[Debian-med-packaging] Bug#820062: Bug#820062: orthanc and orthanc-doc: error when trying to install together

Sébastien Jodogne s.jodogne at chu.ulg.ac.be
Tue Apr 5 07:06:57 UTC 2016 

Hello,

Thank for reporting this issue. However, I need help: I am indeed unable to reproduce it...

According to your report, the file "/usr/lib/orthanc/libModalityWorklists.so.1.0.0" lies both in package "orthanc" and "orthanc-doc":

>>>>>
/var/cache/apt/archives/orthanc-doc_1.0.0+dfsg-2_all.deb (--unpack):
 trying to overwrite '/usr/lib/orthanc/libModalityWorklists.so.1.0.0', which
 is also in package orthanc 1.0.0+dfsg-2
<<<<<

However, when I list the content of the "orthanc-doc" generated by my local pbuilder, this file is not present inside the package:

>>>>>
jodogne at unstable:~/Subversion/Debian/orthanc/debian$ dpkg -c /var/cache/pbuilder/result/orthanc-doc_1.0.0+dfsg-2_all.deb | grep ModalityWorklists
drwxr-xr-x root/root         0 2016-04-04 15:20 ./usr/share/doc/orthanc/OrthancPluginSamples/ModalityWorklists/
-rw-r--r-- root/root      7932 2016-04-04 15:20 ./usr/share/doc/orthanc/OrthancPluginSamples/ModalityWorklists/Plugin.cpp
-rw-r--r-- root/root      1561 2016-04-04 15:20 ./usr/share/doc/orthanc/OrthancPluginSamples/ModalityWorklists/README
drwxr-xr-x root/root         0 2016-04-04 15:20 ./usr/share/doc/orthanc/OrthancPluginSamples/ModalityWorklists/WorklistsDatabase/
-rw-r--r-- root/root       740 2016-04-04 15:20 ./usr/share/doc/orthanc/OrthancPluginSamples/ModalityWorklists/WorklistsDatabase/wklist2.wl
-rw-r--r-- root/root       748 2016-04-04 15:20 ./usr/share/doc/orthanc/OrthancPluginSamples/ModalityWorklists/WorklistsDatabase/wklist7.wl
-rw-r--r-- root/root       742 2016-04-04 15:20 ./usr/share/doc/orthanc/OrthancPluginSamples/ModalityWorklists/WorklistsDatabase/wklist5.wl
-rw-r--r-- root/root       756 2016-04-04 15:20 ./usr/share/doc/orthanc/OrthancPluginSamples/ModalityWorklists/WorklistsDatabase/wklist1.wl
-rw-r--r-- root/root       750 2016-04-04 15:20 ./usr/share/doc/orthanc/OrthancPluginSamples/ModalityWorklists/WorklistsDatabase/wklist6.wl
-rw-r--r-- root/root       752 2016-04-04 15:20 ./usr/share/doc/orthanc/OrthancPluginSamples/ModalityWorklists/WorklistsDatabase/wklist9.wl
-rw-r--r-- root/root       740 2016-04-04 15:20 ./usr/share/doc/orthanc/OrthancPluginSamples/ModalityWorklists/WorklistsDatabase/wklist3.wl
-rw-r--r-- root/root       467 2016-04-04 15:20 ./usr/share/doc/orthanc/OrthancPluginSamples/ModalityWorklists/WorklistsDatabase/Generate.py
-rw-r--r-- root/root       746 2016-04-04 15:20 ./usr/share/doc/orthanc/OrthancPluginSamples/ModalityWorklists/WorklistsDatabase/wklist10.wl
-rw-r--r-- root/root       752 2016-04-04 15:20 ./usr/share/doc/orthanc/OrthancPluginSamples/ModalityWorklists/WorklistsDatabase/wklist8.wl
-rw-r--r-- root/root       728 2016-04-04 15:20 ./usr/share/doc/orthanc/OrthancPluginSamples/ModalityWorklists/WorklistsDatabase/wklist4.wl
-rw-r--r-- root/root      1250 2016-04-04 15:20 ./usr/share/doc/orthanc/OrthancPluginSamples/ModalityWorklists/CMakeLists.txt
<<<<<

Could someone give me a hint? Is it because, as Ralf says at the end of his report, the packages are slightly out of sync?

TIA,
Sébastien-


----- Mail original -----
> De: "Ralf Treinen" <treinen at free.fr>
> À: submit at bugs.debian.org
> Envoyé: Mardi 5 Avril 2016 08:44:44
> Objet: [Debian-med-packaging] Bug#820062: orthanc and orthanc-doc: error	when trying to install together
> 
> Package: orthanc-doc,orthanc
> Version: orthanc-doc/1.0.0+dfsg-1
> Version: orthanc/1.0.0+dfsg-1+b1
> Severity: serious
> User: treinen at debian.org
> Usertags: edos-file-overwrite
> 
> Date: 2016-04-05
> Architecture: amd64
> Distribution: sid
> 
> Hi,
> 
> automatic installation tests of packages that share a file and at the
> same time do not conflict by their package dependency relationships has
> detected the following problem:
> 
> 
> 
> Extracting templates from packages: 65%
> Extracting templates from packages: 100%
> Preconfiguring packages ...
> Selecting previously unselected package libwrap0:amd64.
> (Reading database ... 10944 files and directories currently installed.)
> Preparing to unpack .../libwrap0_7.6.q-25_amd64.deb ...
> Unpacking libwrap0:amd64 (7.6.q-25) ...
> Selecting previously unselected package gcc-5-base:amd64.
> Preparing to unpack .../gcc-5-base_5.3.1-13_amd64.deb ...
> Unpacking gcc-5-base:amd64 (5.3.1-13) ...
> Processing triggers for man-db (2.7.5-1) ...
> Setting up gcc-5-base:amd64 (5.3.1-13) ...
> (Reading database ... 10963 files and directories currently installed.)
> Preparing to unpack .../libstdc++6_5.3.1-13_amd64.deb ...
> Unpacking libstdc++6:amd64 (5.3.1-13) over (4.8.2-19) ...
> Processing triggers for libc-bin (2.22-5) ...
> Setting up libstdc++6:amd64 (5.3.1-13) ...
> Processing triggers for libc-bin (2.22-5) ...
> Selecting previously unselected package libcharls1:amd64.
> (Reading database ... 10977 files and directories currently installed.)
> Preparing to unpack .../libcharls1_1.0-6_amd64.deb ...
> Unpacking libcharls1:amd64 (1.0-6) ...
> Selecting previously unselected package libjbig0:amd64.
> Preparing to unpack .../libjbig0_2.1-3.1_amd64.deb ...
> Unpacking libjbig0:amd64 (2.1-3.1) ...
> Selecting previously unselected package libssl1.0.2:amd64.
> Preparing to unpack .../libssl1.0.2_1.0.2g-1_amd64.deb ...
> Unpacking libssl1.0.2:amd64 (1.0.2g-1) ...
> Selecting previously unselected package libdb5.3:amd64.
> Preparing to unpack .../libdb5.3_5.3.28-11_amd64.deb ...
> Unpacking libdb5.3:amd64 (5.3.28-11) ...
> Selecting previously unselected package libgcrypt20:amd64.
> Preparing to unpack .../libgcrypt20_1.6.5-2_amd64.deb ...
> Unpacking libgcrypt20:amd64 (1.6.5-2) ...
> Selecting previously unselected package libgmp10:amd64.
> Preparing to unpack .../libgmp10_2%3a6.1.0+dfsg-2_amd64.deb ...
> Unpacking libgmp10:amd64 (2:6.1.0+dfsg-2) ...
> Selecting previously unselected package libnettle6:amd64.
> Preparing to unpack .../libnettle6_3.2-1_amd64.deb ...
> Unpacking libnettle6:amd64 (3.2-1) ...
> Selecting previously unselected package libhogweed4:amd64.
> Preparing to unpack .../libhogweed4_3.2-1_amd64.deb ...
> Unpacking libhogweed4:amd64 (3.2-1) ...
> Selecting previously unselected package libffi6:amd64.
> Preparing to unpack .../libffi6_3.2.1-4_amd64.deb ...
> Unpacking libffi6:amd64 (3.2.1-4) ...
> Preparing to unpack .../libp11-kit0_0.23.2-3_amd64.deb ...
> Unpacking libp11-kit0:amd64 (0.23.2-3) over (0.18.5-3) ...
> Selecting previously unselected package libtasn1-6:amd64.
> Preparing to unpack .../libtasn1-6_4.7-3_amd64.deb ...
> Unpacking libtasn1-6:amd64 (4.7-3) ...
> Selecting previously unselected package libgnutls30:amd64.
> Preparing to unpack .../libgnutls30_3.4.10-4_amd64.deb ...
> Unpacking libgnutls30:amd64 (3.4.10-4) ...
> Selecting previously unselected package libkeyutils1:amd64.
> Preparing to unpack .../libkeyutils1_1.5.9-8_amd64.deb ...
> Unpacking libkeyutils1:amd64 (1.5.9-8) ...
> Selecting previously unselected package libkrb5support0:amd64.
> Preparing to unpack .../libkrb5support0_1.13.2+dfsg-5_amd64.deb ...
> Unpacking libkrb5support0:amd64 (1.13.2+dfsg-5) ...
> Selecting previously unselected package libk5crypto3:amd64.
> Preparing to unpack .../libk5crypto3_1.13.2+dfsg-5_amd64.deb ...
> Unpacking libk5crypto3:amd64 (1.13.2+dfsg-5) ...
> Selecting previously unselected package libkrb5-3:amd64.
> Preparing to unpack .../libkrb5-3_1.13.2+dfsg-5_amd64.deb ...
> Unpacking libkrb5-3:amd64 (1.13.2+dfsg-5) ...
> Selecting previously unselected package libgssapi-krb5-2:amd64.
> Preparing to unpack .../libgssapi-krb5-2_1.13.2+dfsg-5_amd64.deb ...
> Unpacking libgssapi-krb5-2:amd64 (1.13.2+dfsg-5) ...
> Selecting previously unselected package libsasl2-modules-db:amd64.
> Preparing to unpack .../libsasl2-modules-db_2.1.26.dfsg1-15_amd64.deb ...
> Unpacking libsasl2-modules-db:amd64 (2.1.26.dfsg1-15) ...
> Selecting previously unselected package libsasl2-2:amd64.
> Preparing to unpack .../libsasl2-2_2.1.26.dfsg1-15_amd64.deb ...
> Unpacking libsasl2-2:amd64 (2.1.26.dfsg1-15) ...
> Selecting previously unselected package libldap-2.4-2:amd64.
> Preparing to unpack .../libldap-2.4-2_2.4.42+dfsg-2+b2_amd64.deb ...
> Unpacking libldap-2.4-2:amd64 (2.4.42+dfsg-2+b2) ...
> Selecting previously unselected package libicu55:amd64.
> Preparing to unpack .../libicu55_55.1-7_amd64.deb ...
> Unpacking libicu55:amd64 (55.1-7) ...
> Selecting previously unselected package libxml2:amd64.
> Preparing to unpack .../libxml2_2.9.3+dfsg1-1_amd64.deb ...
> Unpacking libxml2:amd64 (2.9.3+dfsg1-1) ...
> Selecting previously unselected package libpng12-0:amd64.
> Preparing to unpack .../libpng12-0_1.2.54-4_amd64.deb ...
> Unpacking libpng12-0:amd64 (1.2.54-4) ...
> Selecting previously unselected package libjpeg62-turbo:amd64.
> Preparing to unpack .../libjpeg62-turbo_1%3a1.4.2-2_amd64.deb ...
> Unpacking libjpeg62-turbo:amd64 (1:1.4.2-2) ...
> Selecting previously unselected package libtiff5:amd64.
> Preparing to unpack .../libtiff5_4.0.6-1_amd64.deb ...
> Unpacking libtiff5:amd64 (4.0.6-1) ...
> Selecting previously unselected package libdcmtk5.
> Preparing to unpack .../libdcmtk5_3.6.1~20150924-5_amd64.deb ...
> Unpacking libdcmtk5 (3.6.1~20150924-5) ...
> Selecting previously unselected package dcmtk.
> Preparing to unpack .../dcmtk_3.6.1~20150924-5_amd64.deb ...
> Unpacking dcmtk (3.6.1~20150924-5) ...
> Selecting previously unselected package libboost-system1.58.0:amd64.
> Preparing to unpack .../libboost-system1.58.0_1.58.0+dfsg-5+b1_amd64.deb ...
> Unpacking libboost-system1.58.0:amd64 (1.58.0+dfsg-5+b1) ...
> Selecting previously unselected package libboost-chrono1.58.0:amd64.
> Preparing to unpack .../libboost-chrono1.58.0_1.58.0+dfsg-5+b1_amd64.deb ...
> Unpacking libboost-chrono1.58.0:amd64 (1.58.0+dfsg-5+b1) ...
> Selecting previously unselected package libboost-filesystem1.58.0:amd64.
> Preparing to unpack .../libboost-filesystem1.58.0_1.58.0+dfsg-5+b1_amd64.deb
> ...
> Unpacking libboost-filesystem1.58.0:amd64 (1.58.0+dfsg-5+b1) ...
> Selecting previously unselected package libboost-thread1.58.0:amd64.
> Preparing to unpack .../libboost-thread1.58.0_1.58.0+dfsg-5+b1_amd64.deb ...
> Unpacking libboost-thread1.58.0:amd64 (1.58.0+dfsg-5+b1) ...
> Selecting previously unselected package libboost-locale1.58.0:amd64.
> Preparing to unpack .../libboost-locale1.58.0_1.58.0+dfsg-5+b1_amd64.deb ...
> Unpacking libboost-locale1.58.0:amd64 (1.58.0+dfsg-5+b1) ...
> Selecting previously unselected package libboost-regex1.58.0:amd64.
> Preparing to unpack .../libboost-regex1.58.0_1.58.0+dfsg-5+b1_amd64.deb ...
> Unpacking libboost-regex1.58.0:amd64 (1.58.0+dfsg-5+b1) ...
> Selecting previously unselected package libnghttp2-14:amd64.
> Preparing to unpack .../libnghttp2-14_1.9.1-1_amd64.deb ...
> Unpacking libnghttp2-14:amd64 (1.9.1-1) ...
> Selecting previously unselected package librtmp1:amd64.
> Preparing to unpack .../librtmp1_2.4+20151223.gitfa8646d-1+b1_amd64.deb ...
> Unpacking librtmp1:amd64 (2.4+20151223.gitfa8646d-1+b1) ...
> Selecting previously unselected package libssh2-1:amd64.
> Preparing to unpack .../libssh2-1_1.5.0-2.1_amd64.deb ...
> Unpacking libssh2-1:amd64 (1.5.0-2.1) ...
> Selecting previously unselected package libcurl3:amd64.
> Preparing to unpack .../libcurl3_7.47.0-1_amd64.deb ...
> Unpacking libcurl3:amd64 (7.47.0-1) ...
> Selecting previously unselected package libjs-jquery.
> Preparing to unpack .../libjs-jquery_1.11.3+dfsg-4_all.deb ...
> Unpacking libjs-jquery (1.11.3+dfsg-4) ...
> Selecting previously unselected package liblua5.1-0:amd64.
> Preparing to unpack .../liblua5.1-0_5.1.5-8_amd64.deb ...
> Unpacking liblua5.1-0:amd64 (5.1.5-8) ...
> Selecting previously unselected package libpugixml1v5:amd64.
> Preparing to unpack .../libpugixml1v5_1.7-2_amd64.deb ...
> Unpacking libpugixml1v5:amd64 (1.7-2) ...
> Selecting previously unselected package libjsoncpp1:amd64.
> Preparing to unpack .../libjsoncpp1_1.7.2-1_amd64.deb ...
> Unpacking libjsoncpp1:amd64 (1.7.2-1) ...
> Selecting previously unselected package orthanc.
> Preparing to unpack .../orthanc_1.0.0+dfsg-2_amd64.deb ...
> Unpacking orthanc (1.0.0+dfsg-2) ...
> Selecting previously unselected package orthanc-doc.
> Preparing to unpack .../orthanc-doc_1.0.0+dfsg-2_all.deb ...
> Unpacking orthanc-doc (1.0.0+dfsg-2) ...
> dpkg: error processing archive
> /var/cache/apt/archives/orthanc-doc_1.0.0+dfsg-2_all.deb (--unpack):
>  trying to overwrite '/usr/lib/orthanc/libModalityWorklists.so.1.0.0', which
>  is also in package orthanc 1.0.0+dfsg-2
> dpkg-deb: error: subprocess paste was killed by signal (Broken pipe)
> Processing triggers for libc-bin (2.22-5) ...
> Processing triggers for man-db (2.7.5-1) ...
> Errors were encountered while processing:
>  /var/cache/apt/archives/orthanc-doc_1.0.0+dfsg-2_all.deb
> E: Sub-process /usr/bin/dpkg returned an error code (1)
> 
> 
> This is a serious bug as it makes installation fail, and violates
> sections 7.6.1 and 10.1 of the policy. An optimal solution would
> consist in only one of the packages installing that file, and renaming
> or removing the file in the other package. Depending on the
> circumstances you might also consider Replace relations or file
> diversions. If the conflicting situation cannot be resolved then, as a
> last resort, the two packages have to declare a mutual
> Conflict. Please take into account that Replaces, Conflicts and
> diversions should only be used when packages provide different
> implementations for the same functionality.
> 
> Here is a list of files that are known to be shared by both packages
> (according to the Contents file for sid/amd64, which may be
> slightly out of sync):
> 
>   /usr/lib/orthanc/libModalityWorklists.so.1.0.0
>   /usr/lib/orthanc/libServeFolders.so.1.0.0
>   /usr/sbin/Orthanc
>   /usr/share/orthanc/plugins/libModalityWorklists.so
>   /usr/share/orthanc/plugins/libServeFolders.so
> 
> This bug has been filed against both packages. If you, the maintainers of
> the two packages in question, have agreed on which of the packages will
> resolve the problem please reassign the bug to that package. You may then
> also register in the BTS that the other package is affected by the bug.
> 
> -Ralf.
> 
> PS: for more information about the detection of file overwrite errors
> of this kind see http://qa.debian.org/dose/file-overwrites.html.
> 
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