Bug 836910 – sci-libs/netcdf-4.8.1-r1 - automagic dependency on dev-libs/libzip

• Product: Gentoo Linux
• Status: UNCONFIRMED ---

[Description Bernd 2022-04-06 10:11:26 UTC]

This error is from a multilib testing chroot.

While investigating bug #820593 I encountered this error:

>>> Source configured.
>>> Compiling source in /var/tmp/portage-ondisk/portage/sci-libs/vtk-9.0.3-r4/work/VTK-9.0.3 ...
 * Source directory (CMAKE_USE_DIR): "/var/tmp/portage-ondisk/portage/sci-libs/vtk-9.0.3-r4/work/VTK-9.0.3"
 * Build directory  (BUILD_DIR):     "/var/tmp/portage-ondisk/portage/sci-libs/vtk-9.0.3-r4/work/vtk-9.0.3_build"
ninja -v -j2
ninja: error: '/usr/lib64/libzip.so', needed by 'lib64/libvtkIONetCDF-9.0.so.9.0.3', missing and no known rule to make it
 * ERROR: sci-libs/vtk-9.0.3-r4::gentoo-git failed (compile phase):
 *   ninja -v -j2 failed

Not sure, what change in the tree caused this to happen. Looking through the git log for the netcdf package, didn't help either.

Installing dev-libs/libzip solves the issue.


Reproducible: Always




emerge --info =vtk-9.0.3-r4

(chroot-multi) artus /var/db/repos/gentoo-git/sci-libs/vtk # emerge --info =vtk-9.0.3-r4
Portage 3.0.30 (python 3.9.12-final-0, default/linux/amd64/17.1/systemd, gcc-11.2.1, glibc-2.35-r2, 5.16.18-gentoo-r1-0 x86_64)
=================================================================
                         System Settings
=================================================================
System uname: Linux-5.16.18-gentoo-r1-0-x86_64-AMD_Ryzen_7_3800X_8-Core_Processor-with-glibc2.35
KiB Mem:    32888652 total,   3900072 free
KiB Swap:   33554428 total,  28922724 free
Head commit of repository qt: 07dfab4b3469b6455f543f156b66816602eaf14d

Head commit of repository gentoo-git: 64ffabcdbbdd71f9a3328d252cb033e6579011b9

Head commit of repository waebbl: ed4d21049e449380bd58afa610231d608734cea9

Timestamp of repository gentoo: Wed, 06 Apr 2022 07:34:36 +0000
Head commit of repository gentoo: a23c87788d24d524ae111b8ca87df8e9b084c75d

sh bash 5.1_p16
ld GNU ld (Gentoo 2.38 p3) 2.38
app-misc/pax-utils:        1.3.3::gentoo
app-shells/bash:           5.1_p16::gentoo
dev-lang/perl:             5.34.1::gentoo
dev-lang/python:           3.9.12::gentoo, 3.10.4::gentoo
dev-lang/rust-bin:         1.59.0::gentoo
dev-util/cmake:            3.23.0::gentoo
dev-util/meson:            0.61.4-r2::gentoo
sys-apps/baselayout:       2.8::gentoo
sys-apps/sandbox:          2.29::gentoo
sys-apps/systemd:          250.4-r1::gentoo
sys-devel/autoconf:        2.71-r1::gentoo
sys-devel/automake:        1.16.5::gentoo
sys-devel/binutils:        2.38-r1::gentoo
sys-devel/binutils-config: 5.4.1::gentoo
sys-devel/gcc:             11.2.1_p20220115::gentoo
sys-devel/gcc-config:      2.5-r1::gentoo
sys-devel/libtool:         2.4.7::gentoo
sys-devel/llvm:            13.0.1::gentoo, 14.0.0::gentoo
sys-devel/make:            4.3::gentoo
sys-kernel/linux-headers:  5.16::gentoo (virtual/os-headers)
sys-libs/glibc:            2.35-r2::gentoo
Repositories:

qt
    location: /var/db/repos/qt
    sync-type: git
    sync-uri: https://github.com/gentoo-mirror/qt.git
    masters: gentoo
    priority: 60

gentoo-git
    location: /var/db/repos/gentoo-git
    sync-type: git
    sync-uri: https://github.com/waebbl/gentoo.git
    masters: gentoo
    priority: 99

waebbl
    location: /var/db/repos/waebbl
    sync-type: git
    sync-uri: https://github.com/waebbl/waebbl-gentoo.git
    masters: gentoo
    priority: 99

gentoo
    location: /var/db/repos/gentoo
    sync-type: git
    sync-uri: https://github.com/gentoo-mirror/gentoo.git
    priority: 100

Installed sets: @tools
ACCEPT_KEYWORDS="amd64 ~amd64"
ACCEPT_LICENSE="@FREE"
CBUILD="x86_64-pc-linux-gnu"
CFLAGS="-O2 -pipe -march=znver2 -frecord-gcc-switches -fstack-protector-strong -fstack-check"
CHOST="x86_64-pc-linux-gnu"
CONFIG_PROTECT="/etc /usr/share/gnupg/qualified.txt"
CONFIG_PROTECT_MASK="/etc/ca-certificates.conf /etc/env.d /etc/fonts/fonts.conf /etc/gconf /etc/gentoo-release /etc/revdep-rebuild /etc/sandbox.d /etc/terminfo"
CXXFLAGS="-O2 -pipe -march=znver2 -frecord-gcc-switches -fstack-protector-strong -fstack-check"
DISTDIR="/var/cache/distfiles"
EMERGE_DEFAULT_OPTS="--complete-graph --keep-going --fail-clean --usepkg --buildpkg --buildpkg-exclude='x11-drivers/nvidia-drivers virtual/* acct-group/* acct-user/* app-eselect/* dev-util/nvidia-cuda-toolkit' --autounmask=n --binpkg-respect-use=y --binpkg-changed-deps=y"
ENV_UNSET="CARGO_HOME DBUS_SESSION_BUS_ADDRESS DISPLAY GOBIN GOPATH PERL5LIB PERL5OPT PERLPREFIX PERL_CORE PERL_MB_OPT PERL_MM_OPT XAUTHORITY XDG_CACHE_HOME XDG_CONFIG_HOME XDG_DATA_HOME XDG_RUNTIME_DIR"
FCFLAGS="-O2 -pipe -march=znver2 -frecord-gcc-switches -fstack-protector-strong -fstack-check"
FEATURES="assume-digests binpkg-docompress binpkg-dostrip binpkg-logs buildpkg buildpkg-live buildsyspkg cgroup clean-logs config-protect-if-modified distlocks ebuild-locks fail-clean fixlafiles ipc-sandbox merge-sync multilib-strict network-sandbox news parallel-fetch pid-sandbox preserve-libs protect-owned qa-unresolved-soname-deps sandbox sfperms sign split-elog split-log strict strict-keepdir unknown-features-warn unmerge-logs unmerge-orphans userfetch userpriv usersandbox usersync xattr"
FFLAGS="-O2 -pipe -march=znver2 -frecord-gcc-switches -fstack-protector-strong -fstack-check"
GENTOO_MIRRORS="https://ftp.fau.de/gentoo/ https://ftp-stud.hs-esslingen.de/pub/Mirrors/Gentoo/"
LANG="C.UTF8"
LDFLAGS="-Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0"
MAKEOPTS="-j2"
PKGDIR="/var/cache/binpkgs"
PORTAGE_CONFIGROOT="/"
PORTAGE_RSYNC_OPTS="--recursive --links --safe-links --perms --times --omit-dir-times --compress --force --whole-file --delete --stats --human-readable --timeout=180 --exclude=/distfiles --exclude=/local --exclude=/packages --exclude=/.git"
PORTAGE_TMPDIR="/var/tmp/portage-ondisk"
SHELL="/bin/bash"
USE="X acl amd64 bzip2 cli crypt dri fortran gdbm iconv ipv6 libglvnd libtirpc multilib ncurses nls nptl openmp pam pcre readline seccomp split-usr ssl systemd udev unicode xattr zlib" ABI_X86="64" ADA_TARGET="gnat_2020" APACHE2_MODULES="authn_core authz_core socache_shmcb unixd actions alias auth_basic authn_alias authn_anon authn_dbm authn_default authn_file authz_dbm authz_default authz_groupfile authz_host authz_owner authz_user autoindex cache cgi cgid dav dav_fs dav_lock deflate dir disk_cache env expires ext_filter file_cache filter headers include info log_config logio mem_cache mime mime_magic negotiation rewrite setenvif speling status unique_id userdir usertrack vhost_alias" CALLIGRA_FEATURES="karbon sheets words" COLLECTD_PLUGINS="df interface irq load memory rrdtool swap syslog" CPU_FLAGS_X86="aes avx avx2 f16c fma3 mmx mmxext pclmul popcnt rdrand sha sse sse2 sse3 sse4_1 sse4_2 sse4a ssse3" ELIBC="glibc" GPSD_PROTOCOLS="ashtech aivdm earthmate evermore fv18 garmin garmintxt gpsclock greis isync itrax mtk3301 nmea ntrip navcom oceanserver oldstyle oncore rtcm104v2 rtcm104v3 sirf skytraq superstar2 timing tsip tripmate tnt ublox ubx" INPUT_DEVICES="libinput" KERNEL="linux" LCD_DEVICES="bayrad cfontz cfontz633 glk hd44780 lb216 lcdm001 mtxorb ncurses text" LIBREOFFICE_EXTENSIONS="presenter-console presenter-minimizer" LUA_SINGLE_TARGET="lua5-1" LUA_TARGETS="lua5-1" OFFICE_IMPLEMENTATION="libreoffice" PHP_TARGETS="php7-4 php8-0" POSTGRES_TARGETS="postgres12 postgres13" PYTHON_SINGLE_TARGET="python3_9" PYTHON_TARGETS="python3_9" RUBY_TARGETS="ruby26 ruby27" USERLAND="GNU" VIDEO_CARDS="amdgpu fbdev intel nouveau radeon radeonsi vesa dummy v4l" XTABLES_ADDONS="quota2 psd pknock lscan length2 ipv4options ipset ipp2p iface geoip fuzzy condition tee tarpit sysrq proto steal rawnat logmark ipmark dhcpmac delude chaos account"
Unset:  ADDR2LINE, AR, ARFLAGS, AS, ASFLAGS, CC, CCLD, CONFIG_SHELL, CPP, CPPFLAGS, CTARGET, CXX, CXXFILT, ELFEDIT, EXTRA_ECONF, F77FLAGS, FC, GCOV, GPROF, INSTALL_MASK, LC_ALL, LD, LEX, LFLAGS, LIBTOOL, LINGUAS, MAKE, MAKEFLAGS, NM, OBJCOPY, OBJDUMP, PORTAGE_BINHOST, PORTAGE_BUNZIP2_COMMAND, PORTAGE_COMPRESS, PORTAGE_COMPRESS_FLAGS, PORTAGE_RSYNC_EXTRA_OPTS, RANLIB, READELF, RUSTFLAGS, SIZE, STRINGS, STRIP, YACC, YFLAGS

[Comment 1 Bernd 2022-04-06 10:12:11 UTC]

Created attachment 769010 [details]
vtk-9.0.3-r4:20220406-092357.log

build log

[Comment 2 Bernd 2022-04-06 10:30:43 UTC]

Some things, I discovered.

I guess, this has to do with installing a binary version of netcdf. Unmerging dev-libs/libzip leaves preserved libs, which then wants to re-merge netcdf. Building netcdf from sources, solves the preserved libs.

Rebuilding netcdf from source and then libzip from source, I can unmerge libzip without preserved libs, while first emerging libzip from source and the netcdf from source, gives a preserved libs warning, when libzip gets unmerged.

From my point of view, this looks, like netcdf has an automagic dependency on libzip.

Build log of netcdf with libzip installed:

-- Found Math library: /usr/lib64/libm.so
-- Found Zip: headers at /usr/include, libraries at /usr/lib
--      library is /usr/lib64/libzip.so
-- Enabling use of fill value when NC_ERANGE

Build log of netcdf without libzip installed:

-- Found Math library: /usr/lib64/libm.so
-- Enabling use of fill value when NC_ERANGE

[Comment 3 Bernd 2022-04-06 10:32:49 UTC]

Created attachment 769012 [details]
netcdf-4.8.1-r1:20220406-102200.log

build log without dev-libz/libzip installed

[Comment 4 Bernd 2022-04-06 10:33:28 UTC]

Created attachment 769014 [details]
netcdf-4.8.1-r1:20220406-102546.log

build log with dev-libs/libzip installed

[Comment 5 Andreas Sturmlechner 2022-04-06 11:36:30 UTC]

Not a kde package.