in sci-chemistry/vmd-1.9.3.ebuild there is a missing .gz at the end of the second line of SRC_URI specification
Just in case somebody needs emerge --info (after fixing the typo vmd works fine) Portage 2.3.17 (python 3.6.3-final-0, default/linux/amd64/17.0/systemd, gcc-7.2.0, glibc-2.26-r3, 4.14.3-gentoo x86_64) ================================================================= System Settings ================================================================= System uname: Linux-4.14.3-gentoo-x86_64-Intel-R-_Xeon-R-_CPU_E31245_@_3.30GHz-with-gentoo-2.4.1 KiB Mem: 16324916 total, 9938356 free KiB Swap: 62545212 total, 61904068 free Timestamp of repository gentoo: Sat, 09 Dec 2017 21:30:01 +0000 Head commit of repository gentoo: d552d9c3e55d9434785c397f53280168310fb2fa sh bash 4.4_p12 ld GNU ld (Gentoo 2.29.1 p3) 2.29.1 distcc 3.2rc1 x86_64-pc-linux-gnu [disabled] app-shells/bash: 4.4_p12::gentoo dev-java/java-config: 2.2.0-r3::gentoo dev-lang/perl: 5.26.1-r1::gentoo dev-lang/python: 2.7.14-r1::gentoo, 3.5.4-r1::gentoo, 3.6.3-r1::gentoo dev-util/cmake: 3.10.0::gentoo dev-util/pkgconfig: 0.29.2::gentoo sys-apps/baselayout: 2.4.1-r2::gentoo sys-apps/openrc: 0.34.11::gentoo sys-apps/sandbox: 2.12::gentoo sys-devel/autoconf: 2.13::gentoo, 2.69-r4::gentoo sys-devel/automake: 1.11.6-r2::gentoo, 1.15.1-r1::gentoo sys-devel/binutils: 2.29.1-r1::gentoo sys-devel/gcc: 4.8.5::gentoo, 5.4.0-r3::gentoo, 6.4.0::gentoo, 7.2.0::gentoo sys-devel/gcc-config: 1.9.0-r1::gentoo sys-devel/libtool: 2.4.6-r4::gentoo sys-devel/make: 4.2.1-r1::gentoo sys-kernel/linux-headers: 4.13::gentoo (virtual/os-headers) sys-libs/glibc: 2.26-r3::gentoo Repositories: gentoo location: /usr/portage sync-type: rsync sync-uri: rsync://s6/portage priority: -1000 sync-rsync-extra-opts: local location: /usr/local/portage masters: gentoo priority: 0 flatpak-overlay location: /var/lib/layman/flatpak-overlay masters: gentoo priority: 50 kde location: /var/lib/layman/kde masters: gentoo priority: 50 matrix location: /var/lib/layman/matrix masters: gentoo priority: 50 rion location: /var/lib/layman/rion masters: gentoo priority: 50 science location: /var/lib/layman/science masters: gentoo priority: 50 Installed sets: @kde-apps-next, @kde-frameworks-live, @kde-plasma-live, @mykde ACCEPT_KEYWORDS="amd64 ~amd64" ACCEPT_LICENSE="* -@EULA" CBUILD="x86_64-pc-linux-gnu" CFLAGS="-O2 -pipe -march=corei7" CHOST="x86_64-pc-linux-gnu" CONFIG_PROTECT="/etc /etc/stunnel/stunnel.conf /usr/lib64/libreoffice/program/sofficerc /usr/share/config /usr/share/gnupg/qualified.txt" CONFIG_PROTECT_MASK="/etc/ca-certificates.conf /etc/dconf /etc/env.d /etc/fonts/fonts.conf /etc/gconf /etc/gentoo-release /etc/php/apache2-php7.2/ext-active/ /etc/php/cgi-php7.2/ext-active/ /etc/php/cli-php7.2/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 -march=corei7" DISTDIR="/usr/portage/distfiles" EMERGE_DEFAULT_OPTS="--quiet-build=n --with-bdeps=y" FCFLAGS="-O2 -pipe" FEATURES="assume-digests binpkg-logs candy config-protect-if-modified distlocks ebuild-locks fixlafiles merge-sync multilib-strict news parallel-fetch preserve-libs protect-owned sandbox sfperms splitdebug strict unknown-features-warn unmerge-logs unmerge-orphans userfetch userpriv usersandbox usersync xattr" FFLAGS="-O2 -pipe -march=corei7" GENTOO_MIRRORS="http://distfiles.gentoo.org" LANG="en_US.utf8" LC_ALL="en_US.utf8" LDFLAGS="-Wl,-O1 -Wl,--as-needed" MAKEOPTS="-j 8" 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 --exclude=/.git" PORTAGE_TMPDIR="/var/tmp" USE="X a52 aac aacplus aalib acl alac alsa amd64 amr ansi apache2 apng applet assistant audiofile autoipd avahi berkdb bitmapfonts bittorrent boost branding btrfs bzip2 cairo canna cdda cdio cdr cjk clang cli clozurecl clucene cracklib crossdev crypt css curl cxx daap dbus dconf dcraw declarative demosaic device-mapper dga dirac dri dv dvd dvdr dvdread eds emacs emovix encode eps exif extensions extra extras f77 faac faad fastcgi fdk ffmpeg flac fltk fontconfig foomaticdb fortran fortran2003 fortran95 frei0r g3dvl gcj gd gdbm gdu gif gimp gimpprint gkrellm glib gnuplot gphoto2 gsf gstreamer gtk gtk3 gudev gzip hdri hwdb hwinfo iconv icu imagemagick introspection ipv6 java javascript jbig jpeg jpeg2k kde kdenlive kdepim kdrive lapack latex lcms ldap legacy-systray libinput libkms libxml2 lxc mad matplotlib matroska mbox mdnsresponder-compat melt minizip mjpeg mng modemmanager modules mozilla mp3 mp4 mpm-itk multilib multiuser musepack musicbrainz mysql native-exceptions ncurses network networkmanager nftables nls nptl nsplugin nss numpy objc offensive ogg oggvorbis openbabel openexr opengl openmp opus pam pcntl pcre pcre16 pdf perl plasma plotutils png pnm policykit posix postscript preview-latex printsupport private-headers pstricks pulseaudio python python3 qml qt5 rar readline rendering rle romio rtc sasl schroedinger scipy script scripttools sdl seccomp session smp smpeg sna sndfile sockets socks5 sox speex spell sql sqlite ssl staging static-libs svc svg systemd tagwriting tbb tcl tcltk tcpd tetex tga theora threads tiff tk tracker truetype udev udisks unicode upcall usb user-session uvm vaapi vala vcd vdr vhosts vim vim-pager vorbis vpx wav wavpack webm webp widgets winbind wmf wxgtk1 x264 xattr xcb xetex xft xinerama xkb xml xmp xorg xvfb xvid xvmc yv12 zlib" ABI_X86="64 32" 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="krita stage words" COLLECTD_PLUGINS="df interface irq load memory rrdtool swap syslog" CPU_FLAGS_X86="aes avx mmx mmxext popcnt sse sse2 sse3 sse4_1 sse4_2 ssse3" CURL_SSL="nss" ELIBC="glibc" GPSD_PROTOCOLS="ashtech aivdm earthmate evermore fv18 garmin garmintxt gpsclock isync itrax mtk3301 nmea ntrip navcom oceanserver oldstyle oncore rtcm104v2 rtcm104v3 sirf skytraq superstar2 timing tsip tripmate tnt ublox ubx" GRUB_PLATFORMS="efi-64 pc" INPUT_DEVICES="libinput" KERNEL="linux" L10N="us" LCD_DEVICES="bayrad cfontz cfontz633 glk hd44780 lb216 lcdm001 mtxorb ncurses text" LIBREOFFICE_EXTENSIONS="presenter-console presenter-minimizer" LINGUAS="us" OFFICE_IMPLEMENTATION="libreoffice" PHP_TARGETS="php5-6 php7-0" POSTGRES_TARGETS="postgres9_5" PYTHON_SINGLE_TARGET="python3_6" PYTHON_TARGETS="python2_7 python3_6" RUBY_TARGETS="ruby24" USERLAND="GNU" VIDEO_CARDS="intel i965" 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: CC, CPPFLAGS, CTARGET, CXX, INSTALL_MASK, PORTAGE_BUNZIP2_COMMAND, PORTAGE_COMPRESS, PORTAGE_COMPRESS_FLAGS, PORTAGE_RSYNC_EXTRA_OPTS ================================================================= Package Settings ================================================================= sci-chemistry/vmd-1.9.3::gentoo was built with the following: USE="sqlite xinerama -cuda -gromacs -msms -povray -tachyon" ABI_X86="(64)" PYTHON_TARGETS="python2_7"
confirmed: SRC_URI=" https://dev.gentoo.org/~jlec/distfiles/${P}-gentoo-patches.tar.xz ${P}.src.tar" ... pkg_nofetch() { elog "Please download ${P}.src.tar.gz from"
No, the src.tar.gz (124MB) from http://www.ks.uiuc.edu/Development/Download/download.cgi?PackageName=VMD is actually a uncompressed tarball, so src.tar is correct.
(In reply to Christoph Junghans from comment #3) > No, the src.tar.gz (124MB) from > http://www.ks.uiuc.edu/Development/Download/download.cgi?PackageName=VMD is > actually a uncompressed tarball, so src.tar is correct. Yes, but out of ~4500 compressed tars on distfiles folder only 2 are not compressed, so why is this exception?
(In reply to milan hodoscek from comment #4) > (In reply to Christoph Junghans from comment #3) > > No, the src.tar.gz (124MB) from > > http://www.ks.uiuc.edu/Development/Download/download.cgi?PackageName=VMD is > > actually a uncompressed tarball, so src.tar is correct. > > Yes, but out of ~4500 compressed tars on distfiles folder only 2 are not > compressed, so why is this exception? Upstream! If you go to http://www.ks.uiuc.edu/Development/Download/download.cgi?PackageName=VMD it will downloads a vmd-1.9.3.src.tar.gz, but $ file vmd-1.9.3.src.tar.gz vmd-1.9.3.src.tar.gz: POSIX tar archive (GNU) so we have to rename it for portage to handle the unpack correctly. "For problems, questions, or suggestions, send e-mail to 'vmd@ks.uiuc.edu'." is what the website says.
I have just downloaded the source tarball. It is a real tar.gz, 42M. The download started automatically after agreeing to the license. Maybe it is fixed upstream?
(In reply to Michelangelo Scopelliti from comment #6) > I have just downloaded the source tarball. It is a real tar.gz, 42M. The > download started automatically after agreeing to the license. Maybe it is > fixed upstream? Actually it depends on the browser that you use for download. Some want to be smart and decompress the file on the fly, but apparently some also forget to drop gz then ?? Just guessing but I've seen this before...
if user needs to rename the file it should be explained by error message
(In reply to milan hodoscek from comment #7) > (In reply to Michelangelo Scopelliti from comment #6) > > I have just downloaded the source tarball. It is a real tar.gz, 42M. The > > download started automatically after agreeing to the license. Maybe it is > > fixed upstream? > > Actually it depends on the browser that you use for download. Some want to > be smart and decompress the file on the fly, but apparently some also forget > to drop gz then ?? Just guessing but I've seen this before... Still, I do not understand. The site offers a proper tar.gz (see my previous comment). Since my browser(s) do not compress on the fly, I assume the 42M file is the official one. Now, maybe some (weird) smart browser makes the wrong conversion/unpacking/whatever; but this is on the user, and should not be on the ebuild. Looking at the sizes, I should download the tar.gz, gunzip (but not untar) it, and then put it in distfiles. I think it's weird.
(In reply to Michelangelo Scopelliti from comment #9) > (In reply to milan hodoscek from comment #7) > > (In reply to Michelangelo Scopelliti from comment #6) > > > I have just downloaded the source tarball. It is a real tar.gz, 42M. The > > > download started automatically after agreeing to the license. Maybe it is > > > fixed upstream? > > > > Actually it depends on the browser that you use for download. Some want to > > be smart and decompress the file on the fly, but apparently some also forget > > to drop gz then ?? Just guessing but I've seen this before... > > Still, I do not understand. The site offers a proper tar.gz (see my previous > comment). Since my browser(s) do not compress on the fly, I assume the 42M > file is the official one. > Now, maybe some (weird) smart browser makes the wrong > conversion/unpacking/whatever; but this is on the user, and should not be on > the ebuild. > > Looking at the sizes, I should download the tar.gz, gunzip (but not untar) > it, and then put it in distfiles. I think it's weird. If I go through the website I get a 124MB uncompressed tarball, but if I wget http://www.ks.uiuc.edu/Research/vmd/vmd-1.9.3/files/final/vmd-1.9.3.src.tar.gz directly I get a 42MB compressed tarball, very strang.
Could this be caused by the browser suffering the same issue as latest wget? https://bugs.gentoo.org/640930
Any news on this? curl -IL http://www.ks.uiuc.edu/Research/vmd/vmd-1.9.3/files/final/vmd-1.9.3.src.tar.gz gives HTTP/1.1 200 OK Date: Wed, 10 Jan 2018 12:58:36 GMT Server: Apache/1.3.37 (Unix) mod_perl/1.29 PHP/5.2.1 mod_ssl/2.8.28 OpenSSL/0.9.7l Last-Modified: Thu, 01 Dec 2016 07:13:41 GMT ETag: "64612-29f1a02-583fcda5" Accept-Ranges: bytes Content-Length: 43981314 Content-Type: application/x-tar Content-Encoding: x-gzip Is that the same problem referenced in comment 11 ?
Its related to HTTP header Content-Encoding: x-gzip It says browser that content is compressed and browser should uncompress it. Direct download with wget works just because wget ignores this header.
*** Bug 653526 has been marked as a duplicate of this bug. ***
(In reply to Alexey Shvetsov from comment #13) > Its related to HTTP header > > Content-Encoding: x-gzip > > It says browser that content is compressed and browser should uncompress it. > Direct download with wget works just because wget ignores this header. Maybe as a workaround the message to download the file could point directly to a "wget ..." command to get the "expected" file to be downloaded
(In reply to Alexey Shvetsov from comment #13) > Its related to HTTP header > > Content-Encoding: x-gzip > > It says browser that content is compressed and browser should uncompress it. > Direct download with wget works just because wget ignores this header. I am still confused. wget, curl, aria2c and firefox, all get a 42MiB tar gz file. No decompression whatsoever. Is there a way to test/download the tar one? I am not able to reproduce that.
*** Bug 682850 has been marked as a duplicate of this bug. ***
The bug has been referenced in the following commit(s): https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=3e2a2a3baebbc26bdcd1ee23a765bf04ebed7ee3 commit 3e2a2a3baebbc26bdcd1ee23a765bf04ebed7ee3 Author: Pacho Ramos <pacho@gentoo.org> AuthorDate: 2019-05-30 11:14:56 +0000 Commit: Pacho Ramos <pacho@gentoo.org> CommitDate: 2019-05-30 11:14:56 +0000 sci-chemistry/vmd: Multiple fixes and update ebuild - Longer explanation to download sources files (#640440) - Fix tachyon support (#644122) - Install netcdf plugin (#661636) Bug: https://bugs.gentoo.org/640440 Closes: https://bugs.gentoo.org/644122 Closes: https://bugs.gentoo.org/661636 Package-Manager: Portage-2.3.66, Repoman-2.3.12 Signed-off-by: Pacho Ramos <pacho@gentoo.org> .../vmd/files/vmd-1.9.1-cuda-device_ptr.patch | 8 +- .../vmd/files/vmd-1.9.3-configure-libtachyon.patch | 13 + sci-chemistry/vmd/vmd-1.9.3-r1.ebuild | 262 +++++++++++++++++++++ 3 files changed, 279 insertions(+), 4 deletions(-)
is anyone still able to reproduce this? I have tried with firefox, chromium and webkit-based browsers and all download the proper tar.gz file
The bug has been closed via the following commit(s): https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=3b1941d5039ebc6b665882de5bca60934b366814 commit 3b1941d5039ebc6b665882de5bca60934b366814 Author: Pacho Ramos <pacho@gentoo.org> AuthorDate: 2021-02-12 12:30:59 +0000 Commit: Pacho Ramos <pacho@gentoo.org> CommitDate: 2021-02-12 12:30:59 +0000 sci-chemistry/vmd: Bump to 1.9.4_alpha51 Also stop pushing people to play with tar vs tar.gz file as most web browsers properly download tar.gz file at present time, bug #640440 Closes: https://bugs.gentoo.org/640440 Package-Manager: Portage-3.0.14, Repoman-3.0.2 Signed-off-by: Pacho Ramos <pacho@gentoo.org> sci-chemistry/vmd/Manifest | 2 + sci-chemistry/vmd/vmd-1.9.4_alpha51.ebuild | 270 +++++++++++++++++++++++++++++ 2 files changed, 272 insertions(+)
