Created attachment 387622 [details] build.log 'MAKEOPTS=-j1 emerge -v1 astropy' fails with: ... /usr/lib64/python2.7/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:15:2: warning: #warning "Using deprecated NumPy API, disable it by " "#defining NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp] #warning "Using deprecated NumPy API, disable it by " ... changing mode of /var/tmp/portage/dev-python/astropy-0.4/work/astropy-0.4-python2_7/scripts/fitsdiff from 644 to 755 * python2_7: running distutils-r1_run_phase python_compile_all /usr/bin/python2.7 setup.py build_sphinx Traceback (most recent call last): File "setup.py", line 8, in <module> import ah_bootstrap File "/var/tmp/portage/dev-python/astropy-0.4/work/astropy-0.4/ah_bootstrap.py", line 716, in <module> _main() File "/var/tmp/portage/dev-python/astropy-0.4/work/astropy-0.4/ah_bootstrap.py", line 713, in _main use_astropy_helpers(**kwargs) File "/var/tmp/portage/dev-python/astropy-0.4/work/astropy-0.4/ah_bootstrap.py", line 245, in use_astropy_helpers upgrade = _do_upgrade(dist, index_url) File "/var/tmp/portage/dev-python/astropy-0.4/work/astropy-0.4/ah_bootstrap.py", line 346, in _do_upgrade return _do_download(version=upgrade.version, index_url=index_url) File "/var/tmp/portage/dev-python/astropy-0.4/work/astropy-0.4/ah_bootstrap.py", line 328, in _do_download raise Exception(msg.format(source, repr(e))) Exception: Error retrieving astropy helpers from https://pypi.python.org/simple: DistutilsError("Setup script exited with error: SandboxViolation: open('/var/tmp/portage/dev-python/astropy-0.4/work/astropy-0.4-python2_7/astropy_helpers.egg-info/PKG-INFO', 'w') {}\n\nThe package setup script has attempted to modify files on your system\nthat are not within the EasyInstall build area, and has been aborted.\n\nThis package cannot be safely installed by EasyInstall, and may not\nsupport alternate installation locations even if you run its setup\nscript by hand. Please inform the package's author and the EasyInstall\nmaintainers to find out if a fix or workaround is available.",) * ERROR: dev-python/astropy-0.4::gentoo failed (compile phase): root@lynx2:/root(18)# emerge --info '=dev-python/astropy-0.4::gentoo' Portage 2.2.14 (python 2.7.8-final-0, default/linux/amd64/13.0/desktop/gnome/systemd, gcc-4.8.3, glibc-2.19-r1, 3.17.1-gentoo x86_64) ================================================================= System Settings ================================================================= System uname: Linux-3.17.1-gentoo-x86_64-Intel-R-_Core-TM-2_Duo_CPU_T7500_@_2.20GHz-with-gentoo-2.2 KiB Mem: 3972528 total, 318644 free KiB Swap: 12582908 total, 10863460 free Timestamp of tree: Tue, 28 Oct 2014 03:30:01 +0000 ld GNU ld (GNU Binutils) 2.24 app-shells/bash: 4.3_p30 dev-java/java-config: 2.2.0 dev-lang/perl: 5.20.1-r2 dev-lang/python: 2.7.8, 3.3.5-r1, 3.4.2 dev-util/cmake: 3.0.2 dev-util/pkgconfig: 0.28-r2 sys-apps/baselayout: 2.2 sys-apps/openrc: 0.13.2 sys-apps/sandbox: 2.6-r1 sys-devel/autoconf: 2.13, 2.69 sys-devel/automake: 1.9.6-r3, 1.10.3, 1.11.6, 1.12.6, 1.14.1 sys-devel/binutils: 2.24-r3 sys-devel/gcc: 4.8.3 sys-devel/gcc-config: 1.8 sys-devel/libtool: 2.4.3 sys-devel/make: 4.1-r1 sys-kernel/linux-headers: 3.17 (virtual/os-headers) sys-libs/glibc: 2.19-r1 Repositories: gentoo sunrise x11 sage-on-gentoo science tlp x-portage g-cpan g-octave ACCEPT_KEYWORDS="amd64 ~amd64" ACCEPT_LICENSE="* -@EULA PUEL Intel-SDP dlj-1.1 skype-eula skype-4.0.0.7-copyright googleearth AdobeFlash-11.x cadsoft Oracle-BCLA-JavaSE MakeMKV-EULA NVIDIA-CUDA Nero-AAC-EULA GIMPS" CBUILD="x86_64-pc-linux-gnu" CFLAGS="-march=native -O2 -pipe -fomit-frame-pointer" CHOST="x86_64-pc-linux-gnu" CONFIG_PROTECT="/etc /usr/kde/3.5/env /usr/kde/3.5/share/config /usr/kde/3.5/shutdown /usr/share/config /usr/share/gnupg/qualified.txt /var/lib/hsqldb" CONFIG_PROTECT_MASK="/etc/ca-certificates.conf /etc/dconf /etc/env.d /etc/fonts/fonts.conf /etc/gconf /etc/gentoo-release /etc/php/apache2-php5.6/ext-active/ /etc/php/apache2-php5/ext-active/ /etc/php/cgi-php5.6/ext-active/ /etc/php/cgi-php5/ext-active/ /etc/php/cli-php5.6/ext-active/ /etc/php/cli-php5/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 /etc/udev/rules.d" CXXFLAGS="-march=native -O2 -pipe -fomit-frame-pointer" DISTDIR="/usr/portage/distfiles" 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 xattr" FFLAGS="-march=native -O2 -pipe -fomit-frame-pointer" GENTOO_MIRRORS="http://distfiles.gentoo.org" LANG="en_US.UTF-8" LC_ALL="" LDFLAGS="-Wl,-O1 -Wl,--as-needed" MAKEOPTS="-j3" 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_lynx2" PORTDIR_OVERLAY="/var/lib/layman/sunrise /var/lib/layman/x11 /var/lib/layman/sage-on-gentoo /var/lib/layman/science /var/lib/layman/tlp /usr/local/portage /var/lib/cpan /var/lib/g-octave" USE="64bit R X Xaw3d a52 aac acl acpi admin afs alsa amd64 ao apache2 apng applet archive armadillo arpack asf aspell atlas audacious audiofile automap automount bash-completion berkdb blas blast bluetooth bluray boost branding bzip2 cairo cdda cddb cdf cdio cdparanoia cdr cgi chm cli cmake colord cracklib crypt css cups curl cxx daap db dbi dbm dbus declarative designer devhelp device-mapper dga dia dirac djvu doc dot dri ds2490 ds9097 ds9097u dts dv dvb dvd dvdr dvi dynamicplugin eds egl elf emacs emboss emf encode epiphany evo examples exif expat extensions extra extras faac faad fam ffmpeg fftw firefox fits flac fltk fontconfig foomaticdb fortran fortran95 fpm fpx fuse g3dvl garmin gcj gd gdal gdbm gdu gedit geoip geolocation geos gfortran gif gimp git glade glamor glib glpk gml gmp gnome gnome-keyring gnome-online-accounts gnome-print gnuplot gnutls gold gphoto2 gpm grammar graphics graphtft graphviz grass gsl gsm gstreamer gtk gtk3 gudev guile hdaps hddtemp hdf hdf5 hdri html http httpd hvm hwdb iconv icq icu id3tag ide imagemagick imap inotify introspection ipod ipv6 irda ithreads jabber jadetex java jbig jit john jpeg jpeg2k kate kde kdepim kdrive kerberos keymap kpathsea kvm ladspa lame lapack laptop latex lcms ldap lensfun libffi libkms libnotify libsamplerate libsecret lirc live lua lzma lzo mad mail maildir mapnik math matroska media-library mercurial mikmod mkl mmx mmxext mng mod modules mono motif mozilla mp3 mp4 mpeg mpi mplayer mtp multilib multimedia musepack musicbrainz mysql mysqli nautilus ncurses netcdf netpbm network networking nfs nls nntp nptl nsplugin ntfs ntp numpy obex objc ocaml ocr octave odbc ofa ogdi ogg openexr opengl openmp openvg pam pango pcre pda pdf pdl2 perl plasma plotutils plugins png podcast policykit portaudio posix postgres postscript ppds preview-latex proj projectm pstricks pulseaudio python python-bindings q32 qemu qhull qt3support qt4 quicktime raw readline reiserfs reports rle romio rpc rrdcgi rrdtool sage samba sasl schroedinger science sdk sdl secure-delete semantic-desktop server session shout sip slang slp smart smbclient smp sms sndfile snmp soap socialweb sockets sound soup sox speex spell sql sqlite sse sse2 ssl ssse3 startup-notification stlport subtitles subversion sudo suexec svg svm swig systemd szip t1lib tcl tcpd tex tex4ht texmacs theora thesaurus thinkpad threads thunderbird tidy tiff tk tools truetype udev udisks unicode upower usb utempter v4l vaapi vala valgrind vdpau video virt-network virtualbox visio vorbis vpx vtk wav webdav webdav-serf webkit wifi wmf wxwidgets x264 xa xattr xcb xetex xext xft xine xml xmlreader xmlrpc xpm xv xvid xvmc yaml youtube zlib zvbi" ABI_X86="64" ALSA_CARDS="intel8x0" APACHE2_MODULES="actions alias auth_basic auth_digest authn_anon authn_dbd authn_core authn_dbm authn_default authn_file authz_core authz_dbm authz_default authz_groupfile authz_host authz_owner authz_user autoindex cache cgid dav dav_fs dav_lock dbd deflate dir disk_cache env expires ext_filter file_cache filter headers ident imagemap include info lbmethod_byrequests log_config logio mem_cache mime mime_magic negotiation proxy proxy_ajp proxy_balancer proxy_connect proxy_http rewrite setenvif slotmem_shm so socache_shmcb speling status unique_id unixd userdir usertrack vhost_alias" CALLIGRA_FEATURES="kexi words flow plan sheets stage tables krita karbon braindump author" CAMERAS="canon fuji ptp2" COLLECTD_PLUGINS="df interface irq load memory rrdtool swap syslog" CURL_SSL="nss" DVB_CARDS="usb-wt220u" 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 synaptics void" KERNEL="linux" LCD_DEVICES="cfontz hd44780 mtxorb ncurses X lcd2usb lcdlinux png usblcd" LIBREOFFICE_EXTENSIONS="presenter-console presenter-minimizer" LINGUAS="de fr ru" NETBEANS_MODULES="apisupport cnd dlight enterprise ergonomics groovy gsf harness ide identity j2ee java mobility nb php profiler websvccommon xml" OFFICE_IMPLEMENTATION="libreoffice" PYTHON_SINGLE_TARGET="python2_7" PYTHON_TARGETS="python2_7 python3_3" QEMU_SOFTMMU_TARGETS="arm i386 x86_64" QEMU_USER_TARGETS="arm i386 x86_64" RUBY_TARGETS="ruby19 ruby20" USERLAND="GNU" VIDEO_CARDS="intel displaylink" 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, EMERGE_DEFAULT_OPTS, INSTALL_MASK, PORTAGE_BUNZIP2_COMMAND, PORTAGE_COMPRESS, PORTAGE_COMPRESS_FLAGS, PORTAGE_RSYNC_EXTRA_OPTS, SYNC, USE_PYTHON ================================================================= Package Settings ================================================================= dev-python/astropy-0.4 was built with the following: USE="doc -test" ABI_X86="64" PYTHON_TARGETS="python2_7 python3_3 -python3_2 -python3_4" CFLAGS="-march=native -O2 -pipe" CXXFLAGS="-march=native -O2 -pipe" root@lynx2:/root(19)# emerge -pqv '=dev-python/astropy-0.4::gentoo' [ebuild R ] dev-python/astropy-0.4 USE="doc {-test}" PYTHON_TARGETS="python2_7 python3_3 (-python3_2) -python3_4"
This is fixed by adding the following to the astropy ebuild: python_prepare_all() { distutils-r1_python_prepare_all sed -e '/import ah_bootstrap/d' -i setup.py || die "Removing ah_bootstrap failed" } The problem is that astropy doesn't check if astropy-helpers is installed before building its bundled version. This build results in the SandboxViolation you get. Since portage handles the deps (although astropy-helpers should probably just be in RDEPEND), it's fine to ignore the astropy-helper bootstrap script.
@Juergen is it still an issue? I cannot reproduce it with astropy-helpers installed
(In reply to Kacper Kowalik (Xarthisius) from comment #2) > @Juergen is it still an issue? I cannot reproduce it with astropy-helpers > installed I just hit the issue again on several systems.
(In reply to Juergen Rose from comment #3) > (In reply to Kacper Kowalik (Xarthisius) from comment #2) > > @Juergen is it still an issue? I cannot reproduce it with astropy-helpers > > installed > > I just hit the issue again on several systems. I just hit it with aplpy while bumping, but astropy installs just fine. I hate random bugs...
(In reply to Joseph Booker from comment #1) > This is fixed by adding the following to the astropy ebuild: > > python_prepare_all() { > distutils-r1_python_prepare_all > sed -e '/import ah_bootstrap/d' -i setup.py || die "Removing ah_bootstrap > failed" > } > > The problem is that astropy doesn't check if astropy-helpers is installed > before building its bundled version. This build results in the > SandboxViolation you get. > > Since portage handles the deps (although astropy-helpers should probably > just be in RDEPEND), it's fine to ignore the astropy-helper bootstrap script. "astropy-helpers" is installed, but nevertheless I see this error. I don't have any python_prepare_all in astropy-0.4.ebuild. Should I add it?
(In reply to Juergen Rose from comment #5) > (In reply to Joseph Booker from comment #1) > > This is fixed by adding the following to the astropy ebuild: > > > > python_prepare_all() { > > distutils-r1_python_prepare_all > > sed -e '/import ah_bootstrap/d' -i setup.py || die "Removing ah_bootstrap > > failed" > > } > > > > The problem is that astropy doesn't check if astropy-helpers is installed > > before building its bundled version. This build results in the > > SandboxViolation you get. > > > > Since portage handles the deps (although astropy-helpers should probably > > just be in RDEPEND), it's fine to ignore the astropy-helper bootstrap script. > > "astropy-helpers" is installed, but nevertheless I see this error. > > I don't have any python_prepare_all in astropy-0.4.ebuild. Should I add it? I'll push new version (without revision bump) with fix suggested by Joseph in just a few minutes. Wait for it to hit the rsync servers and please try it out.
(In reply to Kacper Kowalik (Xarthisius) from comment #6) > (In reply to Juergen Rose from comment #5) > > (In reply to Joseph Booker from comment #1) > > > This is fixed by adding the following to the astropy ebuild: > > > > > > python_prepare_all() { > > > distutils-r1_python_prepare_all > > > sed -e '/import ah_bootstrap/d' -i setup.py || die "Removing ah_bootstrap > > > failed" > > > } > > > > > > The problem is that astropy doesn't check if astropy-helpers is installed > > > before building its bundled version. This build results in the > > > SandboxViolation you get. > > > > > > Since portage handles the deps (although astropy-helpers should probably > > > just be in RDEPEND), it's fine to ignore the astropy-helper bootstrap script. > > > > "astropy-helpers" is installed, but nevertheless I see this error. > > > > I don't have any python_prepare_all in astropy-0.4.ebuild. Should I add it? > > I'll push new version (without revision bump) with fix suggested by Joseph > in just a few minutes. Wait for it to hit the rsync servers and please try > it out. I've figured it out. You were building docs, and setup.py was missing --offline in that phase. + 27 Nov 2014; Kacper Kowalik <xarthisius@gentoo.org> astropy-0.4.ebuild: + Pass --offline to setup.py during all phases. Fixes bug #527196 by Juergen + Rose <rose@rz.uni-potsdam.de>, fix dependency on wcslib +
