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Bug 594254 - sci-biology/abyss-1.3.6-r1 : ../.../FastaReader.h:49:35: error: cannot convert ‘std::istream {aka std::basic_istream<char>}’ to ‘void*’ in return
Summary: sci-biology/abyss-1.3.6-r1 : ../.../FastaReader.h:49:35: error: cannot conver...
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:
Keywords:
Depends on:
Blocks: gcc-6
  Show dependency tree
 
Reported: 2016-09-18 17:54 UTC by Toralf Förster
Modified: 2016-09-18 21:43 UTC (History)
1 user (show)

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


Attachments
emerge-history.txt (emerge-history.txt,241.82 KB, text/plain)
2016-09-18 17:54 UTC, Toralf Förster
Details
environment (environment,68.90 KB, text/plain)
2016-09-18 17:54 UTC, Toralf Förster
Details
sci-biology:abyss-1.3.6-r1:20160918-174649.log (sci-biology:abyss-1.3.6-r1:20160918-174649.log,10.34 KB, text/plain)
2016-09-18 17:54 UTC, Toralf Förster
Details

Note You need to log in before you can comment on or make changes to this bug.
Description Toralf Förster gentoo-dev 2016-09-18 17:54:09 UTC
In file included from AssemblyAlgorithms.cpp:4:0:
../DataLayer/FastaReader.h: In member function ‘FastaReader::operator void*() const’:
../DataLayer/FastaReader.h:49:35: error: cannot convert ‘std::istream {aka std::basic_istream<char>}’ to ‘void*’ in return
   operator void*() const { return m_in; }
                                   ^~~~
make[2]: *** [Makefile:374: libassembly_a-AssemblyAlgorithms.o] Error 1


$ cat emerge-info.txt
  -----------------------------------------------------------------

  This is an unstable amd64 chroot image (named amd64-hardened-no-multilib-unstable_20160914-150349) at a hardened host acting as a tinderbox.

  -----------------------------------------------------------------
  USE flags ...

  ... in make.conf:
USE="  pax_kernel xtpax -cdinstall -oci8 -bindist apache -cgi cgroups csc dec_av2 dot -dvb extra ffmpeg freetds gd git -gnome-keyring -gtkstyle havege help hpn imlib -introspection ithreads javascript jpeg kerberos mikmod -mpeg2 networking opencv -opus osc pkcs11 -plasma plotutils pwquality sdl source sqlite ssh ssh-askpass sslv2 system-libs system-sqlite szip tracepath usb usbredir vala -wav webstart wma x264 xa xkb xvfb zenmap ziffy"

  ... in /etc/portage/package.use/*:
  mail-mta/ssmtp      ssl mta
  net-misc/wget       ssl
  app-crypt/pinentry  -qt4
  app-editors/emacs   -dbus -svg -ssl -gtk -gtk3
  app-text/xmlto      -latex
  dev-libs/boehm-gc   threads
  dev-libs/libpcre    pcre16
  dev-qt/qtgui        egl eglfs
  net-nds/openldap    -sasl
  dev-util/cmake      -qt4 -qt5
  dev-vcs/git         -perl
  gnome-base/librsvg  -tools
  media-libs/mesa     -vaapi
  sys-apps/kmod       tools
  <=net-misc/openssh-7.3_p1-r2    -hpn
  net-misc/iputils -caps -filecaps
  >=dev-lang/python-2.7.12:2.7 ssl
  >=dev-lang/python-3.4.5:3.4 ssl

  entries in /etc/portage/package.unmask/*:
  sys-devel/gcc:6.2.0
  -----------------------------------------------------------------

gcc-config -l:
 [1] x86_64-pc-linux-gnu-6.2.0 *

Available Python interpreters, in order of preference:
  [1]   python2.7
  [2]   python3.4

  -----------------------------------------------------------------

Portage 2.3.0 (python 2.7.12-final-0, hardened/linux/amd64/no-multilib, gcc-6.2.0, glibc-2.23-r2, 4.7.4-hardened x86_64)
=================================================================
                         System Settings
=================================================================
System uname: Linux-4.7.4-hardened-x86_64-Intel-R-_Core-TM-_i7-3930K_CPU_@_3.20GHz-with-gentoo-2.3
KiB Mem:    65285480 total,   4959196 free
KiB Swap:   67108860 total,  67107240 free
Timestamp of repository gentoo: Sun, 18 Sep 2016 16:07:02 +0000
sh bash 4.3_p46
ld GNU ld (Gentoo 2.26.1 p1.0) 2.26.1
ccache version 3.2.7 [disabled]
app-shells/bash:          4.3_p46::gentoo
dev-lang/perl:            5.24.0-r1::gentoo
dev-lang/python:          2.7.12::gentoo, 3.4.5::gentoo
dev-util/ccache:          3.2.7::gentoo
dev-util/cmake:           3.6.2::gentoo
dev-util/pkgconfig:       0.29.1::gentoo
sys-apps/baselayout:      2.3::gentoo
sys-apps/openrc:          0.21.7::gentoo
sys-apps/sandbox:         2.10-r2::gentoo
sys-devel/autoconf:       2.13::gentoo, 2.69-r2::gentoo
sys-devel/automake:       1.9.6-r4::gentoo, 1.11.6-r2::gentoo, 1.12.6-r1::gentoo, 1.13.4-r1::gentoo, 1.14.1-r1::gentoo, 1.15-r2::gentoo
sys-devel/binutils:       2.26.1::gentoo
sys-devel/gcc:            6.2.0::gentoo
sys-devel/gcc-config:     1.8-r1::gentoo
sys-devel/libtool:        2.4.6-r2::gentoo
sys-devel/make:           4.2.1::gentoo
sys-kernel/linux-headers: 4.7::gentoo (virtual/os-headers)
sys-libs/glibc:           2.23-r2::gentoo
Repositories:

gentoo
    location: /usr/portage
    sync-type: rsync
    sync-uri: rsync://rsync.gentoo.org/gentoo-portage
    priority: 1

local
    location: /usr/local/portage
    masters: gentoo
    priority: 2

ACCEPT_KEYWORDS="amd64 ~amd64"
ACCEPT_LICENSE="*"
CBUILD="x86_64-pc-linux-gnu"
CFLAGS="-march=native -O2 -pipe"
CHOST="x86_64-pc-linux-gnu"
CONFIG_PROTECT="/etc /etc/omega.conf /usr/lib64/fax /usr/share/config /usr/share/gnupg/qualified.txt /var/rancid/.cloginrc /var/spool/fax/etc /var/yp/Makefile"
CONFIG_PROTECT_MASK="/etc/ca-certificates.conf /etc/env.d /etc/fonts/fonts.conf /etc/gconf /etc/gentoo-release /etc/php/apache2-php5.6/ext-active/ /etc/php/apache2-php7.0/ext-active/ /etc/php/cgi-php5.6/ext-active/ /etc/php/cgi-php7.0/ext-active/ /etc/php/cli-php5.6/ext-active/ /etc/php/cli-php7.0/ext-active/ /etc/revdep-rebuild /etc/sandbox.d /etc/terminfo"
CXXFLAGS="-march=native -O2 -pipe"
DISTDIR="/var/tmp/distfiles"
EMERGE_DEFAULT_OPTS="--verbose --verbose-conflicts --color=n --nospinner --tree --quiet-build"
FCFLAGS="-O2 -pipe"
FEATURES="assume-digests binpkg-logs config-protect-if-modified distlocks ebuild-locks fixlafiles ipc-sandbox merge-sync network-sandbox parallel-fetch preserve-libs protect-owned sandbox sfperms strict test-fail-continue unknown-features-warn unmerge-logs unmerge-orphans userfetch userpriv usersandbox usersync xattr"
FFLAGS="-O2 -pipe"
GENTOO_MIRRORS="http://ftp.uni-erlangen.de/pub/mirrors/gentoo rsync://mirror.netcologne.de/gentoo/ ftp://sunsite.informatik.rwth-aachen.de/pub/Linux/gor.bytemark.co.uk/gentoo/ rsync://ftp.snt.utwente.nl/gentoo"
LANG="en_US.utf8"
LDFLAGS="-Wl,-O1 -Wl,--as-needed"
MAKEOPTS="-j1"
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="acl amd64 apache berkdb bzip2 cgroups cli cracklib crypt csc cxx dec_av2 dot dri extra ffmpeg freetds gd gdbm git hardened havege help hpn iconv imlib ipv6 ithreads javascript jpeg justify kerberos mikmod mmx mmxext modules ncurses networking nls nptl opencv openmp osc pam pax_kernel pcre pie pkcs11 plotutils pwquality readline sdl seccomp session source sqlite sse sse2 ssh ssh-askpass ssl sslv2 ssp system-libs system-sqlite szip tcpd tracepath unicode urandom usb usbredir vala webstart wma x264 xa xattr xkb xtpax xvfb zenmap ziffy 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" CPU_FLAGS_X86="aes avx mmx mmxext popcnt sse sse2 sse3 sse4_1 sse4_2 ssse3" 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" KERNEL="linux" L10N="ca chr en-US eo fr hy pl pt" LCD_DEVICES="bayrad cfontz cfontz633 glk hd44780 lb216 lcdm001 mtxorb ncurses text" LIBREOFFICE_EXTENSIONS="presenter-console presenter-minimizer" OFFICE_IMPLEMENTATION="libreoffice" PHP_TARGETS="php5-6" PYTHON_SINGLE_TARGET="python2_7" PYTHON_TARGETS="python2_7 python3_4" RUBY_TARGETS="ruby20 ruby21" USERLAND="GNU" VIDEO_CARDS="amdgpu fbdev intel nouveau radeon radeonsi vesa dummy v4l" 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, LC_ALL, PORTAGE_BUNZIP2_COMMAND, PORTAGE_COMPRESS, PORTAGE_COMPRESS_FLAGS, PORTAGE_RSYNC_EXTRA_OPTS, USE_PYTHON
Comment 1 Toralf Förster gentoo-dev 2016-09-18 17:54:17 UTC
Created attachment 446450 [details]
emerge-history.txt
Comment 2 Toralf Förster gentoo-dev 2016-09-18 17:54:20 UTC
Created attachment 446452 [details]
environment
Comment 3 Toralf Förster gentoo-dev 2016-09-18 17:54:23 UTC
Created attachment 446454 [details]
sci-biology:abyss-1.3.6-r1:20160918-174649.log
Comment 4 Sergei Trofimovich gentoo-dev 2016-09-18 19:44:58 UTC
It's a c++98 vs c++11 API change. Real example from db-csv.cpp:

   static bool existFile(const char* f)
   {
        ifstream file(f);
        return file;
   }

c++98 provides file->operator void*()
c++11 provides file->operator bool()

Thus the build failure from #comment1.

One of the workarounds is to use 'bool' expression context:

   static bool existFile(const char* f)
   {
        ifstream file(f);
        return file ? true : false;
   }

Another is to use -std=c++98 but the program uses boost.
Better port it over to c++11.
Comment 5 Sergei Trofimovich gentoo-dev 2016-09-18 19:56:27 UTC
Proposed example fix for ::sci abyss-1.9.0:
    https://github.com/gentoo-science/sci/pull/681
Comment 6 Sergei Trofimovich gentoo-dev 2016-09-18 21:43:51 UTC
Pushed version bump and gcc-6 tweak as:

https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=e5fd69e7be7b26a7b7481453553393865d823906

Thanks!