[Bio-linux-dev] [Bio-Linux] How to Install all packages on Ubuntu?

[Jasmine Lognnes]

Dear Tony,

That is good news. I have now tried it on a fresh Ubuntu 12.04 64bit, and
it exits with pasted in at the bottom. More complete output attached.

What can you gather from this?

Hugs,
Jasmine =)



The following NEW packages will be installed:
  bio-linux-artemis
0 upgraded, 1 newly installed, 0 to remove and 14 not upgraded.
Need to get 11.8 MB of archives.
After this operation, 47.7 MB of additional disk space will be used.
Get:1 http://nebc.nerc.ac.uk/bio-linux/ unstable/bio-linux
bio-linux-artemis all 15.1.1-1 [11.8 MB]
Fetched 11.8 MB in 2s (5,111 kB/s)
Selecting previously unselected package bio-linux-artemis.
(Reading database ... 162928 files and directories currently installed.)
Unpacking bio-linux-artemis (from .../bio-linux-artemis_15.1.1-1_all.deb)
...
Processing triggers for bamfdaemon ...
Rebuilding /usr/share/applications/bamf.index...
Processing triggers for desktop-file-utils ...
Processing triggers for gnome-menus ...
Setting up bio-linux-artemis (15.1.1-1) ...
Reading package lists... Done
Building dependency tree
Reading state information... Done
E: Unable to locate package bio-linux-assembly-conversion-tools
Not all packages installed properly - exiting.







On 12 February 2014 16:32, Tony Travis <tony.travis at abdn.ac.uk> wrote:

> On 12/02/14 15:03, Jasmine Lognnes wrote:
> > Dear Tim,
> >
> > That's a very impressive script. Wow!
> >
> > By going through the script I have cherry picked what looks like to be
> > needed on a plain Ubuntu 12.04 64bit. I have attached it as a script.
> > Can you verify that it is the correct procedure?
> >
> > On the liveUSB I did
> >
> > grep "^Packages: bio-linux" /var/lib/dpkg/status | awk '{print $2}'
> >
> > and got the attached list of packages. On a successful installation,
> > should I end up these exact packages?
>
> Hi, Jasmine.
>
> I've used Tim's 6>7 script to install Bio-Linux on pre-existing Ubuntu
> 12.04 LTS systems without any problems. You don't need to grep things
> out like you did. Just run the script in its entirety and please email
> any bug reports to the bio-linux-dev list.
>
> HTH,
>
>   Tony.
>
> --
> Dr. A.J.Travis, University of Aberdeen, Institute of Biological and
> Environmental Sciences, Cruickshank Building, St. Machar Drive, Aberdeen
> AB24 3UU, Scotland, UK. tel +44(0)1224 272700, fax +44 (0)1224 272 396
> http://www.abdn.ac.uk, mailto:tony.travis at abdn.ac.uk, skype:ajtravis
> The University of Aberdeen is a charity registered in Scotland, No
> SC013683.
> _______________________________________________
> Bio-Linux mailing list
> Bio-Linux at nebclists.nerc.ac.uk
> http://nebclists.nerc.ac.uk/mailman/listinfo/bio-linux
>
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  ca-certificates-java icedtea-6-jre-cacao icedtea-6-jre-jamvm icedtea-netx
  icedtea-netx-common java-common libatk-wrapper-java libatk-wrapper-java-jni
  libgif4 libnss3-1d openjdk-6-jre openjdk-6-jre-headless openjdk-6-jre-lib
  ttf-dejavu-extra tzdata-java
Suggested packages:
  default-jre equivs icedtea-plugin sun-java6-fonts fonts-ipafont-gothic
  fonts-ipafont-mincho ttf-telugu-fonts ttf-oriya-fonts ttf-kannada-fonts
  ttf-bengali-fonts
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update-alternatives: using /usr/lib/jvm/java-6-openjdk-i386/jre/bin/orbd to provide /usr/bin/orbd (orbd) in auto mode.
update-alternatives: using /usr/lib/jvm/java-6-openjdk-i386/jre/bin/servertool to provide /usr/bin/servertool (servertool) in auto mode.
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Setting up ca-certificates-java (20110912ubuntu6) ...
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Adding debian:Starfield_Root_Certificate_Authority_-_G2.pem
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Adding debian:AddTrust_Public_Services_Root.pem
Adding debian:Swisscom_Root_CA_1.pem
Adding debian:Firmaprofesional_Root_CA.pem
Adding debian:DigiCert_High_Assurance_EV_Root_CA.pem
Adding debian:Deutsche_Telekom_Root_CA_2.pem
Adding debian:TC_TrustCenter_Class_2_CA_II.pem
Adding debian:GeoTrust_Global_CA.pem
Adding debian:Network_Solutions_Certificate_Authority.pem
Adding debian:Starfield_Services_Root_Certificate_Authority_-_G2.pem
Adding debian:NetLock_Arany_=Class_Gold=_F?tanúsítvány.pem
Adding debian:VeriSign_Class_3_Public_Primary_Certification_Authority_-_G4.pem
Adding debian:Security_Communication_Root_CA.pem
Adding debian:Verisign_Class_1_Public_Primary_Certification_Authority_-_G2.pem
Adding debian:Staat_der_Nederlanden_Root_CA_-_G2.pem
Adding debian:RSA_Root_Certificate_1.pem
Adding debian:SecureSign_RootCA11.pem
Adding debian:Starfield_Class_2_CA.pem
Adding debian:Taiwan_GRCA.pem
Adding debian:Chambers_of_Commerce_Root_-_2008.pem
Adding debian:Verisign_Class_4_Public_Primary_Certification_Authority_-_G2.pem
Adding debian:QuoVadis_Root_CA_3.pem
Adding debian:Hongkong_Post_Root_CA_1.pem
Adding debian:Comodo_Trusted_Services_root.pem
Adding debian:Root_CA_Generalitat_Valenciana.pem
Adding debian:America_Online_Root_Certification_Authority_2.pem
Adding debian:ePKI_Root_Certification_Authority.pem
Adding debian:Microsec_e-Szigno_Root_CA.pem
Adding debian:Entrust.net_Premium_2048_Secure_Server_CA.pem
Adding debian:AddTrust_Qualified_Certificates_Root.pem
Adding debian:TURKTRUST_Certificate_Services_Provider_Root_1.pem
Adding debian:Equifax_Secure_Global_eBusiness_CA.pem
Adding debian:Verisign_Class_2_Public_Primary_Certification_Authority_-_G3.pem
Adding debian:ssl-cert-snakeoil.pem
Adding debian:Digital_Signature_Trust_Co._Global_CA_1.pem
Adding debian:Verisign_Class_1_Public_Primary_Certification_Authority.pem
Adding debian:AffirmTrust_Commercial.pem
Adding debian:Secure_Global_CA.pem
Adding debian:UTN_DATACorp_SGC_Root_CA.pem
Adding debian:XRamp_Global_CA_Root.pem
Adding debian:NetLock_Notary_=Class_A=_Root.pem
Adding debian:Wells_Fargo_Root_CA.pem
Adding debian:DigiCert_Assured_ID_Root_CA.pem
Adding debian:Microsec_e-Szigno_Root_CA_2009.pem
Adding debian:Security_Communication_EV_RootCA1.pem
Adding debian:Certum_Trusted_Network_CA.pem
Adding debian:TC_TrustCenter__Germany__Class_2_CA.pem
Adding debian:GTE_CyberTrust_Global_Root.pem
Adding debian:AC_Raíz_Certicámara_S.A..pem
Adding debian:Verisign_Class_1_Public_Primary_Certification_Authority_-_G3.pem
Adding debian:DigiCert_Global_Root_CA.pem
Adding debian:GlobalSign_Root_CA_-_R2.pem
Adding debian:OISTE_WISeKey_Global_Root_GA_CA.pem
Adding debian:CNNIC_ROOT.pem
Adding debian:RSA_Security_2048_v3.pem
Adding debian:ValiCert_Class_2_VA.pem
Adding debian:TDC_Internet_Root_CA.pem
Adding debian:TC_TrustCenter__Germany__Class_3_CA.pem
Adding debian:Cybertrust_Global_Root.pem
Adding debian:GeoTrust_Global_CA_2.pem
Adding debian:GeoTrust_Primary_Certification_Authority.pem
Adding debian:GeoTrust_Universal_CA.pem
Adding debian:Buypass_Class_2_CA_1.pem
Adding debian:Certum_Root_CA.pem
Adding debian:thawte_Primary_Root_CA.pem
Adding debian:Sonera_Class_1_Root_CA.pem
Adding debian:Entrust.net_Secure_Server_CA.pem
Adding debian:Verisign_Class_4_Public_Primary_Certification_Authority_-_G3.pem
Adding debian:Buypass_Class_3_CA_1.pem
Adding debian:E-Guven_Kok_Elektronik_Sertifika_Hizmet_Saglayicisi.pem
Adding debian:Verisign_Class_3_Public_Primary_Certification_Authority.pem
Adding debian:Equifax_Secure_eBusiness_CA_1.pem
Adding debian:QuoVadis_Root_CA.pem
Adding debian:spi-cacert-2008.pem
Adding debian:Comodo_AAA_Services_root.pem
Adding debian:VeriSign_Class_3_Public_Primary_Certification_Authority_-_G5.pem
Adding debian:Verisign_Class_3_Public_Primary_Certification_Authority_-_G2.pem
Adding debian:ValiCert_Class_1_VA.pem
Adding debian:AffirmTrust_Premium_ECC.pem
Adding debian:TC_TrustCenter_Class_3_CA_II.pem
Adding debian:Staat_der_Nederlanden_Root_CA.pem
Adding debian:ACEDICOM_Root.pem
Adding debian:ComSign_Secured_CA.pem
Adding debian:CA_Disig.pem
Adding debian:GlobalSign_Root_CA.pem
Adding debian:Izenpe.com.pem
Adding debian:AddTrust_External_Root.pem
Adding debian:Visa_eCommerce_Root.pem
Adding debian:GeoTrust_Universal_CA_2.pem
Adding debian:UTN_USERFirst_Email_Root_CA.pem
Adding debian:VeriSign_Universal_Root_Certification_Authority.pem
Adding debian:AffirmTrust_Networking.pem
Adding debian:Verisign_Class_3_Public_Primary_Certification_Authority_-_G3.pem
Adding debian:StartCom_Certification_Authority.pem
Adding debian:Juur-SK.pem
Adding debian:TURKTRUST_Certificate_Services_Provider_Root_2.pem
Adding debian:Baltimore_CyberTrust_Root.pem
Adding debian:America_Online_Root_Certification_Authority_1.pem
Adding debian:SwissSign_Silver_CA_-_G2.pem
Adding debian:thawte_Primary_Root_CA_-_G2.pem
Adding debian:Autoridad_de_Certificacion_Firmaprofesional_CIF_A62634068.pem
Adding debian:SwissSign_Gold_CA_-_G2.pem
Adding debian:Entrust_Root_Certification_Authority.pem
Adding debian:SecureTrust_CA.pem
Adding debian:QuoVadis_Root_CA_2.pem
Adding debian:Sonera_Class_2_Root_CA.pem
Adding debian:UTN_USERFirst_Hardware_Root_CA.pem
Adding debian:Thawte_Server_CA.pem
Adding debian:Verisign_Class_2_Public_Primary_Certification_Authority.pem
done.
Setting up libatk-wrapper-java (0.30.4-0ubuntu2) ...
Setting up icedtea-6-jre-cacao (6b27-1.12.6-1ubuntu0.12.04.4) ...
Setting up icedtea-6-jre-jamvm (6b27-1.12.6-1ubuntu0.12.04.4) ...
Setting up openjdk-6-jre-lib (6b27-1.12.6-1ubuntu0.12.04.4) ...
Setting up libatk-wrapper-java-jni (0.30.4-0ubuntu2) ...
Setting up openjdk-6-jre (6b27-1.12.6-1ubuntu0.12.04.4) ...
update-alternatives: using /usr/lib/jvm/java-6-openjdk-i386/jre/bin/policytool to provide /usr/bin/policytool (policytool) in auto mode.
Setting up bio-linux-archaeopteryx (0.972.beta9M-3) ...
Setting up icedtea-netx (1.2.3-0ubuntu0.12.04.3) ...
update-alternatives: using /usr/lib/jvm/java-6-openjdk-i386/jre/bin/javaws to provide /usr/bin/javaws (javaws) in auto mode.
update-alternatives: using /usr/lib/jvm/java-6-openjdk-i386/jre/bin/itweb-settings to provide /usr/bin/itweb-settings (itweb-settings) in auto mode.
Processing triggers for libc-bin ...
ldconfig deferred processing now taking place
Reading package lists... Done
Building dependency tree       
Reading state information... Done
The following NEW packages will be installed:
  bio-linux-artemis
0 upgraded, 1 newly installed, 0 to remove and 14 not upgraded.
Need to get 11.8 MB of archives.
After this operation, 47.7 MB of additional disk space will be used.
Get:1 http://nebc.nerc.ac.uk/bio-linux/ unstable/bio-linux bio-linux-artemis all 15.1.1-1 [11.8 MB]
Fetched 11.8 MB in 2s (5,111 kB/s)            
Selecting previously unselected package bio-linux-artemis.
(Reading database ... 162928 files and directories currently installed.)
Unpacking bio-linux-artemis (from .../bio-linux-artemis_15.1.1-1_all.deb) ...
Processing triggers for bamfdaemon ...
Rebuilding /usr/share/applications/bamf.index...
Processing triggers for desktop-file-utils ...
Processing triggers for gnome-menus ...
Setting up bio-linux-artemis (15.1.1-1) ...
Reading package lists... Done
Building dependency tree       
Reading state information... Done
E: Unable to locate package bio-linux-assembly-conversion-tools
Not all packages installed properly - exiting.