Hi,
i installed a new CSS server, and I installed some apps :
net-analyzer/fail2ban
app-editors/vim
dev-db/mariadb
www-servers/apache
dev-lang/php
sys-process/nmon
sys-process/htop
sys-process/glances
sys-apps/inxi
app-admin/rsyslog
logrotate
When i update my system, all is up to date but packages are uninstalled, and installed again …
cluster1 adrien # cl-update
Synchronisation des dépôts
* Checking Distros updates ... [ ok ]
* Checking Calculate updates ... [ ok ]
* Checking Gentoo updates ... [ ok ]
* Synchronisation terminée
Configuration système
* Update server http://mirror.yandex.ru/calculate
Mise à jour des paquets
* Calcul des dépendances ...
* Le système est à jour
Suppression des paquets devenus inutiles
* Calcul des dépendances ...
* Liste des paquets à supprimer
* The GLib library of C routines dev-libs/glib-2.50.3-r1
* A shared library tool for developers dev-libs/libltdl-2.4.6
* Package config system that manages compile/link flags dev-util/pkgconfig-0.28-r2
* Used to create autoconfiguration files sys-devel/autoconf-2.69
* Wrapper for autoconf to manage multiple autoconf versions sys-devel/autoconf-wrapper-13
* Used to generate Makefile.in from Makefile.am sys-devel/automake-1.15-r2
* Wrapper for automake to manage multiple automake versions sys-devel/automake-wrapper-10
* A general-purpose (yacc-compatible) parser generator sys-devel/bison-3.0.4-r1
* The Fast Lexical Analyzer sys-devel/flex-2.6.1
* A shared library tool for developers sys-devel/libtool-2.4.6-r3
* GNU macro processor sys-devel/m4-1.4.17
* Virtual for the pkg-config implementation virtual/pkgconfig-0-r1
Would you like to unmerge these unused packages (recommended)? (Yes/No): y
* Suppression de (1 sur 12) sys-devel/bison-3.0.4-r1 ... [ ok ]
* Suppression de (2 sur 12) virtual/pkgconfig-0-r1 ... [ ok ]
* Suppression de (3 sur 12) dev-util/pkgconfig-0.28-r2 ... [ ok ]
* Suppression de (4 sur 12) sys-devel/flex-2.6.1 ... [ ok ]
* Suppression de (5 sur 12) dev-libs/glib-2.50.3-r1 ... [ ok ]
* Suppression de (6 sur 12) sys-devel/libtool-2.4.6-r3 ... [ ok ]
* Suppression de (7 sur 12) dev-libs/libltdl-2.4.6 ... [ ok ]
* Suppression de (8 sur 12) sys-devel/automake-1.15-r2 ... [ ok ]
* Suppression de (9 sur 12) sys-devel/automake-wrapper-10 ... [ ok ]
* Suppression de (10 sur 12) sys-devel/autoconf-2.69 ... [ ok ]
* Suppression de (11 sur 12) sys-devel/autoconf-wrapper-13 ... [ ok ]
* Suppression de (12 sur 12) sys-devel/m4-1.4.17 ... [ ok ]
Recompilation des modules dépendants
* Mise à jour des bibliothèques réservées ... [ ok ]
* (1 sur 13) GNU macro processor
* Compilation de sys-devel/m4-1.4.17 ... [ ok ]
* (2 sur 13) A shared library tool for developers
* Compilation de dev-libs/libltdl-2.4.6 ... [ ok ]
* (3 sur 13) Wrapper for automake to manage multiple automake versions
* Compilation de sys-devel/automake-wrapper-10 ... [ ok ]
* (4 sur 13) Wrapper for autoconf to manage multiple autoconf versions
* Compilation de sys-devel/autoconf-wrapper-13 ... [ ok ]
* Installation de dev-libs/libltdl-2.4.6 ... [ ok ]
* (5 sur 13) The GLib library of C routines
* Compilation de dev-libs/glib-2.50.3-r1 ... [ ok ]
* Installation de sys-devel/autoconf-wrapper-13 ... [ ok ]
* Installation de sys-devel/m4-1.4.17 ... [ ok ]
* Installation de sys-devel/automake-wrapper-10 ... [ ok ]
* Installation de dev-libs/glib-2.50.3-r1 ... [ ok ]
* (6 sur 13) Used to create autoconfiguration files
* Compilation de sys-devel/autoconf-2.69 ... [ ok ]
* (7 sur 13) The Fast Lexical Analyzer
* Compilation de sys-devel/flex-2.6.1 ... [ ok ]
* (8 sur 13) A general-purpose (yacc-compatible) parser generator
* Compilation de sys-devel/bison-3.0.4-r1 ... [ ok ]
* Installation de sys-devel/autoconf-2.69 ... [ ok ]
* Installation de sys-devel/bison-3.0.4-r1 ... [ ok ]
* (9 sur 13) Package config system that manages compile/link flags
* Compilation de dev-util/pkgconfig-0.28-r2 ... [ ok ]
* Installation de sys-devel/flex-2.6.1 ... [ ok ]
* Installation de dev-util/pkgconfig-0.28-r2 ... [ ok ]
* (10 sur 13) Used to generate Makefile.in from Makefile.am
* Compilation de sys-devel/automake-1.15-r2 ... [ ok ]
* Installation de sys-devel/automake-1.15-r2 ... [ ok ]
* (11 sur 13) Virtual for the pkg-config implementation
* Compilation de virtual/pkgconfig-0-r1 ... [ ok ]
* Installation de virtual/pkgconfig-0-r1 ... [ ok ]
* (12 sur 13) A shared library tool for developers
* Compilation de sys-devel/libtool-2.4.6-r3 ... [ ok ]
* Installation de sys-devel/libtool-2.4.6-r3 ... [ ok ]
* (13 sur 13) The PHP language runtime engine
* Compilation de dev-lang/php-7.0.21 ...
Why ?
I try a classical update …
cluster1 adrien # eix-sync && emerge -avuDN --with-bdeps=y @world
* Running !-hooks
* Running /usr/sbin/cl-core --method update --sync-only --skip-eix-update
Synchronisation des dépôts
* Checking Distros updates ... [ ok ]
* Checking Calculate updates ... [ ok ]
* Checking Gentoo updates ... [ ok ]
* Synchronisation terminée
Configuration système
* Update server http://mirror.yandex.ru/calculate
* Votre système a bien été mis à jour !
* Copying old database to /var/cache/eix/previous.eix
* Running eix-update
Reading Portage settings...
Building database (/var/cache/eix/portage.eix)...
[0] "gentoo" /usr/portage/ (cache: metadata-md5-or-flat)
Reading category 164|164 (100) Finished
[1] "distros" /var/lib/layman/distros (cache: parse|ebuild*#metadata-md5#metadata-flat#assign)
Reading category 164|164 (100) EMPTY!
[2] "calculate" /var/lib/layman/calculate (cache: parse|ebuild*#metadata-md5#metadata-flat#assign)
Reading category 164|164 (100) Finished
Applying masks...
Calculating hash tables...
Writing database file /var/cache/eix/portage.eix...
Database contains 19633 packages in 164 categories.
* Calling eix-diff
* Time statistics:
4 seconds for syncing
28 seconds for eix-update
2 seconds for eix-diff
35 seconds total
Local copy of remote index is up-to-date and will be used.
* IMPORTANT: 4 news items need reading for repository 'gentoo'.
* Use eselect news read to view new items.
These are the packages that would be merged, in order:
Calculating dependencies... done!
[binary N ] app-text/sgml-common-0.6.3-r5::gentoo 62 KiB
[binary N ] dev-util/boost-build-1.62.0-r1::gentoo USE="-examples -python {-test}" PYTHON_TARGETS="python2_7" 408 KiB
[binary N ] dev-util/gperf-3.0.4::gentoo 149 KiB
[binary N ] sys-devel/autoconf-archive-2016.03.20-r1::gentoo 548 KiB
[binary N ] app-portage/elt-patches-20170422::gentoo 43 KiB
[binary N ] virtual/yacc-0::gentoo 8 KiB
[binary N ] dev-libs/libnatspec-0.2.6-r1::gentoo USE="-doc -python" PYTHON_TARGETS="python2_7" 104 KiB
[binary N ] app-arch/unzip-6.0_p20::gentoo USE="bzip2 natspec unicode" 210 KiB
[binary N ] app-text/opensp-1.5.2-r3::gentoo USE="nls -doc -static-libs {-test}" 1081 KiB
[binary N ] app-text/openjade-1.3.2-r7::gentoo USE="-static-libs" 1063 KiB
[binary N ] x11-proto/xproto-7.0.31::gentoo USE="-doc" ABI_X86="(64) -32 (-x32)" 130 KiB
[binary NS ] app-text/docbook-xml-dtd-4.5-r1:4.5::gentoo [4.1.2-r6:4.1.2::gentoo, 4.2-r2:4.2::gentoo] 83 KiB
[binary N ] dev-libs/libuv-1.10.2:0/1::gentoo USE="-static-libs" ABI_X86="(64) -32 (-x32)" 145 KiB
[binary N ] virtual/perl-ExtUtils-MakeMaker-7.100.200_rc-r1::gentoo 10 KiB
[binary N ] virtual/perl-CPAN-Meta-YAML-0.18.0-r2::gentoo 9 KiB
[binary N ] virtual/perl-Parse-CPAN-Meta-1.441.700.100_rc-r1::gentoo 10 KiB
[binary N ] dev-perl/SGMLSpm-1.03-r7::gentoo 46 KiB
[binary N ] dev-perl/Text-CharWidth-0.40.0-r1::gentoo 36 KiB
[binary N ] dev-perl/XML-Parser-2.440.0::gentoo 193 KiB
[binary N ] virtual/perl-Text-ParseWords-3.300.0-r3::gentoo 9 KiB
[binary N ] virtual/perl-Perl-OSType-1.9.0-r1::gentoo 9 KiB
[binary N ] virtual/perl-Module-Metadata-1.0.31-r1::gentoo 9 KiB
[binary N ] virtual/perl-ExtUtils-ParseXS-3.310.0-r1::gentoo 9 KiB
[binary N ] virtual/perl-ExtUtils-Manifest-1.700.0-r4::gentoo 9 KiB
[binary N ] virtual/perl-ExtUtils-Install-2.40.0-r3::gentoo 9 KiB
[binary N ] virtual/perl-ExtUtils-CBuilder-0.280.225-r2::gentoo 9 KiB
[binary N ] virtual/perl-JSON-PP-2.273.0.100_rc-r3::gentoo 10 KiB
[binary N ] virtual/perl-version-0.991.600-r1::gentoo 9 KiB
[binary N ] dev-libs/klibc-2.0.4-r3::calculate USE="-custom-cflags -debug {-test}" 366 KiB
[binary N ] dev-perl/Text-WrapI18N-0.60.0-r1::gentoo 34 KiB
[binary N ] virtual/perl-CPAN-Meta-2.150.5-r1::gentoo 9 KiB
[binary N ] dev-perl/Module-Build-0.421.600::gentoo USE="{-test}" 170 KiB
[binary N ] dev-libs/libatomic_ops-7.4.2::gentoo 95 KiB
[binary N ] dev-util/gtk-doc-am-1.25-r1::gentoo 30 KiB
[binary N ] x11-misc/makedepend-1.0.5::gentoo 61 KiB
[binary N ] virtual/awk-1::gentoo 8 KiB
[binary N ] dev-lang/swig-3.0.12::gentoo USE="pcre -ccache -doc" 1375 KiB
[binary N ] dev-libs/boost-1.62.0-r1:0/1.62.0::gentoo USE="icu nls python threads -context -debug -doc -mpi -static-libs -tools" ABI_X86="(64) -32 (-x32)" PYTHON_TARGETS="python2_7 python3_4 (-python3_5)" 11129 KiB
[binary N ] dev-python/pygments-2.2.0::gentoo USE="-doc {-test}" PYTHON_TARGETS="python2_7 python3_4 (-pypy) (-pypy3) (-python3_5) (-python3_6)" 4261 KiB
[binary N ] dev-python/docutils-0.12::gentoo PYTHON_TARGETS="python2_7 python3_4 (-pypy) (-pypy3) (-python3_5) (-python3_6)" 2835 KiB
[binary N ] dev-perl/Locale-gettext-1.50.0-r1::gentoo 41 KiB
[binary N ] dev-util/intltool-0.51.0-r1::gentoo 73 KiB
[binary N ] sys-apps/help2man-1.46.6::gentoo USE="nls" 142 KiB
[binary N ] app-text/po4a-0.47-r1::gentoo USE="{-test}" LINGUAS="cs da de es et fr hr it nl pl pt pt_BR ru sl sv uk -af -ca -eo -eu -id -ja -kn -ko -nb -vi -zh_CN -zh_HK" 1194 KiB
[binary N ] app-text/asciidoc-8.6.9-r2::gentoo USE="-examples -graphviz -highlight {-test}" PYTHON_SINGLE_TARGET="python2_7 (-pypy)" PYTHON_TARGETS="python2_7 (-pypy)" 254 KiB
[binary N ] dev-util/cmake-3.7.2::gentoo USE="ncurses -doc -emacs -qt5 -system-jsoncpp {-test}" 7806 KiB
Total: 46 packages (45 new, 1 in new slot, 46 binaries), Size of downloads: 34284 KiB
Would you like to merge these packages? [Yes/No] y
>>> Emerging binary (1 of 46) app-text/sgml-common-0.6.3-r5::gentoo
>>> Emerging binary (2 of 46) dev-util/boost-build-1.62.0-r1::gentoo
>>> Emerging binary (3 of 46) dev-util/gperf-3.0.4::gentoo
>>> Emerging binary (4 of 46) sys-devel/autoconf-archive-2016.03.20-r1::gentoo
>>> Installing (1 of 46) app-text/sgml-common-0.6.3-r5::gentoo
>>> Emerging binary (5 of 46) app-portage/elt-patches-20170422::gentoo
>>> Installing (3 of 46) dev-util/gperf-3.0.4::gentoo
>>> Installing (2 of 46) dev-util/boost-build-1.62.0-r1::gentoo
>>> Installing (4 of 46) sys-devel/autoconf-archive-2016.03.20-r1::gentoo
>>> Installing (5 of 46) app-portage/elt-patches-20170422::gentoo
>>> Emerging binary (6 of 46) virtual/yacc-0::gentoo
>>> Installing (6 of 46) virtual/yacc-0::gentoo
>>> Emerging binary (7 of 46) dev-libs/libnatspec-0.2.6-r1::gentoo
>>> Installing (7 of 46) dev-libs/libnatspec-0.2.6-r1::gentoo
>>> Emerging binary (8 of 46) app-arch/unzip-6.0_p20::gentoo
>>> Installing (8 of 46) app-arch/unzip-6.0_p20::gentoo
>>> Emerging binary (9 of 46) app-text/opensp-1.5.2-r3::gentoo
>>> Emerging binary (10 of 46) x11-proto/xproto-7.0.31::gentoo
>>> Emerging binary (11 of 46) app-text/docbook-xml-dtd-4.5-r1::gentoo
>>> Emerging binary (12 of 46) dev-libs/libuv-1.10.2::gentoo
>>> Installing (10 of 46) x11-proto/xproto-7.0.31::gentoo
>>> Emerging binary (13 of 46) virtual/perl-ExtUtils-MakeMaker-7.100.200_rc-r1::gentoo
>>> Installing (9 of 46) app-text/opensp-1.5.2-r3::gentoo
>>> Installing (12 of 46) dev-libs/libuv-1.10.2::gentoo
>>> Installing (11 of 46) app-text/docbook-xml-dtd-4.5-r1::gentoo
>>> Installing (13 of 46) virtual/perl-ExtUtils-MakeMaker-7.100.200_rc-r1::gentoo
After installation, all packages are identified as unused …
cluster1 adrien # cl-update
Synchronisation des dépôts
* Checking Distros updates ... [ ok ]
* Checking Calculate updates ... [ ok ]
* Checking Gentoo updates ... [ ok ]
* Synchronisation terminée
Configuration système
* Update server http://mirror.yandex.ru/calculate
Mise à jour des paquets
* Calcul des dépendances ...
* Le système est à jour
Suppression des paquets devenus inutiles
* Calcul des dépendances ...
* Liste des paquets à supprimer
* Unzipper for pkzip-compressed files app-arch/unzip-6.0_p20
* Collection of patches for libtool.eclass app-portage/elt-patches-20170422
* AsciiDoc is a plain text human readable/writable document format app-text/asciidoc-8.6.9-r2
* Docbook DTD for XML app-text/docbook-xml-dtd-4.5-r1
* Jade is an implementation of DSSSL for formatting SGML and XML documents app-text/openjade-1.3.2-r7
* A free, object-oriented toolkit for SGML parsing and entity management app-text/opensp-1.5.2-r3
* Tools for helping translation of documentation app-text/po4a-0.47-r1
* Base ISO character entities and utilities for SGML app-text/sgml-common-0.6.3-r5
* Simplified Wrapper and Interface Generator dev-lang/swig-3.0.12
* Boost Libraries for C++ dev-libs/boost-1.62.0-r1
* The GLib library of C routines dev-libs/glib-2.50.3-r1
* A minimal libc subset for use with initramfs dev-libs/klibc-2.0.4-r3
* Implementation for atomic memory update operations dev-libs/libatomic_ops-7.4.2
* A shared library tool for developers dev-libs/libltdl-2.4.6
* Library to smooth charset/localization issues dev-libs/libnatspec-0.2.6-r1
* Cross-platform asychronous I/O dev-libs/libuv-1.10.2
* A Perl module for accessing the GNU locale utilities dev-perl/Locale-gettext-1.50.0-r1
* Build and install Perl modules dev-perl/Module-Build-0.421.600
* Perl library for parsing the output of nsgmls dev-perl/SGMLSpm-1.03-r7
* Get number of occupied columns of a string on terminal dev-perl/Text-CharWidth-0.40.0-r1
* Internationalized substitute of Text::Wrap dev-perl/Text-WrapI18N-0.60.0-r1
* A Perl extension interface to James Clark's XML parser, expat dev-perl/XML-Parser-2.440.0
* Python Documentation Utilities dev-python/docutils-0.12
* Pygments is a syntax highlighting package written in Python dev-python/pygments-2.2.0
* A system for large project software construction, simple to use and powerful dev-util/boost-build-1.62.0-r1
* Cross platform Make dev-util/cmake-3.7.2
* A perfect hash function generator dev-util/gperf-3.0.4
* Automake files from gtk-doc dev-util/gtk-doc-am-1.25-r1
* Internationalization Tool Collection dev-util/intltool-0.51.0-r1
* Package config system that manages compile/link flags dev-util/pkgconfig-0.28-r2
* GNU utility to convert program --help output to a man page sys-apps/help2man-1.46.6
* Used to create autoconfiguration files sys-devel/autoconf-2.69
* GNU Autoconf Macro Archive sys-devel/autoconf-archive-2016.03.20-r1
* Wrapper for autoconf to manage multiple autoconf versions sys-devel/autoconf-wrapper-13
* Used to generate Makefile.in from Makefile.am sys-devel/automake-1.15-r2
* Wrapper for automake to manage multiple automake versions sys-devel/automake-wrapper-10
* A general-purpose (yacc-compatible) parser generator sys-devel/bison-3.0.4-r1
* The Fast Lexical Analyzer sys-devel/flex-2.6.1
* A shared library tool for developers sys-devel/libtool-2.4.6-r3
* GNU macro processor sys-devel/m4-1.4.17
* Virtual for awk implementation virtual/awk-1
* Virtual for CPAN-Meta virtual/perl-CPAN-Meta-2.150.5-r1
* Virtual for CPAN-Meta-YAML virtual/perl-CPAN-Meta-YAML-0.18.0-r2
* Virtual for ExtUtils-CBuilder virtual/perl-ExtUtils-CBuilder-0.280.225-r2
* Virtual for ExtUtils-Install virtual/perl-ExtUtils-Install-2.40.0-r3
* Virtual for ExtUtils-MakeMaker virtual/perl-ExtUtils-MakeMaker-7.100.200_rc-r1
* Virtual for ExtUtils-Manifest virtual/perl-ExtUtils-Manifest-1.700.0-r4
* Virtual for ExtUtils-ParseXS virtual/perl-ExtUtils-ParseXS-3.310.0-r1
* Virtual for JSON-PP virtual/perl-JSON-PP-2.273.0.100_rc-r3
* Virtual for Module-Metadata virtual/perl-Module-Metadata-1.0.31-r1
* Virtual for Parse-CPAN-Meta virtual/perl-Parse-CPAN-Meta-1.441.700.100_rc-r1
* Virtual for Perl-OSType virtual/perl-Perl-OSType-1.9.0-r1
* Virtual for Text-ParseWords virtual/perl-Text-ParseWords-3.300.0-r3
* Virtual for version virtual/perl-version-0.991.600-r1
* Virtual for the pkg-config implementation virtual/pkgconfig-0-r1
* Virtual for yacc (yet another compiler compiler) virtual/yacc-0
* Create dependencies in makefiles x11-misc/makedepend-1.0.5
* X.Org xproto protocol headers x11-proto/xproto-7.0.31
Would you like to unmerge these unused packages (recommended)? (Yes/No):
Hummm bug with calculate-utilities variables …
cl-core-variables --set update.cl_update_other_set=on
cl-core-variables --set update.cl_update_with_bdeps_set=on
and solved
We fixed different behaviour on package updating and preserved rebuild. Now cl-update
setups --with-bdeps by variable update.cl_update_with_bdeps_set
only.