82455 2005-02-18 05:57 0000 Treeviewx doesn't compile on amd64 2005-02-28 08:28:11 0000 1 1 1 Unclassified Gentoo Linux Applications unspecified AMD64 Linux RESOLVED FIXED P2 enhancement --- 1 daniel@molbio.su.se sci@gentoo.org amd64@gentoo.org daniel@molbio.su.se 2005-02-18 05:57:03 0000 When I try to emerge treeviewx I get the following error: In file included from /usr/lib/gcc/x86_64-pc-linux-gnu/3.4.3/include/g++-v3/backward/strstream:51, from TreeLib.h:40, from treereader.h:27, from treereader.cpp:24: /usr/lib/gcc/x86_64-pc-linux-gnu/3.4.3/include/g++-v3/backward/backward_warning.h:32:2: warning: #warning This file includes at least one deprecated or antiquated header. Please consider using one of the 32 headers found in section 17.4.1.2 of the C++ standard. Examples include substituting the <X> header for the <X.h> header for C++ includes, or <iostream> instead of the deprecated header <iostream.h>. To disable this warning use -Wno-deprecated. In file included from /usr/lib/gcc/x86_64-pc-linux-gnu/3.4.3/include/g++-v3/backward/strstream:51, from TreeLib.h:40, from treewriter.h:27, from treewriter.cpp:24: /usr/lib/gcc/x86_64-pc-linux-gnu/3.4.3/include/g++-v3/backward/backward_warning.h:32:2: warning: #warning This file includes at least one deprecated or antiquated header. Please consider using one of the 32 headers found in section 17.4.1.2 of the C++ standard. Examples include substituting the <X> header for the <X.h> header for C++ includes, or <iostream> instead of the deprecated header <iostream.h>. To disable this warning use -Wno-deprecated. In file included from treewriter.h:28, from treewriter.cpp:24: nodeiterator.h: In member function `virtual N* PreorderIterator<N>::begin()': nodeiterator.h:131: error: `cur' undeclared (first use this function) nodeiterator.h:131: error: (Each undeclared identifier is reported only once for each function it appears in.) nodeiterator.h:131: error: `root' undeclared (first use this function) nodeiterator.h: In member function `virtual N* PreorderIterator<N>::next()': nodeiterator.h:137: error: `cur' undeclared (first use this function) nodeiterator.h:139: error: `stk' undeclared (first use this function) make[1]: *** [treewriter.o] Error 1 make: *** [all-recursive] Error 1 !!! ERROR: sci-biology/treeviewx-0.4 failed. !!! Function src_compile, Line 41, Exitcode 2 !!! (no error message) !!! If you need support, post the topmost build error, NOT this status message. I've added x86 as a keyword for this app, but to med it doesn't look like it would compile on 32 bit x86 either. Reproducible: Always Steps to Reproduce: 1. Add "sci-biology/treeviewx x86" to package.keywords 2. emerge treeviewx Actual Results: Compilationan terminated with the error above. Expected Results: Compile cleanly. emerge info: Portage 2.0.51-r15 (default-linux/amd64/2004.3, gcc-3.4.3, glibc-2.3.4.20041102-r0, 2.6.9-gentoo-r6 x86_64) ================================================================= System uname: 2.6.9-gentoo-r6 x86_64 AMD Opteron(tm) Processor 246 Gentoo Base System version 1.4.16 Python: dev-lang/python-2.3.4-r1 [2.3.4 (#1, Feb 18 2005, 11:11:45)] dev-lang/python: 2.3.4-r1 sys-devel/autoconf: 2.13, 2.59-r6 sys-devel/automake: 1.5, 1.6.3, 1.7.9-r1, 1.4_p6, 1.8.5-r3, 1.9.4 sys-devel/binutils: 2.15.92.0.2-r1 sys-devel/libtool: 1.5.10-r4 virtual/os-headers: 2.6.8.1-r2 ACCEPT_KEYWORDS="amd64" AUTOCLEAN="yes" CFLAGS="-march=opteron -mtune=opteron -O2 -pipe" CHOST="x86_64-pc-linux-gnu" CONFIG_PROTECT="/etc /usr/kde/2/share/config /usr/kde/3.3/env /usr/kde/3.3/share/config /usr/kde/3.3/shutdown /usr/kde/3/share/config /usr/lib/X11/xkb /usr/lib/mozilla/defaults/pref /usr/share/config /usr/share/texmf/dvipdfm/config/ /usr/share/texmf/dvips/config/ /usr/share/texmf/tex/generic/config/ /usr/share/texmf/tex/platex/config/ /usr/share/texmf/xdvi/ /var/qmail/control" CONFIG_PROTECT_MASK="/etc/gconf /etc/terminfo /etc/env.d" CXXFLAGS="-march=opteron -mtune=opteron -O2 -pipe" DISTDIR="/usr/portage/distfiles" FEATURES="autoaddcvs autoconfig ccache distlocks sandbox" GENTOO_MIRRORS="http://distfiles.gentoo.org http://distro.ibiblio.org/pub/Linux/distributions/gentoo" LC_ALL="sv_SE" MAKEOPTS="-j3" PKGDIR="/usr/portage/packages" PORTAGE_TMPDIR="/var/tmp" PORTDIR="/usr/portage" SYNC="rsync://rsync.europe.gentoo.org/gentoo-portage" USE="amd64 X acpi alsa arts berkdb bitmap-fonts cdr crypt cups curl emboss esd f77 fam font-server foomaticdb fortran gdbm gif gnome gpm gstreamer gtk gtk2 imagemagick imap imlib ipv6 java jp2 jpeg junit kde libwww lzw lzw-tiff mad mikmod motif mozilla mozsvg mpi multilib ncurses nls oggvorbis opengl oss pam perl png postgres ppds python qt readline slang ssl tcltk tcpd tetex tiff tlctk truetype truetype-fonts type1-fonts usb userlocales xml xml2 xmms xpm xrandr xv zlib" Unset: ASFLAGS, CBUILD, CTARGET, LANG, LDFLAGS, PORTDIR_OVERLAY ribosome@gentoo.org 2005-02-19 18:40:57 0000 Thanks for reporting. TreeViewX does compile and run on 32 bit x86. I used it last week and just recompiled it on two machines. The problem seems to be specific to a certain configuration. (I was not able to reproduce it.) If you look carefully at the output you provided, you will see that the antiquated headers only produce warnings. The real problems are the undefined identifiers. It might be a gcc 3.4 problem, so I added a patch that might help you. Try to sync your Portage tree in an hour, and try to install again. I expect there will still be (different) error messages; please paste them here. cryos: You are a lot better than me at porting code to gcc 3.4. Could you try compiling TreeViewX on amd64? daniel@molbio.su.se 2005-02-20 12:03:21 0000 Created an attachment (id=51709) Error log from patch attempt Your patch (nodeiterator.h.patch) didn't apply. See attached log file. ribosome@gentoo.org 2005-02-20 16:22:13 0000 My dumb mistake. Please try again (in an hour). daniel@molbio.su.se 2005-02-20 23:45:18 0000 Essentially the same error, but with new line numbers, after your patch: In file included from treeorder.h:47, from treeorder.cpp:24: nodeiterator.h: In member function `virtual N* PreorderIterator<N>::next()': nodeiterator.h:139: error: `cur' undeclared (first use this function) nodeiterator.h:139: error: (Each undeclared identifier is reported only once for each function it appears in.) nodeiterator.h:145: error: `stk' undeclared (first use this function) treedrawer.cpp: In member function `virtual void PhylogramDrawer::CalcCoordinates()': treedrawer.cpp:409: error: `fabs' is not a member of `std' make[1]: *** [treeorder.o] Error 1 make[1]: *** [treedrawer.o] Error 1 make: *** [all-recursive] Error 1 I also tried compiling after setting gcc to 3.3.4, but that seems broken on my system. From configure: checking for C++ compiler default output... configure: error: C++ compiler cannot create executables ribosome@gentoo.org 2005-02-22 20:39:27 0000 I was able to compile TreeViewX using gcc 3.4 (on x86), so it is not a gcc 3.4 problem. I do not have access to an amd64 machine, so I will CC the amd64 team on this bug. Sorry for wasting your time with that patch, Daniel. cryos@gentoo.org 2005-02-23 06:40:38 0000 It fails for me I am afraid, In file included from /usr/lib/gcc/x86_64-pc-linux-gnu/3.4.3/include/g++-v3/backward/strstream:51, from TreeLib.h:40, from treewriter.h:27, from treewriter.cpp:24: /usr/lib/gcc/x86_64-pc-linux-gnu/3.4.3/include/g++-v3/backward/backward_warning.h:32:2: warning: #warning This file includes at least one deprecated or antiquated header. Please consider using one of the 32 headers found in section 17.4.1.2 of the C++ standard. Examples include substituting the <X> header for the <X.h> header for C++ includes, or <iostream> instead of the deprecated header <iostream.h>. To disable this warning use -Wno-deprecated. In file included from treewriter.h:28, from treewriter.cpp:24: nodeiterator.h: In member function `virtual N* PreorderIterator<N>::next()': nodeiterator.h:139: error: `cur' undeclared (first use this function) nodeiterator.h:139: error: (Each undeclared identifier is reported only once for each function it appears in.) nodeiterator.h:145: error: `stk' undeclared (first use this function) make[1]: *** [treewriter.o] Error 1 make[1]: *** Waiting for unfinished jobs.... In file included from /usr/lib/gcc/x86_64-pc-linux-gnu/3.4.3/include/g++-v3/backward/strstream:51, from TreeLib.h:40, from treedrawer.h:46, from treedrawer.cpp:27: /usr/lib/gcc/x86_64-pc-linux-gnu/3.4.3/include/g++-v3/backward/backward_warning.h:32:2: warning: #warning This file includes at least one deprecated or antiquated header. Please consider using one of the 32 headers found in section 17.4.1.2 of the C++ standard. Examples include substituting the <X> header for the <X.h> header for C++ includes, or <iostream> instead of the deprecated header <iostream.h>. To disable this warning use -Wno-deprecated. In file included from treedrawer.h:47, from treedrawer.cpp:27: nodeiterator.h: In member function `virtual N* PreorderIterator<N>::next()': nodeiterator.h:139: error: `cur' undeclared (first use this function) nodeiterator.h:139: error: (Each undeclared identifier is reported only once for each function it appears in.) nodeiterator.h:145: error: `stk' undeclared (first use this function) treedrawer.cpp: In member function `virtual void PhylogramDrawer::CalcCoordinates()': treedrawer.cpp:409: error: `fabs' is not a member of `std' make[1]: *** [treedrawer.o] Error 1 make[1]: Leaving directory `/var/tmp/portage/treeviewx-0.4/work/tv-0.4/TreeLib' make: *** [all-recursive] Error 1 cryos ~ # emerge info Portage 2.0.51-r15 (default-linux/amd64/2005.0, gcc-3.4.3, glibc-2.3.4.20050125-r0, 2.6.10-gentoo-r7 x86_64) ================================================================= System uname: 2.6.10-gentoo-r7 x86_64 AMD Athlon(tm) 64 Processor 3200+ Gentoo Base System version 1.6.9 Python: dev-lang/python-2.3.4-r1 [2.3.4 (#1, Feb 17 2005, 19:58:23)] distcc 2.18.3 x86_64-pc-linux-gnu (protocols 1 and 2) (default port 3632) [disabled] ccache version 2.3 [enabled] dev-lang/python: 2.3.4-r1 sys-devel/autoconf: 2.59-r6, 2.13 sys-devel/automake: 1.7.9-r1, 1.8.5-r3, 1.5, 1.4_p6, 1.6.3, 1.9.4 sys-devel/binutils: 2.15.92.0.2-r2, 2.15.92.0.2-r3 sys-devel/libtool: 1.5.10-r4 virtual/os-headers: 2.6.8.1-r4 ACCEPT_KEYWORDS="amd64" AUTOCLEAN="yes" CFLAGS="-march=k8 -O2 -pipe" CHOST="x86_64-pc-linux-gnu" CONFIG_PROTECT="/etc /usr/kde/2/share/config /usr/kde/3.3/env /usr/kde/3.3/share/config /usr/kde/3.3/shutdown /usr/kde/3.4/env /usr/kde/3.4/share/config /usr/kde/3.4/shutdown /usr/kde/3/share/config /usr/lib/X11/xkb /usr/share/config /var/qmail/control" CONFIG_PROTECT_MASK="/etc/gconf /etc/terminfo /etc/texmf/web2c /etc/env.d" CXXFLAGS="-march=k8 -O2 -pipe" DISTDIR="/usr/portage/distfiles" FEATURES="autoaddcvs autoconfig buildpkg ccache collision-protect cvs digest distlocks sandbox sign" GENTOO_MIRRORS="http://distfiles.gentoo.org http://distro.ibiblio.org/pub/Linux/distributions/gentoo" MAKEOPTS="-j2" PKGDIR="/usr/portage/packages" PORTAGE_TMPDIR="/var/tmp" PORTDIR="/usr/portage" PORTDIR_OVERLAY="/usr/local/portage" SYNC="rsync://rsync.gentoo.org/gentoo-portage" USE="amd64 X aalib acpi aim alsa apache2 audiofile avi bash-completion berkdb bitmap-fonts blas bootsplash cdparanoia cdr crypt cscope cups curl directfb divx4linux doc dvd dvdr encode esd ethereal evo f77 fam fbcon fftw flac flash foomaticdb fortran gb gd gdbm gif gimpprint ginac gmp gphoto2 gpm graphviz gstreamer gtk gtk2 gtkhtml icq imagemagick imap imlib innodb ipv6 jabber java jikes joystick jp2 jpeg junit kde lcms ldap libg++ libwww lzw lzw-tiff mad mcal motif mpeg mpi msn mysql ncurses netcdf nls nptl octave odbc offensive oggvorbis opengl oscar oss pam pdflib perl plotutils png postgres povray ppds python qt quicktime readline samba sasl scanner sdl slp snmp spell sqlite ssl svg tcltk tcpd tetex tiff truetype truetype-fonts type1-fonts unicode usb vhosts videos wmf wxwindows xine xinerama xml2 xmms xpm xrandr xscreensaver xv xvid yahoo zlib linguas_en_GB" Unset: ASFLAGS, CBUILD, CTARGET, LANG, LC_ALL, LDFLAGS ribosome@gentoo.org 2005-02-27 11:55:23 0000 I just added "sci-biology/treeviewx-0.4-r1" to Portage and "package.mask". It might solve (some) compilation problems on amd64. Please sync (in an hour or so), unmask the new version, and test it. Thanks. daniel@molbio.su.se 2005-02-28 00:32:10 0000 Compiled, not without warnings, but works nicely. I've tested the basic functionality and it seems OK. As far as I'm concerned this bug could be closed. (Or am I supposed to do that?) Thank you very much for your work! ribosome@gentoo.org 2005-02-28 08:28:11 0000 Great! Closing. 51709 2005-02-20 12:03 0000 Error log from patch attempt nodeiterator.h.patch-30594.out text/plain KioqKiogbm9kZWl0ZXJhdG9yLmgucGF0Y2ggKioqKioKCj09PT09PT09PT09PT09PT09PT09PT09 PT09PT09PT09CgpQQVRDSCBDT01NQU5EOiAgcGF0Y2ggLXAwIC1nMCA8IC91c3IvcG9ydGFnZS9z Y2ktYmlvbG9neS90cmVldmlld3gvZmlsZXMvbm9kZWl0ZXJhdG9yLmgucGF0Y2gKCj09PT09PT09 PT09PT09PT09PT09PT09PT09PT09PT09CnBhdGNoaW5nIGZpbGUgbm9kZWl0ZXJhdG9yLmgKSHVu ayAjMSBGQUlMRUQgYXQgMjAuCjEgb3V0IG9mIDIgaHVua3MgRkFJTEVEIC0tIHNhdmluZyByZWpl Y3RzIHRvIGZpbGUgbm9kZWl0ZXJhdG9yLmgucmVqCj09PT09PT09PT09PT09PT09PT09PT09PT09 PT09PT09CgpQQVRDSCBDT01NQU5EOiAgcGF0Y2ggLXAxIC1nMCA8IC91c3IvcG9ydGFnZS9zY2kt YmlvbG9neS90cmVldmlld3gvZmlsZXMvbm9kZWl0ZXJhdG9yLmgucGF0Y2gKCj09PT09PT09PT09 PT09PT09PT09PT09PT09PT09PT09Cm1pc3NpbmcgaGVhZGVyIGZvciB1bmlmaWVkIGRpZmYgYXQg bGluZSAzIG9mIHBhdGNoCmNhbid0IGZpbmQgZmlsZSB0byBwYXRjaCBhdCBpbnB1dCBsaW5lIDMK UGVyaGFwcyB5b3UgdXNlZCB0aGUgd3JvbmcgLXAgb3IgLS1zdHJpcCBvcHRpb24/ClRoZSB0ZXh0 IGxlYWRpbmcgdXAgdG8gdGhpcyB3YXM6Ci0tLS0tLS0tLS0tLS0tLS0tLS0tLS0tLS0tCnwtLS0g bm9kZWl0ZXJhdG9yLmgub2xkCTIwMDItMDItMjQgMTU6Mzc6MTcuMDAwMDAwMDAwIC0wNTAwCnwr Kysgbm9kZWl0ZXJhdG9yLmgJMjAwNS0wMi0xOSAyMTowOTozMS4wMDAwMDAwMDAgLTA1MDAKLS0t LS0tLS0tLS0tLS0tLS0tLS0tLS0tLS0KTm8gZmlsZSB0byBwYXRjaC4gIFNraXBwaW5nIHBhdGNo LgoyIG91dCBvZiAyIGh1bmtzIGlnbm9yZWQKPT09PT09PT09PT09PT09PT09PT09PT09PT09PT09 PT0KClBBVENIIENPTU1BTkQ6ICBwYXRjaCAtcDIgLWcwIDwgL3Vzci9wb3J0YWdlL3NjaS1iaW9s b2d5L3RyZWV2aWV3eC9maWxlcy9ub2RlaXRlcmF0b3IuaC5wYXRjaAoKPT09PT09PT09PT09PT09 PT09PT09PT09PT09PT09PT0KbWlzc2luZyBoZWFkZXIgZm9yIHVuaWZpZWQgZGlmZiBhdCBsaW5l IDMgb2YgcGF0Y2gKY2FuJ3QgZmluZCBmaWxlIHRvIHBhdGNoIGF0IGlucHV0IGxpbmUgMwpQZXJo YXBzIHlvdSB1c2VkIHRoZSB3cm9uZyAtcCBvciAtLXN0cmlwIG9wdGlvbj8KVGhlIHRleHQgbGVh ZGluZyB1cCB0byB0aGlzIHdhczoKLS0tLS0tLS0tLS0tLS0tLS0tLS0tLS0tLS0KfC0tLSBub2Rl aXRlcmF0b3IuaC5vbGQJMjAwMi0wMi0yNCAxNTozNzoxNy4wMDAwMDAwMDAgLTA1MDAKfCsrKyBu b2RlaXRlcmF0b3IuaAkyMDA1LTAyLTE5IDIxOjA5OjMxLjAwMDAwMDAwMCAtMDUwMAotLS0tLS0t LS0tLS0tLS0tLS0tLS0tLS0tLQpObyBmaWxlIHRvIHBhdGNoLiAgU2tpcHBpbmcgcGF0Y2guCjIg b3V0IG9mIDIgaHVua3MgaWdub3JlZAo9PT09PT09PT09PT09PT09PT09PT09PT09PT09PT09PQoK UEFUQ0ggQ09NTUFORDogIHBhdGNoIC1wMyAtZzAgPCAvdXNyL3BvcnRhZ2Uvc2NpLWJpb2xvZ3kv dHJlZXZpZXd4L2ZpbGVzL25vZGVpdGVyYXRvci5oLnBhdGNoCgo9PT09PT09PT09PT09PT09PT09 PT09PT09PT09PT09PQptaXNzaW5nIGhlYWRlciBmb3IgdW5pZmllZCBkaWZmIGF0IGxpbmUgMyBv ZiBwYXRjaApjYW4ndCBmaW5kIGZpbGUgdG8gcGF0Y2ggYXQgaW5wdXQgbGluZSAzClBlcmhhcHMg eW91IHVzZWQgdGhlIHdyb25nIC1wIG9yIC0tc3RyaXAgb3B0aW9uPwpUaGUgdGV4dCBsZWFkaW5n IHVwIHRvIHRoaXMgd2FzOgotLS0tLS0tLS0tLS0tLS0tLS0tLS0tLS0tLQp8LS0tIG5vZGVpdGVy YXRvci5oLm9sZAkyMDAyLTAyLTI0IDE1OjM3OjE3LjAwMDAwMDAwMCAtMDUwMAp8KysrIG5vZGVp dGVyYXRvci5oCTIwMDUtMDItMTkgMjE6MDk6MzEuMDAwMDAwMDAwIC0wNTAwCi0tLS0tLS0tLS0t LS0tLS0tLS0tLS0tLS0tCk5vIGZpbGUgdG8gcGF0Y2guICBTa2lwcGluZyBwYXRjaC4KMiBvdXQg b2YgMiBodW5rcyBpZ25vcmVkCj09PT09PT09PT09PT09PT09PT09PT09PT09PT09PT09CgpQQVRD SCBDT01NQU5EOiAgcGF0Y2ggLXA0IC1nMCA8IC91c3IvcG9ydGFnZS9zY2ktYmlvbG9neS90cmVl dmlld3gvZmlsZXMvbm9kZWl0ZXJhdG9yLmgucGF0Y2gKCj09PT09PT09PT09PT09PT09PT09PT09 PT09PT09PT09Cm1pc3NpbmcgaGVhZGVyIGZvciB1bmlmaWVkIGRpZmYgYXQgbGluZSAzIG9mIHBh dGNoCmNhbid0IGZpbmQgZmlsZSB0byBwYXRjaCBhdCBpbnB1dCBsaW5lIDMKUGVyaGFwcyB5b3Ug dXNlZCB0aGUgd3JvbmcgLXAgb3IgLS1zdHJpcCBvcHRpb24/ClRoZSB0ZXh0IGxlYWRpbmcgdXAg dG8gdGhpcyB3YXM6Ci0tLS0tLS0tLS0tLS0tLS0tLS0tLS0tLS0tCnwtLS0gbm9kZWl0ZXJhdG9y Lmgub2xkCTIwMDItMDItMjQgMTU6Mzc6MTcuMDAwMDAwMDAwIC0wNTAwCnwrKysgbm9kZWl0ZXJh dG9yLmgJMjAwNS0wMi0xOSAyMTowOTozMS4wMDAwMDAwMDAgLTA1MDAKLS0tLS0tLS0tLS0tLS0t LS0tLS0tLS0tLS0KTm8gZmlsZSB0byBwYXRjaC4gIFNraXBwaW5nIHBhdGNoLgoyIG91dCBvZiAy IGh1bmtzIGlnbm9yZWQK