Calculate Linux is a great distro, but in this x86_64 installation the Calculate Linux Update facility keeps removing and reinstalling the same files at nearly every daily update. Some of the files, I am under the impression, may be dependencies to app-text/xiphos-4.0.6a, a Bible study package.
Note 1: Xiphos required some flags to be set on another recent Calculate Linux installation when xiphos was being installed with many other packages; however, in the current installation for some reason only two other packages reported needing flags to be set - clamtk and thermald - (not xiphos) for which autounmask-write and dispatch-conf were applied with root privileges.
Note 2: The system was installed a few days ago using the ‘overnight’ updated iso file cldxe-20180817-x86_64.iso. (The jwm window manager was very easily installed and it is the environment being used).
Today, the Calculate Linux Update facility only offered what seems to be the removal and rebuild of the same packages, as often happens:
Sep 3 2018:
"Listing packages for removal
- Tools to convert docbook to man and info app-text/docbook2X-0.8.8-r4
- A collection of documentation utilities for the Gnome project app-text/gnome-doc-utils-0.20.10-r1
- A documentation metadata library app-text/rarian-0.8.1-r3
- Perl binding for libxml2 dev-perl/XML-LibXML-2.13.200
- A Perl module that offers a simple to process namespaced XML names dev-perl/XML-NamespaceSupport-1.120.0
- Perl module for using and building Perl SAX2 XML parsers, filters, and drivers dev-perl/XML-SAX-1.0.0
- Base class SAX Drivers and Filters dev-perl/XML-SAX-Base-1.90.0
- Internationalization Tool Collection dev-util/intltool-0.51.0-r2
- A multicast protocol to support Bible software shared co-navigation net-libs/biblesync-1.1.2-r2"
After responding ‘Yes’ to whether to unmerge those packages, the process continues with:
“Rebuilding dependent modules
(1 of 10) A multicast protocol to support Bible software shared co-navigation
Emerging net-libs/biblesync-1.1.2-r2
(2 of 10) A Perl module that offers a simple to process namespaced XML names
Emerging dev-perl/XML-NamespaceSupport-1.120.0
(3 of 10) Base class SAX Drivers and Filters
Emerging dev-perl/XML-SAX-Base-1.90.0
(4 of 10) A collection of documentation utilities for the Gnome project
Emerging app-text/gnome-doc-utils 0.20.10-r1
Installing net-libs/biblesync 1.1.2-r
(5 of 10) A documentation metadata library
Emerging app-text/rarian 0.8.1-r
Installing dev-perl/XML-NamespaceSupport-1.120.0
(6 of 10) Internationalization Tool Collection
Emerging dev-util/intltool 0.51.0-r
Installing dev-perl/XML-SAX-Base-1.90.0
Installing app-text/gnome-doc-utils 0.20.10-r1
Installing app-text/rarian 0.8.1-r
Installing dev-util/intltool 0.51.0-r
(7 of 10) Perl module for using and building Perl SAX2 XML parsers, filters, and drivers
Emerging dev-perl/XML-SAX 1.0.0
Installing dev-perl/XML-SAX 1.0.0
(8 of 10) Perl binding for libxml2
Emerging dev-perl/XML-LibXML 2.13.200
Installing dev-perl/XML-LibXML 2.13.200
(9 of 10) Tools to convert docbook to man and info
Emerging app-text/docbook2X 0.8.8-r4
Installing app-text/docbook2X 0.8.8-r4
(10 of 10) A bible study frontend for Sword (formerly known as GnomeSword)
Emerging app-text/xiphos-4.0.6a
Installing app-text/xiphos-4.0.6a
Updating configuration files
System update finished!”
Note 3: In case this could be relevant, package searches indicate that there are TWO versions available for FOUR of those packages:
[I] net-libs/biblesync
Available versions: 1.1.2-r2{tbz2} ~2.0.1 {static}
Installed versions: 1.1.2-r2{tbz2}(05:11:57 PM 08/28/2018)(-static)
Homepage: http://www.crosswire.org/wiki/BibleSync
Description: A multicast protocol to support Bible software shared co-navigation
[I] dev-perl/XML-SAX
Available versions: 0.990.0-r1 1.0.0{tbz2}
Installed versions: 1.0.0{tbz2}(11:36:02 AM 08/28/2018)
Homepage: http://search.cpan.org/dist/XML-SAX/
Description: Perl module for using and building Perl SAX2 XML parsers, filters, and drivers
[I] dev-perl/XML-LibXML
Available versions: 2.12.800-r1 ~2.12.900 2.13.200{tbz2} {examples minimal test}
Installed versions: 2.13.200{tbz2}(11:44:45 AM 08/28/2018)(-examples -minimal -test)
Homepage: http://search.cpan.org/dist/XML-LibXML/
Description: Perl binding for libxml2
[I] app-text/xiphos
Available versions: 4.0.6a-r1 ~4.1.0-r1 {dbus debug PYTHON_TARGETS="python2_7"}
Installed versions: 4.0.6a-r1(01:15:20 PM 09/03/2018)(dbus -debug PYTHON_TARGETS="python2_7")
Homepage: http://xiphos.org/
Description: A bible study frontend for Sword (formerly known as GnomeSword)
Note 4: Perhaps the output for the following may be helpful when trying to find conflicts, as inspired by another Calculate Linux forum post:
$ emerge -avquDN --with-bdeps=y @world --verbose-conflicts
The output is posted here.
Note 5: This recurring problem had occurred with my previous Calculate Linux installation, which had been regularly updated. In that installation, I don’t think xiphos required any flags to be set either (unlike an even earlier installation of Calculate Linux). From my notes:
Aug 19 2018:
"Listing packages for removal
- Tools to convert docbook to man and info app-text/docbook2X-0.8.8-r4
- A collection of documentation utilities for the Gnome project app-text/gnome-doc-utils-0.20.10-r1
- A documentation metadata library app-text/rarian-0.8.1-r3
- Perl binding for libxml2 dev-perl/XML-LibXML-2.13.200
- A Perl module that offers a simple to process namespaced XML names dev-perl/XML-NamespaceSupport-1.120.0
- Perl module for using and building Perl SAX2 XML parsers, filters, and drivers dev-perl/XML-SAX-0.990.0-r1
- Base class SAX Drivers and Filters dev-perl/XML-SAX-Base-1.90.0
- Internationalization Tool Collection dev-util/intltool-0.51.0-r2"
[…]
Then:
“Rebuilding dependent modules
Updating preserved libraries
(1 of 10) A multicast protocol to support Bible software shared co-navigation
Emerging net-libs/biblesync-1.1.2-r2
(2 of 10) A Perl module that offers a simple to process namespaced XML names
Emerging dev-perl/XML-NamespaceSupport-1.120.0
(3 of 10) Base class SAX Drivers and Filters
Emerging dev-perl/XML-SAX-Base-1.90.0
[etc, up to…]
(10 of 10) A bible study frontend for Sword (formerly known as GnomeSword)
Emerging app-text/xiphos-4.0.6a
Installing app-text/xiphos-4.0.6a
Updating configuration files
System update finished!”
When xiphos was removed in that earlier installation, the problem resolved. The leftover dependencies, presumably, or unneeded packages were offered to be removed also - including ?some of the above, if I remember correctly. However, I would like to preserve Xiphos this time. Could anyone suggest some repair attempts please? Thank you!