I ran into trouble with pdb-extract. (This is durin an emerge -e world, so I assume no dependency issues) x86_64-pc-linux-gnu-gcc -Wl,-O1 -w pdb_extract_sf.o -o pdb_extract_sf x86_64-pc-linux-gnu-gcc: pdb_extract_sf.o: No such file or directory make[1]: *** [pdb_extract_sf] Error 1 make[1]: *** Waiting for unfinished jobs.... make[1]: Leaving directory `/var/tmp/portage/sci-chemistry/pdb-extract-3.004/work/pdb-extract-v3.004-prod-src/pdb-extract-v3.0' make: *** [compile] Error 1 Reproducible: Always build log and emerge --info: * CPV: sci-chemistry/pdb-extract-3.004 * REPO: gentoo * USE: amd64 elibc_glibc kernel_linux userland_GNU >>> Unpacking source... >>> Unpacking pdb-extract-v3.004-prod-src.tar.gz to /var/tmp/portage/sci-chemistry/pdb-extract-3.004/work >>> Source unpacked in /var/tmp/portage/sci-chemistry/pdb-extract-3.004/work >>> Preparing source in /var/tmp/portage/sci-chemistry/pdb-extract-3.004/work/pdb-extract-v3.004-prod-src ... * Applying pdb-extract-3.004-cflags-install.patch ... [ ok ] * Applying pdb-extract-3.004-gcc-4.3.patch ... [ ok ] * Applying pdb-extract-3.004-Makefile.patch ... [ ok ] * Applying pdb-extract-3.004-env.patch ... [ ok ] * Deleting redundant directories ... [ ok ] /var/tmp/portage/sci-chemistry/pdb-extract-3.004/temp/environment: line 2402: eprefixify: command not found >>> Source prepared. >>> Configuring source in /var/tmp/portage/sci-chemistry/pdb-extract-3.004/work/pdb-extract-v3.004-prod-src ... >>> Source configured. >>> Compiling source in /var/tmp/portage/sci-chemistry/pdb-extract-3.004/work/pdb-extract-v3.004-prod-src ... make -j3 Using platform specific configuration for system: gnu4 Platform configuration done. ------------------------------------------------------------ **** Making pdb-extract-v3.0 **** ------------------------------------------------------------ make[1]: Entering directory `/var/tmp/portage/sci-chemistry/pdb-extract-3.004/work/pdb-extract-v3.004-prod-src/pdb-extract-v3.0' x86_64-pc-linux-gnu-g++ -march=native -O2 -pipe -ansi -Wall -Wno-deprecated -DHAVE_STRCASECMP -DINCL_TEMPLATE_SRC -DHAVE_PLACEMENT_NEW -I./include -I../inclu de -I/usr/include/cifparse-obj -c src/pdb_extract.C -o ./obj/pdb_extract.o x86_64-pc-linux-gnu-g++ -march=native -O2 -pipe -ansi -Wall -Wno-deprecated -DHAVE_STRCASECMP -DINCL_TEMPLATE_SRC -DHAVE_PLACEMENT_NEW -I./include -I../inclu de -I/usr/include/cifparse-obj -c src/pdb_extract_sf.C -o ./obj/pdb_extract_sf.o x86_64-pc-linux-gnu-g++ -march=native -O2 -pipe -ansi -Wall -Wno-deprecated -DHAVE_STRCASECMP -DINCL_TEMPLATE_SRC -DHAVE_PLACEMENT_NEW -I./include -I../inclu de -I/usr/include/cifparse-obj -c src/extract.C -o ./obj/extract.o src/pdb_extract.C: In function 'int pdb2cif_maxit(int, char**, char*)': src/pdb_extract.C:300: warning: ignoring return value of 'int system(const char*)', declared with attribute warn_unused_result src/pdb_extract.C: In function 'void merge_files(char*, char*)': src/pdb_extract.C:378: warning: ignoring return value of 'int system(const char*)', declared with attribute warn_unused_result src/extract.C: In function 'void get_mmcif(char*)': src/extract.C:1865: warning: ignoring return value of 'int system(const char*)', declared with attribute warn_unused_result src/extract.C:1873: warning: ignoring return value of 'int system(const char*)', declared with attribute warn_unused_result src/extract.C:1880: warning: ignoring return value of 'int system(const char*)', declared with attribute warn_unused_result src/extract.C:2044: warning: ignoring return value of 'int system(const char*)', declared with attribute warn_unused_result src/pdb_extract_sf.C: In function 'void check_input_error(int, char**, char*, char*, char*)': src/pdb_extract_sf.C:404: warning: suggest parentheses around && within || src/pdb_extract.C: In function 'void extract_seq(int, char**)': src/pdb_extract.C:2154: warning: ignoring return value of 'int system(const char*)', declared with attribute warn_unused_result src/pdb_extract.C:2165: warning: ignoring return value of 'int system(const char*)', declared with attribute warn_unused_result src/pdb_extract.C:2176: warning: ignoring return value of 'int system(const char*)', declared with attribute warn_unused_result src/pdb_extract.C: In function 'void check_version()': src/pdb_extract.C:2368: warning: ignoring return value of 'int system(const char*)', declared with attribute warn_unused_result src/pdb_extract_sf.C: In function 'void merge_I_F(int, char**)': src/pdb_extract_sf.C:644: warning: suggest parentheses around && within || x86_64-pc-linux-gnu-gcc -Wl,-O1 -w pdb_extract_sf.o -o pdb_extract_sf x86_64-pc-linux-gnu-gcc: pdb_extract_sf.o: No such file or directory make[1]: *** [pdb_extract_sf] Error 1 make[1]: *** Waiting for unfinished jobs.... make[1]: Leaving directory `/var/tmp/portage/sci-chemistry/pdb-extract-3.004/work/pdb-extract-v3.004-prod-src/pdb-extract-v3.0' make: *** [compile] Error 1 Portage 2.1.8.3 (default/linux/amd64/10.0/no-multilib, gcc-4.3.4, glibc-2.10.1-r1, 2.6.31-gentoo-r6 x86_64) ================================================================= System uname: Linux-2.6.31-gentoo-r6-x86_64-Intel-R-_Core-TM-_i7_CPU_920_@_2.67GHz-with-gentoo-1.12.13 Timestamp of tree: Sat, 17 Apr 2010 13:00:02 +0000 app-shells/bash: 4.0_p37 dev-java/java-config: 2.1.9-r2 dev-lang/python: 2.6.4 dev-util/cmake: 2.6.4-r3 sys-apps/baselayout: 1.12.13 sys-apps/sandbox: 1.6-r2 sys-devel/autoconf: 2.13, 2.63-r1 sys-devel/automake: 1.6.3-r1, 1.9.6-r2, 1.10.2, 1.11.1 sys-devel/binutils: 2.18-r3 sys-devel/gcc: 4.3.4 sys-devel/gcc-config: 1.4.1 sys-devel/libtool: 2.2.6b virtual/os-headers: 2.6.30-r1 ACCEPT_KEYWORDS="amd64" ACCEPT_LICENSE="* -@EULA dlj-1.1" CBUILD="x86_64-pc-linux-gnu" CFLAGS="-march=native -O2 -pipe" CHOST="x86_64-pc-linux-gnu" CONFIG_PROTECT="/etc /usr/share/X11/xkb /usr/share/config /var/lib/hsqldb" CONFIG_PROTECT_MASK="/etc/ca-certificates.conf /etc/env.d /etc/env.d/java/ /etc/fonts/fonts.conf /etc/gconf /etc/revdep-rebuild /etc/sandbox.d /etc/terminfo" CXXFLAGS="-march=native -O2 -pipe" DISTDIR="/usr/portage/distfiles" FEATURES="assume-digests distlocks fixpackages news parallel-fetch protect-owned sandbox sfperms strict unmerge-logs unmerge-orphans userfetch" GENTOO_MIRRORS="http://linux.rz.ruhr-uni-bochum.de/download/gentoo-mirror/ http://ftp.snt.ipv6.utwente.nl/pub/os/linux/gentoo/ http://www.mirrorservice.org/sites/www.ibiblio.org/gentoo/ " LDFLAGS="-Wl,-O1" LINGUAS="en nl" MAKEOPTS="-j3" PKGDIR="/usr/portage/packages" PORTAGE_CONFIGROOT="/" PORTAGE_RSYNC_OPTS="--recursive --links --safe-links --perms --times --compress --force --whole-file --delete --stats --timeout=180 --exclude=/distfiles --exclude=/local --exclude=/packages" PORTAGE_TMPDIR="/var/tmp" PORTDIR="/usr/portage" SYNC="rsync://rsync.gentoo.org/gentoo-portage" USE="X a52 aac aalib acl acpi alsa amd64 audacious audiocd berkdb blas bzip2 caps cdda cddb cdr cli cracklib crypt cuda cups cxx dbus divx dri dvdnav dvdr encode exif ffmpeg fftw firefox firefox3 fortran gdbm gif gimp gpm hal iconv ieee1394 ipod ipv6 java jpeg kde lame lapack lcms lvm2 mikmod mmx modules mp3 mpeg mudflap mysql ncurses nls nptl nptlonly nsplugin nvidia ogg openexr opengl openmp pam pcre perl png pppd python qt3support qt4 quicktime readline reflection semantic-desktop session spl sql sse sse2 ssl svg sysfs tcpd theora threads tiff timezone tk truetype type1 unicode usb vorbis webkit x264 xinerama xorg xvmc zlib" ALSA_CARDS="hda-intel" ALSA_PCM_PLUGINS="adpcm alaw asym copy dmix dshare dsnoop empty extplug file hooks iec958 ioplug ladspa lfloat linear meter mmap_emul mulaw multi null plug rate route share shm softvol" APACHE2_MODULES="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 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" ELIBC="glibc" INPUT_DEVICES="keyboard mouse wacom evdev" KERNEL="linux" LCD_DEVICES="bayrad cfontz cfontz633 glk hd44780 lb216 lcdm001 mtxorb ncurses text" LINGUAS="en nl" RUBY_TARGETS="ruby18" USERLAND="GNU" VIDEO_CARDS="nv nvidia vesa" Unset: CPPFLAGS, CTARGET, EMERGE_DEFAULT_OPTS, FFLAGS, INSTALL_MASK, LANG, LC_ALL, PORTAGE_COMPRESS, PORTAGE_COMPRESS_FLAGS, PORTAGE_RSYNC_EXTRA_OPTS, PORTDIR_OVERLAY
Looks like a messed up build system.
Same with -j1?
I'd expect this to be a parallel make build problem indeed, but I didn't try with -j1 here yet. I'd suggest adding it anyway, keeping this bug open, and pointing at this.
(In reply to comment #3) > I'd expect this to be a parallel make build problem indeed, but I didn't try > with -j1 here yet. I'd suggest adding it anyway, keeping this bug open, and > pointing at this. > with -j1 it fails at an other point (see below). -j2 on my laptop (also amd64) behaves the same as -j1 on my desktop. On both systems this package/version has been installed previously so I assume there is an issue with more strict checking or something similar. * CPV: sci-chemistry/pdb-extract-3.004 * REPO: gentoo * USE: amd64 elibc_glibc kernel_linux userland_GNU >>> Unpacking source... >>> Unpacking pdb-extract-v3.004-prod-src.tar.gz to /var/tmp/portage/sci-chemistry/pdb-extract-3.004/work >>> Source unpacked in /var/tmp/portage/sci-chemistry/pdb-extract-3.004/work >>> Preparing source in /var/tmp/portage/sci-chemistry/pdb-extract-3.004/work/pdb-extract-v3.004-prod-src ... * Applying pdb-extract-3.004-cflags-install.patch ... [ ok ] * Applying pdb-extract-3.004-gcc-4.3.patch ... [ ok ] * Applying pdb-extract-3.004-Makefile.patch ... [ ok ] * Applying pdb-extract-3.004-env.patch ... [ ok ] * Deleting redundant directories ... [ ok ] /var/tmp/portage/sci-chemistry/pdb-extract-3.004/temp/environment: line 2404: eprefixify: command not found >>> Source prepared. >>> Configuring source in /var/tmp/portage/sci-chemistry/pdb-extract-3.004/work/pdb-extract-v3.004-prod-src ... >>> Source configured. >>> Compiling source in /var/tmp/portage/sci-chemistry/pdb-extract-3.004/work/pdb-extract-v3.004-prod-src ... make -j1 Using platform specific configuration for system: gnu4 Platform configuration done. ------------------------------------------------------------ **** Making pdb-extract-v3.0 **** ------------------------------------------------------------ make[1]: Entering directory `/var/tmp/portage/sci-chemistry/pdb-extract-3.004/work/pdb-extract-v3.004-prod-src/pdb-extract-v3.0' x86_64-pc-linux-gnu-g++ -march=native -O2 -pipe -ansi -Wall -Wno-deprecated -DHAVE_STRCASECMP -DINCL_TEMPLATE_SRC -DHAVE_PLACEMENT_NEW -I./include -I../inclu de -I/usr/include/cifparse-obj -c src/pdb_extract.C -o ./obj/pdb_extract.o src/pdb_extract.C: In function 'int pdb2cif_maxit(int, char**, char*)': src/pdb_extract.C:300: warning: ignoring return value of 'int system(const char*)', declared with attribute warn_unused_result src/pdb_extract.C: In function 'void merge_files(char*, char*)': src/pdb_extract.C:378: warning: ignoring return value of 'int system(const char*)', declared with attribute warn_unused_result src/pdb_extract.C: In function 'void extract_seq(int, char**)': src/pdb_extract.C:2154: warning: ignoring return value of 'int system(const char*)', declared with attribute warn_unused_result src/pdb_extract.C:2165: warning: ignoring return value of 'int system(const char*)', declared with attribute warn_unused_result src/pdb_extract.C:2176: warning: ignoring return value of 'int system(const char*)', declared with attribute warn_unused_result src/pdb_extract.C: In function 'void check_version()': src/pdb_extract.C:2368: warning: ignoring return value of 'int system(const char*)', declared with attribute warn_unused_result x86_64-pc-linux-gnu-gcc -Wl,-O1 -w pdb_extract.o -o pdb_extract x86_64-pc-linux-gnu-gcc: pdb_extract.o: No such file or directory make[1]: *** [pdb_extract] Error 1 make[1]: Leaving directory `/var/tmp/portage/sci-chemistry/pdb-extract-3.004/work/pdb-extract-v3.004-prod-src/pdb-extract-v3.0' make: *** [compile] Error 1
I will investigate that later today.
Could you please sync and try -r1?
(In reply to comment #6) > Could you please sync and try -r1? > That one compiles fine (using -j3, I think). Thanks for the help!
Seems to be fixed.
