Gentoo Websites Logo
Go to: Gentoo Home Documentation Forums Lists Bugs Planet Store Wiki Get Gentoo!
Bug 550148 - =sci-biology/readseq: masked for removal
Summary: =sci-biology/readseq: masked for removal
Status: RESOLVED FIXED
Alias: None
Product: Gentoo Linux
Classification: Unclassified
Component: Current packages (show other bugs)
Hardware: All Linux
: Normal normal (vote)
Assignee: Gentoo Science Biology related packages
URL:
Whiteboard: Removal on 29/03
Keywords: PMASKED
Depends on:
Blocks:
 
Reported: 2015-05-22 09:11 UTC by Martin Mokrejš
Modified: 2016-04-03 21:44 UTC (History)
1 user (show)

See Also:
Package list:
Runtime testing required: ---


Attachments
build.log (build.log,6.34 KB, text/x-log)
2015-05-22 09:11 UTC, Martin Mokrejš
Details

Note You need to log in before you can comment on or make changes to this bug.
Description Martin Mokrejš 2015-05-22 09:11:23 UTC
Created attachment 403752 [details]
build.log

>>> Compiling source in /var/tmp/portage/sci-biology/readseq-20100513/work ...
 * Disabling all optional ANT_TASKS
Buildfile: /var/tmp/portage/sci-biology/readseq-20100513/work/build.xml

prepare:
    [mkdir] Created dir: /var/tmp/portage/sci-biology/readseq-20100513/work/build
    [mkdir] Created dir: /var/tmp/portage/sci-biology/readseq-20100513/work/build/classes

compile:
    [javac] Compiling 110 source files to /var/tmp/portage/sci-biology/readseq-20100513/work/build/classes
    [javac] /var/tmp/portage/sci-biology/readseq-20100513/work/src/flybase/OpenString.java:15: error: package sun.io does not exist
    [javac] import sun.io.ByteToCharConverter;
    [javac]              ^
    [javac] /var/tmp/portage/sci-biology/readseq-20100513/work/src/flybase/OpenString.java:16: error: package sun.io does not exist
    [javac] import sun.io.CharToByteConverter;
    [javac]              ^
    [javac] /var/tmp/portage/sci-biology/readseq-20100513/work/src/flybase/OpenString.java:118: error: cannot find symbol
    [javac]                ByteToCharConverter btc)
    [javac]                ^
    [javac]   symbol:   class ByteToCharConverter
    [javac]   location: class OpenString
    [javac] /var/tmp/portage/sci-biology/readseq-20100513/work/src/flybase/OpenString.java:232: error: cannot find symbol
    [javac]     protected byte[] getBytes(CharToByteConverter ctb) {
    [javac]                               ^
    [javac]   symbol:   class CharToByteConverter
    [javac]   location: class OpenString
    [javac] /var/tmp/portage/sci-biology/readseq-20100513/work/src/flybase/OpenString.java:114: error: reference to OpenString is ambiguous
    [javac]                     this(ascii, hibyte, 0, ascii.length);
    [javac]                     ^
    [javac]   both constructor OpenString(byte[],int,int,int) in OpenString and constructor OpenString(byte[],int,int,ByteToCharConverter) in OpenString match
    [javac] /var/tmp/portage/sci-biology/readseq-20100513/work/src/flybase/OpenString.java:143: error: cannot find symbol
    [javac]                     this(bytes, offset, length, ByteToCharConverter.getConverter(enc));
    [javac]                                                 ^
    [javac]   symbol:   variable ByteToCharConverter
    [javac]   location: class OpenString
    [javac] /var/tmp/portage/sci-biology/readseq-20100513/work/src/flybase/OpenString.java:153: error: cannot find symbol
    [javac]                     this(bytes, offset, length, ByteToCharConverter.getDefault());
    [javac]                                                 ^
    [javac]   symbol:   variable ByteToCharConverter
    [javac]   location: class OpenString
    [javac] /var/tmp/portage/sci-biology/readseq-20100513/work/src/flybase/OpenString.java:157: error: cannot find symbol
    [javac]                     this(bytes, 0, bytes.length, ByteToCharConverter.getDefault());
    [javac]                                                  ^
    [javac]   symbol:   variable ByteToCharConverter
    [javac]   location: class OpenString
    [javac] /var/tmp/portage/sci-biology/readseq-20100513/work/src/flybase/OpenString.java:260: error: cannot find symbol
    [javac]                     return getBytes(CharToByteConverter.getConverter(enc));
    [javac]                                     ^
Comment 1 Martin Mokrejš 2015-05-22 09:11:49 UTC
# emerge --info
Portage 2.2.10 (default/linux/amd64/13.0/desktop, gcc-4.8.3, glibc-2.19-r1, 3.15.6-aufs-r1 x86_64)
=================================================================
System uname: Linux-3.15.6-aufs-r1-x86_64-Intel-R-_Core-TM-_i7-2640M_CPU_@_2.80GHz-with-gentoo-2.2
KiB Mem:     4050712 total,   1853628 free
KiB Swap:   33554428 total,  33326220 free
Timestamp of tree: Tue, 29 Jul 2014 13:30:01 +0000
ld GNU ld (Gentoo 2.24 p1.4) 2.24
distcc 3.1 x86_64-pc-linux-gnu [disabled]
ccache version 3.1.9 [disabled]
app-shells/bash:          4.2_p47
dev-lang/python:          2.7.7, 3.3.5-r1, 3.4.1
dev-util/ccache:          3.1.9-r3
dev-util/cmake:           2.8.12.2-r1
dev-util/pkgconfig:       0.28-r2
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, 1.14.1
sys-devel/binutils:       2.24-r3
sys-devel/gcc:            4.8.3
sys-devel/gcc-config:     1.8
sys-devel/libtool:        2.4.2-r1
sys-devel/make:           4.0-r1
sys-kernel/linux-headers: 3.15 (virtual/os-headers)
sys-libs/glibc:           2.19-r1
Repositories: gentoo
ACCEPT_KEYWORDS="amd64 ~amd64 ~x86"
ACCEPT_LICENSE="* -@EULA @BINARY-REDISTRIBUTABLE"
CBUILD="x86_64-pc-linux-gnu"
CFLAGS="-O2 -pipe"
CHOST="x86_64-pc-linux-gnu"
CONFIG_PROTECT="/etc /usr/share/config /usr/share/gnupg/qualified.txt /usr/share/themes/oxygen-gtk/gtk-2.0"
CONFIG_PROTECT_MASK="/etc/ca-certificates.conf /etc/dconf /etc/env.d /etc/fonts/fonts.conf /etc/gconf /etc/gentoo-release /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"
FCFLAGS="-O2 -pipe"
FEATURES="assume-digests binpkg-logs candy config-protect-if-modified distlocks ebuild-locks fixlafiles merge-sync news nodoc parallel-fetch preserve-libs protect-owned sandbox sfperms strict unknown-features-warn unmerge-logs unmerge-orphans userpriv usersandbox usersync"
FFLAGS="-O2 -pipe"
GENTOO_MIRRORS="http://distfiles.gentoo.org"
LANG="en_US.UTF-8"
LDFLAGS="-Wl,-O1 -Wl,--as-needed"
MAKEOPTS="-j2"
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=""
USE="X aac accessibility acl acpi alsa amd64 atm avahi berkdb bindist bluetooth branding bzip2 cairo cdda cdr cli consolekit cracklib crypt cups cxx dbus dri dts dvd dvdr eds emboss encode exif fam fbcondecor firefox flac fortran gdbm gif gnome gnome-keyring gpm gtk iconv ipv6 jpeg kde lcms ldap libnotify livecd loop-aes mad mmx mng modules mpeg multilib nautilus ncurses nls nouveau nptl ogg opengl openmp pam pango pcre pdf png policykit portaudio ppds qt3support qt4 readline sdl semantic-desktop session socks5 spell sse sse2 ssl startup-notification svg tcpd tiff truetype udev udisks unicode upower usb vino vorbis wxwidgets xcb xml xv 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="evdev keyboard mouse synaptics virtualbox" KERNEL="linux" LCD_DEVICES="bayrad cfontz cfontz633 glk hd44780 lb216 lcdm001 mtxorb ncurses text" LIBREOFFICE_EXTENSIONS="presenter-console presenter-minimizer" LINGUAS="af ar as ast az be bg bn bo br brx bs ca ca@valencia ca_XV cs csb cy da de dgo dz el en en_GB en_ZA eo es et eu fa fi fo fr fy ga gd gl gu gu_IN ha he hi hr hsb hu ia id is it ja ka kk km kn kn_IN ko kok ks ku lb lo lt lv mai mi mk ml mn mni mr ms mt my nb nds ne nl nn nr nso oc om or pa pa_IN pl pt pt_BR ro ru rw sa_IN sat sd se sh si sk sl sq sr ss st sv sw sw_TZ ta ta_IN te tg th tn tr ts tt ug uk uz ve ven vi wa xh zh_CN zh_HK zh_TW zu" 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="i915 i965 r100 r200 r300 r600 qxl virtualbox nouveau glint intel mach64 mga nv r128 radeon savage tdfx trident vesa via vmware cirrus ast chips i128 imstt s3virge tseng v4l vermilion" XFCE_PLUGINS="menu" 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, LC_ALL, PORTAGE_BUNZIP2_COMMAND, PORTAGE_COMPRESS, PORTAGE_COMPRESS_FLAGS, PORTAGE_RSYNC_EXTRA_OPTS, SYNC, USE_PYTHON
Comment 2 Martin Mokrejš 2015-05-22 09:17:19 UTC
This is a newly installed system:


# eselect 
Usage: eselect <global options> <module name> <module options>

Global options:
  --brief                   Make output shorter
  --colour=<yes|no|auto>    Enable or disable colour output (default 'auto')

Built-in modules:
  help                      Display a help message
  usage                     Display a usage message
  version                   Display version information

Extra modules:
  binutils                  Manage installed versions of sys-devel/binutils
  blas                      Manage installed BLAS implementations
  cblas                     Manage installed CBLAS implementations
  ctags                     Manage /usr/bin/ctags implementations
  ecj                       Manage ECJ targets
  editor                    Manage the EDITOR environment variable
  env                       Manage environment variables set in /etc/env.d/
  etags                     Manage /usr/bin/etags implementations
  fontconfig                Manage fontconfig /etc/fonts/conf.d/ symlinks
  java-nsplugin             Manage the Java plugin for Netscape-like Browsers
  java-vm                   Manage the Java system and user VM
  kernel                    Manage the /usr/src/linux symlink
  lapack                    Manage installed LAPACK implementations
  locale                    Manage the LANG environment variable
  maven                     Manage Maven targets
  mesa                      Manage the OpenGL driver architecture used by media-libs/mesa
  modules                   Query eselect modules
  news                      Read Gentoo ("GLEP 42") news items
  notify-send               Manage /usr/bin/notify-send implementation
  opengl                    Manage the OpenGL implementation used by your system
  pager                     Manage the PAGER environment variable
  pinentry                  Manage /usr/bin/pinentry implementation
  profile                   Manage the make.profile symlink
  python                    Manage Python symlinks
  qtgraphicssystem          Manage the system-wide active Qt Graphics System
  rc                        Manage /etc/init.d scripts in runlevels
  vi                        Manage /usr/bin/vi implementations
  visual                    Manage the VISUAL environment variable
  wxwidgets                 Manage the system default wxWidgets profile
  xvmc                      Manage the XvMC implementation used by your system
#
# eselect java-vm list
Available Java Virtual Machines:
  [1]   oracle-jdk-bin-1.8  system-vm

#

But sun-java is gone from portage tree.
Comment 3 Patrice Clement gentoo-dev 2015-05-27 09:40:14 UTC
>>> Compiling source in /var/tmp/portage/sci-biology/readseq-20100513/work ...
 * Disabling all optional ANT_TASKS
Buildfile: /var/tmp/portage/sci-biology/readseq-20100513/work/build.xml

prepare:
    [mkdir] Created dir: /var/tmp/portage/sci-biology/readseq-20100513/work/build
    [mkdir] Created dir: /var/tmp/portage/sci-biology/readseq-20100513/work/build/classes

compile:
    [javac] Compiling 110 source files to /var/tmp/portage/sci-biology/readseq-20100513/work/build/classes
     [copy] Copying 43 files to /var/tmp/portage/sci-biology/readseq-20100513/work/build/classes/rez

jar:
      [jar] Building jar: /var/tmp/portage/sci-biology/readseq-20100513/work/build/readseq.jar

BUILD SUCCESSFUL
Total time: 6 seconds
>>> Source compiled.

epsilon ~ # eselect java-vm list
Available Java Virtual Machines:
  [1]   icedtea-7  system-vm

I have to try to compile this package with oracle-jdk-1.8 and check if it still fails.
Comment 4 James Le Cuirot gentoo-dev 2016-02-29 21:14:30 UTC
(In reply to Patrice Clement from comment #3)
> I have to try to compile this package with oracle-jdk-1.8 and check if it
> still fails.

It doesn't. I have last-rited it now.
Comment 5 Patrice Clement gentoo-dev 2016-03-02 23:34:54 UTC
# James Le Cuirot <chewi@gentoo.org> (29 Feb 2016)
# Dead upstream and doesn't build with Java 8. Removal in 30 days.
sci-biology/readseq
Comment 6 Martin Mokrejš 2016-03-04 11:08:50 UTC
Hi Patrice,
  why is this bug report being twisted into a package removal? IMHO Bugzilla is a tracker of issues and it is not a problem by itself that some issues are opened.

   I may be well off but I think sci-biology is un(der)staffed and has not much  experience with java.

  Would you mind improving the ebuild so that it requires java-1.7 or whichever works fine? I do not know myself how to automatically switch to the required VM on the fly (without requiring the user to switch VM globally just to compile the package).

  In general, I propose if packages are removed due to this, please move them into science overlay instead of dropping from the main tree. A requirement that package must compile with current dev tools is ridiculous and Gentoo in my eyes should stop this bad practice. We just can't fix every package, there are not enough developers and in a long run it only puts off any future package maintainers from joining Gentoo. For no good reason. The package works, is useful and users do not mind if it requires "older" java provided Gentoo offers it. Moreover, other distro's do not cause to themselves such a hassle by requiring that the binary they distribute was compiled with the latest and greatest compiler. Most users will not even care about these technical details but they judge distro's based on the number of packages they provide. This should be of utmost importance to Gentoo and technical glitches should never result in a package removal.

  I already mentioned it in the past elsewhere: I even think old dev-lang/php, python, etc., should be kept available, sometimes one just needs to install an older app. This was the strong advantage of Gentoo in the past and I just personally do not agree that older versions of development packages are being dropped from the tree.

With best regards,
Martin
P.S.: The 30 days limit for 'last rite' sounds maybe good and sufficient but in real, I don't sync my tree anymore more than once in a month ... who is going to realize this in time? I really mean packages should be moved to a different tree so that users can at least add it via layman to their system back (in the middle of the night). Imagine someone was doing 'revdep-rebuild -i' and the package meanwhile disappeared. Filing a bug at Gentoo bugzilla ... causes only extra work to new Gentoo maintainers and takes time. By moving "dropped" packages to a different tree would enable users to "solve" their issue by just running layman in a few seconds without anybody else needed to be involved.
Comment 7 James Le Cuirot gentoo-dev 2016-03-04 11:38:31 UTC
(In reply to Martin Mokrejš from comment #6)
>   why is this bug report being twisted into a package removal? IMHO Bugzilla
> is a tracker of issues and it is not a problem by itself that some issues
> are opened.

Agreed. monsieurp, please stop doing that.

>   Would you mind improving the ebuild so that it requires java-1.7 or
> whichever works fine? I do not know myself how to automatically switch to
> the required VM on the fly (without requiring the user to switch VM globally
> just to compile the package).

Putting virtual/jre:1.7 and virtual/jdk:1.7 in the ebuild will make it work at runtime but we are not going to do that because we would like to remove Java 7 this year. If the project was maintained upstream and stood a chance of being fixed then we'd keep it but there's been no activity in nearly 6 years. We try not to kick genuinely useful software from the tree, even if upstream is dead, but we're only willing to go so far in order to fix it. If you can provide a patch then we'll certainly keep it.

>   In general, I propose if packages are removed due to this, please move
> them into science overlay instead of dropping from the main tree.

We do not have commit access there. You would need to speak to the science team about that but that doesn't change the fact that Java 7 is going away.

> The
> requirement that package must compile with current dev tools is ridiculous
> and Gentoo in my eyes should stop this bad practice. We just can't fix every
> package, there are not enough developers and in a long run it only puts off
> any future package maintainers from joining Gentoo. For no good reason. The
> package works, is useful and users do not mind if it requires "older" java
> provided Gentoo offers it.

Java 7 will not be maintained forever. IcedTea will keep maintaining it until Red Hat stop paying for it. Admittedly this isn't going to happen soon but keeping multiple versions of Java in the tree is a maintenance burden for us. It causes hard to avoid breakages where dependencies get updated and suddenly require newer Java versions than the packages using them. The best way to avoid this is to have as few supported Java versions as possible. Java 9 will make things easier by making it simpler to build against older releases but we're not there yet.

There will be some casualties but very few of these packages are actually being used by anyone. I guess this is an exception and that's what last-rites are for, to let us know that someone cares and, if possible, put on the brakes.

> Moreover, other distro's do not cause to
> themselves such a hassle by requiring that the binary they distribute was
> compiled with the latest and greatest compiler.

Binary distros have a much easier life than we do. They can build however they like behind the scenes and not have to worry about supporting these older versions for end users. They also tend to have more manpower.

> Most users will not even
> care about these technical details but they judge distro's based on the
> number of packages they provide.

If you don't care how it's built then just download the jar and run java -jar readseq.jar.

> P.S.: The 30 days limit for 'last rite' sounds maybe good and sufficient but
> in real, I don't sync my tree anymore more than once in a month ... who is
> going to realize this in time?

This has occurred to me but it's the general policy, not Java team's. Feel free to raise it on the mailing list.
Comment 8 James Le Cuirot gentoo-dev 2016-03-07 16:11:28 UTC
(In reply to Martin Mokrejš from comment #6)
> Moreover, other distro's do not cause to
> themselves such a hassle by requiring that the binary they distribute was
> compiled with the latest and greatest compiler. Most users will not even
> care about these technical details but they judge distro's based on the
> number of packages they provide.

One thing to add regarding this point. Other distros don't even package the Java version of readseq at all. Debian and Mandriva package the ancient C version (from 1993!?) and it is heavily patched.
Comment 9 James Le Cuirot gentoo-dev 2016-04-03 21:44:01 UTC
It's gone now, sorry. Please let us know if you manage to patch around it.