Problem with update (CSS) : uninstall packages which reinstall after

Added by Adrien Daugabel 3 months ago

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 ?


Replies (4)

RE: Problem with update (CSS) : uninstall packages which reinstall after - Added by Adrien Daugabel 3 months ago

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

RE: Problem with update (CSS) : uninstall packages which reinstall after - Added by Adrien Daugabel 3 months ago

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): 

RE: Problem with update (CSS) : uninstall packages which reinstall after - Added by Adrien Daugabel 3 months ago

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

RE: Problem with update (CSS) : uninstall packages which reinstall after - Added by Mikhail Hiretsky 3 months ago

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.

(1-4/4)

Thank you!