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Bug 387577

Summary: dev-lang/R refuses to build against medialibs/libpng-1.5.x
Product: Gentoo Linux Reporter: Carter Young <ecyoung>
Component: Current packagesAssignee: Gentoo Linux bug wranglers <bug-wranglers>
Status: RESOLVED DUPLICATE    
Severity: major    
Priority: Normal    
Version: unspecified   
Hardware: All   
OS: Linux   
Whiteboard:
Package list:
Runtime testing required: ---
Attachments: Build Log

Description Carter Young 2011-10-18 17:59:25 UTC 
After reading:
2011-10-15-libpng15
  Title                     Upgrade to libpng15
  Author                    Samuli Suominen <ssuominen@gentoo.org>
  Posted                    2011-10-15
  Revision                  1

After upgrading from libpng14 to libpng15 it's important that you rebuild
cairo and gdk-pixbuf as soon as possible if they are installed.

Then you can proceed with rebuilding the rest of the software against the new
library:

# revdep-rebuild --library libpng14.so.14 -- --keep-going

Note: It might be necessary to run the previous command more than once.

If you find packages not building with the message "ld: cannot find -lpng14",
they are likely caused by broken libtool archives (.la) in your system.

You can identify those files with following one-liner:

# find /usr/ -name '*.la' -exec grep png14 {} +

Once you have identified the broken files, you can either delete them,
edit them in place and replace png14 with png15, or re-emerge the packages
they belong to.

More information and help is available at the following forum post:

http://forums.gentoo.org/viewtopic-t-894950.html
-------------------------------------------------

I updated all my la files by hand and every complaining package except dev-lang/R is now built against media-libs/libpng-1.5.  See attached build log.




Reproducible: Always

Steps to Reproduce:
1. Modify affected Linker Archive files by hand.
2. cave resolve -x1 cairo gdk-pixbuf
3. cave fix-linkage -x -l libpng14.so.14 - equivalent to revdep-rebuild --library libpng14.so.14 -- --keep-going

Actual Results:  
All affected packages are built except dev-lang/R.  R fails with:

<snip>
rbitmap.c: In function 'my_png_error':
rbitmap.c:73: error: dereferencing pointer to incomplete type
rbitmap.c: In function 'R_SaveAsPng':
rbitmap.c:127: error: dereferencing pointer to incomplete type
make[4]: Leaving directory `/var/tmp/paludis/dev-lang-R-2.10.1/work/R-2.10.1/src/modules/X11'
make[3]: Leaving directory `/var/tmp/paludis/dev-lang-R-2.10.1/work/R-2.10.1/src/modules/X11'
make[4]: *** [rbitmap.o] Error 1
make[3]: *** [R] Error 2
make[2]: *** [make.X11] Error 2
make[2]: *** Waiting for unfinished jobs....
x86_64-pc-linux-gnu-gfortran  -fpic  -g -O2 -c dlapack2.f -o dlapack2.o
x86_64-pc-linux-gnu-gfortran  -fpic  -g -O2 -c dlapack3.f -o dlapack3.o
x86_64-pc-linux-gnu-gfortran  -fpic  -g -O2 -c dlapack4.f -o dlapack4.o
x86_64-pc-linux-gnu-gfortran  -fpic  -g -O2 -c cmplx.f -o cmplx.o
x86_64-pc-linux-gnu-gcc -std=gnu99 -shared -Wl,-O1 -Wl,--as-needed -o libRlapack.so dlamch.o dlapack0.o dlapack1.o dlapack2.o dlapack3.o dlapack4.o cmplx.o  -lblas   
make[4]: Leaving directory `/var/tmp/paludis/dev-lang-R-2.10.1/work/R-2.10.1/src/modules/lapack'
make[4]: Entering directory `/var/tmp/paludis/dev-lang-R-2.10.1/work/R-2.10.1/src/modules/lapack'
x86_64-pc-linux-gnu-gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I/usr/local/include -DHAVE_CONFIG_H   -fpic  -march=amdfam10 -O2 -pipe -c Lapack.c -o Lapack.o
x86_64-pc-linux-gnu-gcc -std=gnu99 -shared -Wl,-O1 -Wl,--as-needed -o lapack.so  Lapack.o  -L../../../lib -lR  -L../../../lib -lRlapack -lblas   -lgfortran -lm
make[5]: Entering directory `/var/tmp/paludis/dev-lang-R-2.10.1/work/R-2.10.1/src/modules/lapack'
/var/tmp/paludis/dev-lang-R-2.10.1/work/R-2.10.1/lib/libRlapack.so is unchanged
make[5]: Leaving directory `/var/tmp/paludis/dev-lang-R-2.10.1/work/R-2.10.1/src/modules/lapack'
make[4]: Leaving directory `/var/tmp/paludis/dev-lang-R-2.10.1/work/R-2.10.1/src/modules/lapack'
make[3]: Leaving directory `/var/tmp/paludis/dev-lang-R-2.10.1/work/R-2.10.1/src/modules/lapack'
make[2]: Leaving directory `/var/tmp/paludis/dev-lang-R-2.10.1/work/R-2.10.1/src/modules'
make[1]: Leaving directory `/var/tmp/paludis/dev-lang-R-2.10.1/work/R-2.10.1/src'
make[1]: *** [R] Error 1
make: *** [R] Error 1
/usr/libexec/paludis/utils/emake: emake returned error 2

!!! ERROR in dev-lang/R-2.10.1::gentoo:
!!! In src_compile at line 4515
!!! emake failed

!!! Call stack:
!!!    * src_compile (/var/tmp/paludis/dev-lang-R-2.10.1/temp/loadsaveenv:4515)
!!!    * ebuild_f_compile (/usr/libexec/paludis/2/src_compile.bash:56)
!!!    * ebuild_main (/usr/libexec/paludis/ebuild.bash:646)
!!!    * main (/usr/libexec/paludis/ebuild.bash:672)

diefunc: making ebuild PID 19644 exit with error
die trap: exiting with error.


As a side note, I also tried cave resolve -ex installed-packages, -Cs installed-packages, which is equivalent to emerge -e world --keep-going, to see if I missed a package that the linkage wasn't fixed.  R still fails as package 1088 of 1329 (build log attached.)

Expected Results:  
dev-lang/R should build cleanly.  R does build when USE="-png"

Extra Information for media-libs/libpng-1.5.5::installed:
        >>> Running ebuild phase killold as paludisbuild:paludisbuild...
        >>> Starting builtin_killold
        >>> Done builtin_killold
        >>> Completed ebuild phase killold
        >>> Running ebuild phases initmisc infovars info as paludisbuild:paludisbuild...
        >>> Starting builtin_initmisc
        bunzip2 < /var/db/pkg/media-libs/libpng-1.5.5/environment.bz2 > /var/tmp/paludis/environment-media-libs-libpng-1.5.5-11727
        ebuild_scrub_environment /var/tmp/paludis/environment-media-libs-libpng-1.5.5-11727
        ebuild_safe_source /var/tmp/paludis/environment-media-libs-libpng-1.5.5-11727
        rm /var/tmp/paludis/environment-media-libs-libpng-1.5.5-11727
        >>> Done builtin_initmisc
        >>> Starting builtin_infovars
        ACCEPT_KEYWORDS=amd64
        CBUILD=x86_64-pc-linux-gnu
        CFLAGS=-march=amdfam10 -O2 -pipe
        CHOST=x86_64-pc-linux-gnu
        CONFIG_PROTECT=/etc /usr/share/config /usr/share/gnupg/qualified.txt /var/lib/hsqldb 
        CONFIG_PROTECT_MASK=/etc/ca-certificates.conf /etc/env.d /etc/env.d/java/ /etc/fonts/fonts.conf /etc/gconf /etc/gentoo-release /etc/php/apache2-php5.3/ext-active/ /etc/php/cgi-php5.3/ext-active/ /etc/php/cli-php5.3/ext-active/ /etc/revdep-rebuild /etc/sandbox.d /etc/splash /etc/terminfo /etc/texmf/language.dat.d /etc/texmf/language.def.d /etc/texmf/updmap.d /etc/texmf/web2c 
        CPPFLAGS=
        CTARGET=
        CXXFLAGS=-march=amdfam10 -O2 -pipe
        DISTDIR=/var/db/pkg/media-libs/libpng-1.5.5
        FEATURES=
        FFLAGS=
        GENTOO_MIRRORS=
        INSTALL_MASK=
        LANG=
        LC_ALL=C
        LDFLAGS=-Wl,-O1 -Wl,--as-needed
        LINGUAS=en en_US
        MAKEOPTS=-j3
        PORTAGE_COMPRESS=
        PORTAGE_COMPRESS_FLAGS=
        PORTAGE_CONFIGROOT=
        PORTAGE_RSYNC_EXTRA_OPTS=
        PORTAGE_RSYNC_OPTS=
        PORTAGE_TMPDIR=/var/tmp/paludis
        PORTDIR=/var/db/pkg/media-libs/libpng-1.5.5
        PORTDIR_OVERLAY=
        SYNC=
        USE=apng static-libs amd64 alsa_cards_ali5451 alsa_cards_als4000 alsa_cards_atiixp alsa_cards_atiixp-modem alsa_cards_bt87x alsa_cards_ca0106 alsa_cards_cmipci alsa_cards_emu10k1x alsa_cards_ens1370 alsa_cards_ens1371 alsa_cards_es1938 alsa_cards_es1968 alsa_cards_fm801 alsa_cards_hda-intel alsa_cards_intel8x0 alsa_cards_intel8x0m alsa_cards_maestro3 alsa_cards_trident alsa_cards_usb-audio alsa_cards_via82xx alsa_cards_via82xx-modem alsa_cards_ymfpci alsa_pcm_plugins_adpcm alsa_pcm_plugins_alaw alsa_pcm_plugins_asym alsa_pcm_plugins_copy alsa_pcm_plugins_dmix alsa_pcm_plugins_dshare alsa_pcm_plugins_dsnoop alsa_pcm_plugins_empty alsa_pcm_plugins_extplug alsa_pcm_plugins_file alsa_pcm_plugins_hooks alsa_pcm_plugins_iec958 alsa_pcm_plugins_ioplug alsa_pcm_plugins_ladspa alsa_pcm_plugins_lfloat alsa_pcm_plugins_linear alsa_pcm_plugins_meter alsa_pcm_plugins_mmap_emul alsa_pcm_plugins_mulaw alsa_pcm_plugins_multi alsa_pcm_plugins_null alsa_pcm_plugins_plug alsa_pcm_plugins_rate alsa_pcm_plugins_route alsa_pcm_plugins_share alsa_pcm_plugins_shm alsa_pcm_plugins_softvol apache2_modules_alias apache2_modules_auth_basic apache2_modules_auth_digest apache2_modules_authz_host apache2_modules_cgid apache2_modules_dav apache2_modules_dir apache2_modules_mime apache2_modules_php apache2_modules_rewrite apache2_mpms_worker calligra_features_braindump calligra_features_flow calligra_features_karbon calligra_features_kexi calligra_features_krita calligra_features_plan calligra_features_stage calligra_features_tables calligra_features_words cameras_ptp2 collectd_plugins_df collectd_plugins_interface collectd_plugins_irq collectd_plugins_load collectd_plugins_memory collectd_plugins_rrdtool collectd_plugins_swap collectd_plugins_syslog elibc_glibc gpsd_protocols_aivdm gpsd_protocols_ashtech gpsd_protocols_earthmate gpsd_protocols_evermore gpsd_protocols_fv18 gpsd_protocols_garmin gpsd_protocols_garmintxt gpsd_protocols_gpsclock gpsd_protocols_itrax gpsd_protocols_mtk3301 gpsd_protocols_navcom gpsd_protocols_nmea gpsd_protocols_ntrip gpsd_protocols_oceanserver gpsd_protocols_oldstyle gpsd_protocols_oncore gpsd_protocols_rtcm104v2 gpsd_protocols_rtcm104v3 gpsd_protocols_sirf gpsd_protocols_superstar2 gpsd_protocols_timing gpsd_protocols_tnt gpsd_protocols_tripmate gpsd_protocols_tsip gpsd_protocols_ubx input_devices_evdev input_devices_keyboard input_devices_mouse input_devices_virtualbox kernel_linux lcd_devices_bayrad lcd_devices_cfontz lcd_devices_cfontz633 lcd_devices_glk lcd_devices_hd44780 lcd_devices_lb216 lcd_devices_lcdm001 lcd_devices_mtxorb lcd_devices_ncurses lcd_devices_text linguas_en linguas_en_US php_targets_php5-3 ruby_targets_ruby18 userland_GNU video_cards_nv video_cards_nvidia xtables_addons_account xtables_addons_chaos xtables_addons_condition xtables_addons_delude xtables_addons_dhcpmac xtables_addons_fuzzy xtables_addons_geoip xtables_addons_iface xtables_addons_ipmark xtables_addons_ipp2p xtables_addons_ipset xtables_addons_ipv4options xtables_addons_length2 xtables_addons_logmark xtables_addons_lscan xtables_addons_pknock xtables_addons_psd xtables_addons_quota2 xtables_addons_rawnat xtables_addons_steal xtables_addons_sysrq xtables_addons_tarpit xtables_addons_tee amd64 
        >>> Done builtin_infovars
        >>> Starting pkg_info
        >>> Done pkg_info
        >>> Completed ebuild phases initmisc infovars info
        >>> Running ebuild phase tidyup as paludisbuild:paludisbuild...
        >>> Starting builtin_tidyup
        rm -fr /var/tmp/paludis/media-libs-libpng-1.5.5-info
        >>> Done builtin_tidyup
        >>> Completed ebuild phase tidyup

Extra Information for dev-lang/R-2.10.1::installed:
        >>> Running ebuild phase killold as paludisbuild:paludisbuild...
        >>> Starting builtin_killold
        >>> Done builtin_killold
        >>> Completed ebuild phase killold
        >>> Running ebuild phases initmisc infovars info as paludisbuild:paludisbuild...
        >>> Starting builtin_initmisc
        bunzip2 < /var/db/pkg/dev-lang/R-2.10.1/environment.bz2 > /var/tmp/paludis/environment-dev-lang-R-2.10.1-13728
        ebuild_scrub_environment /var/tmp/paludis/environment-dev-lang-R-2.10.1-13728
        ebuild_safe_source /var/tmp/paludis/environment-dev-lang-R-2.10.1-13728
        rm /var/tmp/paludis/environment-dev-lang-R-2.10.1-13728
        >>> Done builtin_initmisc
        >>> Starting builtin_infovars
        ACCEPT_KEYWORDS=amd64
        CBUILD=x86_64-pc-linux-gnu
        CFLAGS=-march=amdfam10 -O2 -pipe
        CHOST=x86_64-pc-linux-gnu
        CONFIG_PROTECT=/etc /usr/share/config /usr/share/gnupg/qualified.txt /var/lib/hsqldb 
        CONFIG_PROTECT_MASK=/etc/ca-certificates.conf /etc/env.d /etc/env.d/java/ /etc/fonts/fonts.conf /etc/gconf /etc/gentoo-release /etc/php/apache2-php5.3/ext-active/ /etc/php/cgi-php5.3/ext-active/ /etc/php/cli-php5.3/ext-active/ /etc/revdep-rebuild /etc/sandbox.d /etc/splash /etc/terminfo /etc/texmf/language.dat.d /etc/texmf/language.def.d /etc/texmf/updmap.d /etc/texmf/web2c 
        CPPFLAGS=
        CTARGET=
        CXXFLAGS=-march=amdfam10 -O2 -pipe
        DISTDIR=/var/db/pkg/dev-lang/R-2.10.1
        FEATURES=
        FFLAGS=
        GENTOO_MIRRORS=
        INSTALL_MASK=
        LANG=
        LC_ALL=C
        LDFLAGS=-Wl,-O1 -Wl,--as-needed
        LINGUAS=en en_US
        MAKEOPTS=-j3
        PORTAGE_COMPRESS=
        PORTAGE_COMPRESS_FLAGS=
        PORTAGE_CONFIGROOT=
        PORTAGE_RSYNC_EXTRA_OPTS=
        PORTAGE_RSYNC_OPTS=
        PORTAGE_TMPDIR=/var/tmp/paludis
        PORTDIR=/var/db/pkg/dev-lang/R-2.10.1
        PORTDIR_OVERLAY=
        SYNC=
        USE=X bash-completion cairo java jpeg nls readline threads tk amd64 alsa_cards_ali5451 alsa_cards_als4000 alsa_cards_atiixp alsa_cards_atiixp-modem alsa_cards_bt87x alsa_cards_ca0106 alsa_cards_cmipci alsa_cards_emu10k1x alsa_cards_ens1370 alsa_cards_ens1371 alsa_cards_es1938 alsa_cards_es1968 alsa_cards_fm801 alsa_cards_hda-intel alsa_cards_intel8x0 alsa_cards_intel8x0m alsa_cards_maestro3 alsa_cards_trident alsa_cards_usb-audio alsa_cards_via82xx alsa_cards_via82xx-modem alsa_cards_ymfpci alsa_pcm_plugins_adpcm alsa_pcm_plugins_alaw alsa_pcm_plugins_asym alsa_pcm_plugins_copy alsa_pcm_plugins_dmix alsa_pcm_plugins_dshare alsa_pcm_plugins_dsnoop alsa_pcm_plugins_empty alsa_pcm_plugins_extplug alsa_pcm_plugins_file alsa_pcm_plugins_hooks alsa_pcm_plugins_iec958 alsa_pcm_plugins_ioplug alsa_pcm_plugins_ladspa alsa_pcm_plugins_lfloat alsa_pcm_plugins_linear alsa_pcm_plugins_meter alsa_pcm_plugins_mmap_emul alsa_pcm_plugins_mulaw alsa_pcm_plugins_multi alsa_pcm_plugins_null alsa_pcm_plugins_plug alsa_pcm_plugins_rate alsa_pcm_plugins_route alsa_pcm_plugins_share alsa_pcm_plugins_shm alsa_pcm_plugins_softvol apache2_modules_alias apache2_modules_auth_basic apache2_modules_auth_digest apache2_modules_authz_host apache2_modules_cgid apache2_modules_dav apache2_modules_dir apache2_modules_mime apache2_modules_php apache2_modules_rewrite apache2_mpms_worker calligra_features_braindump calligra_features_flow calligra_features_karbon calligra_features_kexi calligra_features_krita calligra_features_plan calligra_features_stage calligra_features_tables calligra_features_words cameras_ptp2 collectd_plugins_df collectd_plugins_interface collectd_plugins_irq collectd_plugins_load collectd_plugins_memory collectd_plugins_rrdtool collectd_plugins_swap collectd_plugins_syslog elibc_glibc gpsd_protocols_aivdm gpsd_protocols_ashtech gpsd_protocols_earthmate gpsd_protocols_evermore gpsd_protocols_fv18 gpsd_protocols_garmin gpsd_protocols_garmintxt gpsd_protocols_gpsclock gpsd_protocols_itrax gpsd_protocols_mtk3301 gpsd_protocols_navcom gpsd_protocols_nmea gpsd_protocols_ntrip gpsd_protocols_oceanserver gpsd_protocols_oldstyle gpsd_protocols_oncore gpsd_protocols_rtcm104v2 gpsd_protocols_rtcm104v3 gpsd_protocols_sirf gpsd_protocols_superstar2 gpsd_protocols_timing gpsd_protocols_tnt gpsd_protocols_tripmate gpsd_protocols_tsip gpsd_protocols_ubx input_devices_evdev input_devices_keyboard input_devices_mouse input_devices_virtualbox kernel_linux lcd_devices_bayrad lcd_devices_cfontz lcd_devices_cfontz633 lcd_devices_glk lcd_devices_hd44780 lcd_devices_lb216 lcd_devices_lcdm001 lcd_devices_mtxorb lcd_devices_ncurses lcd_devices_text linguas_en linguas_en_US php_targets_php5-3 ruby_targets_ruby18 userland_GNU video_cards_nv video_cards_nvidia xtables_addons_account xtables_addons_chaos xtables_addons_condition xtables_addons_delude xtables_addons_dhcpmac xtables_addons_fuzzy xtables_addons_geoip xtables_addons_iface xtables_addons_ipmark xtables_addons_ipp2p xtables_addons_ipset xtables_addons_ipv4options xtables_addons_length2 xtables_addons_logmark xtables_addons_lscan xtables_addons_pknock xtables_addons_psd xtables_addons_quota2 xtables_addons_rawnat xtables_addons_steal xtables_addons_sysrq xtables_addons_tarpit xtables_addons_tee amd64 
        >>> Done builtin_infovars
        >>> Starting pkg_info
        >>> Done pkg_info
        >>> Completed ebuild phases initmisc infovars info
        >>> Running ebuild phase tidyup as paludisbuild:paludisbuild...
        >>> Starting builtin_tidyup
        rm -fr /var/tmp/paludis/dev-lang-R-2.10.1-info
        >>> Done builtin_tidyup
        >>> Completed ebuild phase tidyup
Comment 1 Carter Young 2011-10-18 18:03:19 UTC 
Created attachment 290181 [details]
Build Log
Comment 2 Samuli Suominen (RETIRED) gentoo-dev 2011-10-18 18:04:37 UTC 
already fixed in portage.   sync, or if you already did, change mirrors.

*** This bug has been marked as a duplicate of bug 366223 ***