Bug 534712 – sci-chemistry/molden-4.8-r2 - make -C surf depend: Makefile:47: recipe for target 'depend' failed

• Product: Gentoo Linux
• Status: RESOLVED PKGREMOVED

[Description Toralf Förster 2015-01-04 21:13:56 UTC]

Created attachment 393170 [details]
emerge log

x86_64-pc-linux-gnu-gfortran -o ambfor ambfor.o alloc.o angle.o bond.o charge.o conn.o enegrd.o getinp.o param.o tors.o vdwlj.o math.o optimise.o switch.o wrtout.o pbc.o -lm
x86_64-pc-linux-gnu-gfortran -O2 -pipe  -c -o md.o md.f
x86_64-pc-linux-gnu-gfortran -O2 -pipe  -c -o verlet.o verlet.f
x86_64-pc-linux-gnu-gcc -O2 -pipe -c -I/usr/X11R6/include -DDOBACK -DHASTIMER -DCOLOR_OFFSET=0.0 -DMD -c alloc.c -o allocmd.o
x86_64-pc-linux-gnu-gfortran -o ambmd md.o verlet.o allocmd.o angle.o bond.o charge.o conn.o enegrd.o getinp.o param.o tors.o vdwlj.o math.o optimise.o switch.o wrtout.o pbc.o -lm
make[1]: Leaving directory '/var/tmp/portage/sci-chemistry/molden-4.8-r2/work/molden4.8/ambfor'
make -C surf depend
make[1]: Entering directory '/var/tmp/portage/sci-chemistry/molden-4.8-r2/work/molden4.8/surf'
making dependencies...
Makefile:47: recipe for target 'depend' failed
make[1]: *** [depend] Error 1
make[1]: Leaving directory '/var/tmp/portage/sci-chemistry/molden-4.8-r2/work/molden4.8/surf'
makefile:239: recipe for target 'surf/surf' failed
make: *** [surf/surf] Error 2
 * ERROR: sci-chemistry/molden-4.8-r2::gentoo failed (compile phase):
 *   emake failed
 * 
 * If you need support, post the output of `emerge --info '=sci-chemistry/molden-4.8-r2::gentoo'`,
 * the complete build log and the output of `emerge -pqv '=sci-chemistry/molden-4.8-r2::gentoo'`.
 * The complete build log is located at '/var/log/portage/sci-chemistry:molden-4.8-r2:20150104-195906.log'.
 * For convenience, a symlink to the build log is located at '/var/tmp/portage/sci-chemistry/molden-4.8-r2/temp/build.log'.
 * The ebuild environment file is located at '/var/tmp/portage/sci-chemistry/molden-4.8-r2/temp/environment'.
 * Working directory: '/var/tmp/portage/sci-chemistry/molden-4.8-r2/work/molden4.8'
 * S: '/var/tmp/portage/sci-chemistry/molden-4.8-r2/work/molden4.8'


This chroot image is located at a hardened amd64 host.

Portage 2.2.14 (python 2.7.9-final-0, default/linux/amd64/13.0, gcc-4.8.3, glibc-2.19-r1, 3.17.7-hardened-r1 x86_64)
=================================================================
System uname: Linux-3.17.7-hardened-r1-x86_64-Intel-R-_Core-TM-_i7-3770_CPU_@_3.40GHz-with-gentoo-2.2
KiB Mem:    16166924 total,    445140 free
KiB Swap:   16777212 total,  16766308 free
Timestamp of tree: Sun, 04 Jan 2015 17:45:01 +0000
ld GNU ld (Gentoo 2.24 p1.4) 2.24
ccache version 3.1.9 [disabled]
app-shells/bash:          4.2_p53
dev-lang/perl:            5.18.2-r2
dev-lang/python:          2.7.9-r1, 3.3.5-r1
dev-util/ccache:          3.1.9-r4
dev-util/cmake:           2.8.12.2-r1
dev-util/pkgconfig:       0.28-r1
sys-apps/baselayout:      2.2
sys-apps/openrc:          0.12.4
sys-apps/sandbox:         2.6-r1
sys-devel/autoconf:       2.13, 2.69
sys-devel/automake:       1.11.6-r1, 1.13.4
sys-devel/binutils:       2.24-r3
sys-devel/gcc:            4.8.3
sys-devel/gcc-config:     1.7.3
sys-devel/libtool:        2.4.2-r1
sys-devel/make:           4.0-r1
sys-kernel/linux-headers: 3.16 (virtual/os-headers)
sys-libs/glibc:           2.19-r1
Repositories: gentoo
ACCEPT_KEYWORDS="amd64"
ACCEPT_LICENSE="*"
CBUILD="x86_64-pc-linux-gnu"
CFLAGS="-O2 -pipe"
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/php/apache2-php5.5/ext-active/ /etc/php/cgi-php5.5/ext-active/ /etc/php/cli-php5.5/ext-active/ /etc/revdep-rebuild /etc/sandbox.d /etc/terminfo /etc/texmf/language.dat.d /etc/texmf/language.def.d /etc/texmf/updmap.d /etc/texmf/web2c"
CXXFLAGS="-O2 -pipe"
DISTDIR="/usr/portage/distfiles"
EMERGE_DEFAULT_OPTS="--nospinner --tree --quiet-build --deep --jobs 1"
FCFLAGS="-O2 -pipe"
FEATURES="assume-digests binpkg-logs config-protect-if-modified distlocks ebuild-locks fixlafiles merge-sync news parallel-fetch preserve-libs protect-owned sandbox sfperms strict unknown-features-warn unmerge-logs unmerge-orphans userfetch userpriv usersandbox usersync"
FFLAGS="-O2 -pipe"
GENTOO_MIRRORS="http://mirror.leaseweb.com/gentoo/ http://ftp.uni-erlangen.de/pub/mirrors/gentoo http://ftp-stud.hs-esslingen.de/pub/Mirrors/gentoo/ http://gd.tuwien.ac.at/opsys/linux/gentoo/"
LDFLAGS="-Wl,-O1 -Wl,--as-needed"
MAKEOPTS="-j1"
PKGDIR="/usr/portage/packages"
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"
PORTAGE_TMPDIR="/var/tmp"
PORTDIR="/usr/portage"
PORTDIR_OVERLAY=""
SYNC="rsync://rsync.de.gentoo.org/gentoo-portage"
USE="acl amd64 berkdb bindist bzip2 cli cracklib crypt cxx dri fortran gdbm iconv ipv6 mbox mmx modules multilib ncurses nls nptl openmp pam pax_kernel pcre readline session sse sse2 ssl tcpd unicode zlib" ABI_X86="64" ALSA_CARDS="ali5451 als4000 atiixp atiixp-modem bt87x ca0106 cmipci emu10k1x ens1370 ens1371 es1938 es1968 fm801 hda-intel intel8x0 intel8x0m maestro3 trident usb-audio via82xx via82xx-modem ymfpci" 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="kexi words flow plan sheets stage tables krita karbon braindump author" CAMERAS="ptp2" COLLECTD_PLUGINS="df interface irq load memory rrdtool swap syslog" ELIBC="glibc" GPSD_PROTOCOLS="ashtech aivdm earthmate evermore fv18 garmin garmintxt gpsclock itrax mtk3301 nmea ntrip navcom oceanserver oldstyle oncore rtcm104v2 rtcm104v3 sirf superstar2 timing tsip tripmate tnt ublox ubx" INPUT_DEVICES="keyboard mouse evdev" KERNEL="linux" LCD_DEVICES="bayrad cfontz cfontz633 glk hd44780 lb216 lcdm001 mtxorb ncurses text" LIBREOFFICE_EXTENSIONS="presenter-console presenter-minimizer" OFFICE_IMPLEMENTATION="libreoffice" PHP_TARGETS="php5-5" PYTHON_SINGLE_TARGET="python2_7" PYTHON_TARGETS="python2_7 python3_3" RUBY_TARGETS="ruby19 ruby20" USERLAND="GNU" VIDEO_CARDS="fbdev glint intel mach64 mga nouveau nv r128 radeon savage sis tdfx trident vesa via vmware dummy v4l" XTABLES_ADDONS="quota2 psd pknock lscan length2 ipv4options ipset ipp2p iface geoip fuzzy condition tee tarpit sysrq steal rawnat logmark ipmark dhcpmac delude chaos account"
Unset:  CPPFLAGS, CTARGET, INSTALL_MASK, LANG, LC_ALL, PORTAGE_BUNZIP2_COMMAND, PORTAGE_COMPRESS, PORTAGE_COMPRESS_FLAGS, PORTAGE_RSYNC_EXTRA_OPTS, USE_PYTHON

[Comment 1 Justin Lecher (RETIRED) 2015-01-05 08:12:17 UTC]

Could you please retry with MAKEOPTS=-j1 ?

[Comment 2 Toralf Förster 2015-01-05 13:07:27 UTC]

(In reply to Justin Lecher from comment #1)
> Could you please retry with MAKEOPTS=-j1 ?

rtm :

MAKEOPTS="-j1"

[Comment 3 Justin Lecher (RETIRED) 2016-02-11 19:14:55 UTC]

Does this still happen with version 5 or 5.5?

[Comment 4 Toralf Förster 2016-02-11 19:25:04 UTC]

(In reply to Justin Lecher from comment #3)
don't hink so :

emerge at: amd64-gnome-unstable_20160121-220651
Thu Feb  4 17:44:28 2016 >>> sci-chemistry/molden-5.0

[Comment 5 Toralf Förster 2016-02-11 19:43:51 UTC]

/me wonders if this :


 * Please install currently selected gcc version with USE=fortran.
 * If you intend to use a different compiler then gfortran, please
 * set FC variable accordingly and take care that the necessary
 * fortran dialects are supported.

 * ERROR: sci-chemistry/molden-5.5::gentoo failed (setup phase):
 *   Currently no working fortran compiler is available



at few images could be avoided by a DEPEND definition ?

[Comment 6 Justin Lecher (RETIRED) 2016-02-12 07:13:31 UTC]

(In reply to Toralf Förster from comment #5)
> /me wonders if this :
> 
> 
>  * Please install currently selected gcc version with USE=fortran.
>  * If you intend to use a different compiler then gfortran, please
>  * set FC variable accordingly and take care that the necessary
>  * fortran dialects are supported.
> 
>  * ERROR: sci-chemistry/molden-5.5::gentoo failed (setup phase):
>  *   Currently no working fortran compiler is available
> 
> 
> 
> at few images could be avoided by a DEPEND definition ?

No it can't and you are changing the defaults. gcc[fortran] is the default. And as you can have multiple gcc installed we have no way to express it in the ebuild correctly. So we need to test.

[Comment 7 Justin Lecher (RETIRED) 2016-02-12 07:13:57 UTC]

(In reply to Toralf Förster from comment #4)
> (In reply to Justin Lecher from comment #3)
> don't hink so :
> 
> emerge at: amd64-gnome-unstable_20160121-220651
> Thu Feb  4 17:44:28 2016 >>> sci-chemistry/molden-5.0

Could you please attach an up2date build.log?

[Comment 8 Justin Lecher (RETIRED) 2016-02-12 08:02:17 UTC]

I cannot reproduce this here on a plain stage3 chroot.

[Comment 9 Toralf Förster 2016-02-12 13:09:26 UTC]

(In reply to Justin Lecher from comment #7)
sry - there it emerged fine:

amd64-gnome-unstable_20160121-220651
Thu Feb  4 17:44:28 2016 >>> sci-chemistry/molden-5.0
Thu Feb 11 20:32:23 2016 <<< sci-chemistry/molden-5.0
Thu Feb 11 20:32:32 2016 >>> sci-chemistry/molden-5.5
molden: Thu Feb  4 17:42:39 2016: 1 minute, 49 seconds
molden: Thu Feb 11 20:30:10 2016: 2 minutes, 22 seconds
molden: 2 times

Do you want to have the build.log of a successful build ?

[Comment 10 Toralf Förster 2016-03-31 17:24:56 UTC]

Created attachment 429378 [details]
emerge-info.txt

makefile:291: recipe for target 'surf/surf' failed
make: *** [surf/surf] Error 2
 * ERROR: sci-chemistry/molden-5.5::gentoo failed (compile phase):
 *   emake failed
 * 
 * If you need support, post the output of `emerge --info '=sci-chemistry/molden-5.5::gentoo'`,

[Comment 11 Toralf Förster 2016-03-31 17:24:59 UTC]

Created attachment 429380 [details]
emerge-history.txt

[Comment 12 Toralf Förster 2016-03-31 17:25:02 UTC]

Created attachment 429382 [details]
environment

[Comment 13 Toralf Förster 2016-03-31 17:25:04 UTC]

Created attachment 429384 [details]
sci-chemistry:molden-5.5:20160331-170334.log

[Comment 14 Toralf Förster 2016-10-16 20:06:18 UTC]

Created attachment 450476 [details]
emerge-info.txt

failes here even with USE=fortran

[Comment 15 Toralf Förster 2016-10-16 20:06:23 UTC]

Created attachment 450478 [details]
emerge-history.txt

[Comment 16 Toralf Förster 2016-10-16 20:06:26 UTC]

Created attachment 450480 [details]
environment

[Comment 17 Toralf Förster 2016-10-16 20:06:28 UTC]

Created attachment 450482 [details]
sci-chemistry:molden-5.5:20161016-192154.log

[Comment 18 Pacho Ramos 2019-11-11 21:04:42 UTC]

5.5 builds fine for me with current systems

[Comment 19 Larry the Git Cow 2022-02-19 13:59:10 UTC]

The bug has been referenced in the following commit(s):

https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=ec853626b72f671a8a201bb5472680a9801b3f89

commit ec853626b72f671a8a201bb5472680a9801b3f89
Author:     Andrew Ammerlaan <[e-mail]>
AuthorDate: 2022-02-19 13:58:05 +0000
Commit:     Andrew Ammerlaan <[e-mail]>
CommitDate: 2022-02-19 13:59:03 +0000

    sci-chemistry/molden: add version 6.9
    
    Bug: https://bugs.gentoo.org/831519
    Bug: https://bugs.gentoo.org/822510
    Bug: https://bugs.gentoo.org/775626
    Bug: https://bugs.gentoo.org/610968
    Bug: https://bugs.gentoo.org/534712
    Closes: https://bugs.gentoo.org/721290
    Package-Manager: Portage-3.0.30, Repoman-3.0.3
    Signed-off-by: Andrew Ammerlaan <[e-mail]>

 sci-chemistry/molden/Manifest                      |  1 +
 .../molden/files/molden-6.9-ldflags.patch          | 87 ++++++++++++++++++++++
 sci-chemistry/molden/molden-6.9.ebuild             | 81 ++++++++++++++++++++
 3 files changed, 169 insertions(+)