner4DNA.OverlapType.QueryPrefix2RefSuffix && overlap.get() >= minOverlap) {
    [javac]                                                                                ^
    [javac] /build/megan-ce-0.0+20170515/antbuild/src/megan/classification/data/String2IntegerFileBasedABinMap.java:210: error: cannot find symbol
    [javac]         return Math.abs(MurmurHash3.murmurhash3x8632(key, 0, key.length, 666) & mask);
    [javac]                         ^
    [javac]   symbol:   variable MurmurHash3
    [javac]   location: class String2IntegerFileBasedABinMap
    [javac] /build/megan-ce-0.0+20170515/antbuild/src/megan/classification/data/String2IntegerFileBasedABinMap.java:221: error: cannot find symbol
    [javac]         return Math.abs(MurmurHash3.murmurhash3x8632(key, offset, length, 666) & mask);
    [javac]                         ^
    [javac]   symbol:   variable MurmurHash3
    [javac]   location: class String2IntegerFileBasedABinMap
    [javac] /build/megan-ce-0.0+20170515/antbuild/src/megan/groups/commands/ComputeContrastsCommand.java:114: error: cannot find symbol
    [javac]                     final Contrasts contrasts = new Contrasts();
    [javac]                           ^
    [javac]   symbol:   class Contrasts
    [javac]   location: class ComputeContrastsCommand
    [javac] /build/megan-ce-0.0+20170515/antbuild/src/megan/groups/commands/ComputeContrastsCommand.java:114: error: cannot find symbol
    [javac]                     final Contrasts contrasts = new Contrasts();
    [javac]                                                     ^
    [javac]   symbol:   class Contrasts
    [javac]   location: class ComputeContrastsCommand
    [javac] /build/megan-ce-0.0+20170515/antbuild/src/rusch/megan5client/connector/Megan5ServerConnector.java:72: error: cannot access MultiValueMap
    [javac]         headers.add("Authorization", "Basic " + base64Creds);
    [javac]                ^
    [javac]   class file for org.springframework.util.MultiValueMap not found
    [javac] /build/megan-ce-0.0+20170515/antbuild/src/rusch/megan5client/connector/Megan5ServerConnector.java:73: error: incompatible types: HttpEntity<HttpHeaders> cannot be converted to HttpEntity<String>
    [javac]         request = new HttpEntity<>(headers);
    [javac]                   ^
    [javac] /build/megan-ce-0.0+20170515/antbuild/src/rusch/megan5client/connector/Megan5ServerConnector.java:85: error: cannot access ParameterizedTypeReference
    [javac]             url2response.put(requestURL, restTemplate.exchange(requestURL, HttpMethod.GET, request, RMADataset[].class).getBody());
    [javac]                                                      ^
    [javac]   class file for org.springframework.core.ParameterizedTypeReference not found
    [javac] Note: Some input files use or override a deprecated API.
    [javac] Note: Recompile with -Xlint:deprecation for details.
    [javac] Note: Some input files use unchecked or unsafe operations.
    [javac] Note: Recompile with -Xlint:unchecked for details.
    [javac] 16 errors
    [javac] 1 warning

BUILD FAILED
/build/megan-ce-0.0+20170515/antbuild/build.xml:67: Compile failed; see the compiler error output for details.

Total time: 6 seconds
debian/rules:20: recipe for target 'override_dh_auto_build' failed
make[1]: *** [override_dh_auto_build] Error 1
make[1]: Leaving directory '/build/megan-ce-0.0+20170515'
debian/rules:13: recipe for target 'build' failed
make: *** [build] Error 2
dpkg-buildpackage: error: debian/rules build gave error exit status 2
[0mI: copying local configuration[0m
[0;31mE: Failed autobuilding of package[0m
[0mI: user script /var/cache/pbuilder/build/cow.25760/tmp/hooks/C99_failed_build starting[0m
Installing convenience apps: mc less bash-completion 
20170515/antbuild/src/megan/classification/data/String2IntegerFileBasedABinMap.java:221: error: cannot find symbol
    [javac]         return Math.abs(MurmurHash3.murmurhash3x8632(key, offset, length, 666) & mask);
    [javac]                         ^
    [javac]   symbol:   variable MurmurHash3
    [javac]   location: class String2IntegerFileBasedABinMap
    [javac] /build/megan-ce-0.0+20170515/antbuild/src/megan/groups/commands/ComputeContrastsCommand.java:114: error: cannot find symbol
    [javac]                     final Contrasts contrasts = new Contrasts();
    [javac]                           ^
    [javac]   symbol:   class Contrasts
    [javac]   location: class ComputeContrastsCommand
    [javac] /build/megan-ce-0.0+20170515/antbuild/src/megan/groups/commands/ComputeContrastsCommand.java:114: error: cannot find symbol
    [javac]                     final Contrasts contrasts = new Contrasts();
    [javac]                                                     ^
    [javac]   symbol:   class Contrasts
    [javac]   location: class ComputeContrastsCommand
    [javac] /build/megan-ce-0.0+20170515/antbuild/src/rusch/megan5client/connector/Megan5ServerConnector.java:72: error: cannot access MultiValueMap
    [javac]         headers.add("Authorization", "Basic " + base64Creds);
    [javac]                ^
    [javac]   class file for org.springframework.util.MultiValueMap not found
    [javac] /build/megan-ce-0.0+20170515/antbuild/src/rusch/megan5client/connector/Megan5ServerConnector.java:73: error: incompatible types: HttpEntity<HttpHeaders> cannot be converted to HttpEntity<String>
    [javac]         request = new HttpEntity<>(headers);
    [javac]                   ^
    [javac] /build/megan-ce-0.0+20170515/antbuild/src/rusch/megan5client/connector/Megan5ServerConnector.java:85: error: cannot access ParameterizedTypeReference
    [javac]             url2response.put(requestURL, restTemplate.exchange(requestURL, HttpMethod.GET, request, RMADataset[].class).getBody());
    [javac]                                                      ^
    [javac]   class file for org.springframework.core.ParameterizedTypeReference not found
    [javac] Note: Some input files use or override a deprecated API.
    [javac] Note: Recompile with -Xlint:deprecation for details.
    [javac] Note: Some input files use unchecked or unsafe operations.
    [javac] Note: Recompile with -Xlint:unchecked for details.
    [javac] 16 errors
    [javac] 1 warning

BUILD FAILED
/build/megan-ce-0.0+20170515/antbuild/build.xml:67: Compile failed; see the compiler error output for details.

Total time: 6 seconds
debian/rules:20: recipe for target 'override_dh_auto_build' failed
make[1]: *** [override_dh_auto_build] Error 1
make[1]: Leaving directory '/build/megan-ce-0.0+20170515'
debian/rules:13: recipe for target 'build' failed
make: *** [build] Error 2
dpkg-buildpackage: error: debian/rules build gave error exit status 2
[0mI: copying local configuration[0m
[0;31mE: Failed autobuilding of package[0m
[0mI: user script /var/cache/pbuilder/build/cow.25760/tmp/hooks/C99_failed_build starting[0m
Installing convenience apps: mc less bash-completion 