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Bug 681920

Summary: sci-biology/consed-29: X Error of failed request: BadWindow (invalid Window parameter)
Product: Gentoo Linux Reporter: Martin Mokrejš <mmokrejs>
Component: Current packagesAssignee: Gentoo Science Biology related packages <sci-biology>
Severity: normal    
Priority: Normal    
Version: unspecified   
Hardware: All   
OS: Linux   
Package list:
Runtime testing required: ---
Bug Depends on:    
Bug Blocks: 617524    

Description Martin Mokrejš 2019-03-28 11:07:31 UTC
My problem is that consed (the X11 GUI) does not start for me although I can start xterm from the same shell.

mokrejs@vrapenec$ consed -ace reference.ace.1
CONSED_PARAMETERS is set to /etc/consedrc
no consedrc file so no project-specific resources--that's ok
couldn't open readOrder.txt--that's ok
reading /etc/consedrc/consedtaglib.txt...
not setting XKEYSYMDB.  This is ok if you don't get any errors saying something about "Warning: translation table..."X Error of failed request:  BadWindow (invalid Window parameter)
  Major opcode of failed request:  19 (X_DeleteProperty)
  Resource id in failed request:  0x0
  Serial number of failed request:  230
  Current serial number in output stream:  234
mokrejs@vrapenec$ xterm

You can try:

root# USE=examples emerge consed
$ cp -r /usr/share/consed/examples/align454reads_answer /tmp/
$ cd /tmp/align454reads_answer/edit_dir
$ consed -ace reference.ace.1 &

consed 29 used to work and was compilable with gcc-4.4.7 but not >=sys-devel/gcc-4.6:*. Then the patches to get it compiled with more recent gcc came into portage tree. The list of linked libraries used to be much longer (due to unknown bugs but still there are some unexpected, like png/jpg).

I cannot figure out why I still cannot start consed version 29 due to the Major opcode of failed request: 19 (X_DeleteProperty) error.

I restored consed-29.ebuild from science overlay and went to keep adding changes from current consed-29.ebuild from gentoo repo. In the end there were no diffs, except the emake arguments/env variables overridden and the patches.

I need to add -fpermissive to get the thing compiled with recent gcc-8.2.0.

parseAceFile.cpp:295:24: error: invalid conversion from 'char' to 'char*' [-fpermissive]
       szPossibleComp = '\0';

I think the breakage is in one of the patches.

I tried to remove the

X11_LIBS="$($(tc-getPKG_CONFIG) --libs x11)" 

line to see why this was not needed in earlier ebuilds. I got:

x86_64-pc-linux-gnu-g++ -Wl,-O1 -Wl,--as-needed -O2 -pipe -mpclmul -mpopcnt -march=native -ftree-vectorize -fpermissive -o consed
... -L/usr/lib64 -lXt -lXm  -lbam-0.1-legacy
/usr/lib/gcc/x86_64-pc-linux-gnu/8.3.0/../../../../x86_64-pc-linux-gnu/bin/ld: guiapp.o: undefined reference to symbol 'XCreateColormap'
/usr/lib64/ error adding symbols: DSO missing from command line
collect2: error: ld returned 1 exit status
make: *** [makefile:599: consed] Error 1
Comment 1 Martin Mokrejš 2019-03-28 11:09:10 UTC
The patches were developed at about
Comment 2 Martin Mokrejš 2019-03-28 11:10:38 UTC
Upstream binaries use:

$ ldd consed_linux32bit_dyn (0xf7f7c000) => /usr/lib32/ (0xf7ea4000) => /usr/lib32/ (0xf7d53000) => /usr/lib32/ (0xf7d49000) => /usr/lib32/ (0xf7d2d000) => /usr/lib/gcc/x86_64-pc-linux-gnu/8.3.0/32/ (0xf7b23000) => /lib32/ (0xf7a53000) => /usr/lib/gcc/x86_64-pc-linux-gnu/8.3.0/32/ (0xf7a36000) => /lib32/ (0xf7848000) => /usr/lib32/ (0xf781b000) => /lib32/ (0xf7816000) => /usr/lib32/ (0xf780c000) => /usr/lib32/ (0xf77ec000)
	/lib/ (0xf7f7d000) => /usr/lib32/ (0xf77e7000) => /usr/lib32/ (0xf77e0000) => /lib32/ (0xf77d6000) => /lib32/ (0xf77b5000)
$ ldd consed_linux32bit (0xf7f42000) => /usr/lib32/ (0xf7d82000) => /usr/lib/gcc/x86_64-pc-linux-gnu/8.3.0/32/ (0xf7b78000) => /lib32/ (0xf7aa8000) => /usr/lib/gcc/x86_64-pc-linux-gnu/8.3.0/32/ (0xf7a8b000) => /lib32/ (0xf789d000) => /usr/lib32/ (0xf7870000) => /lib32/ (0xf786b000)
	/lib/ (0xf7f43000) => /usr/lib32/ (0xf7866000) => /usr/lib32/ (0xf785f000) => /usr/lib32/ (0xf783f000) => /lib32/ (0xf7833000) => /lib32/ (0xf7812000)

Gentoo src-based binaries use:

$ ldd consed (0x00007fff5bfd3000) => /usr/lib64/ (0x00007f208b62d000) => /usr/lib64/ (0x00007f208b3c4000) => /usr/lib64/ (0x00007f208aef3000) => /usr/lib64/ (0x00007f208acba000) => /usr/lib/gcc/x86_64-pc-linux-gnu/8.3.0/ (0x00007f208a8b3000) => /lib64/ (0x00007f208a533000) => /usr/lib/gcc/x86_64-pc-linux-gnu/8.3.0/ (0x00007f208a31b000) => /lib64/ (0x00007f2089f4a000) => /usr/lib64/ (0x00007f2089d21000) => /lib64/ (0x00007f2089b1d000) => /usr/lib64/ (0x00007f2089915000) => /usr/lib64/ (0x00007f20896f9000) => /usr/lib64/ (0x00007f20894de000) => /usr/lib64/ (0x00007f20892cc000) => /usr/lib64/ (0x00007f2089042000) => /usr/lib64/ (0x00007f2088e08000) => /lib64/ (0x00007f2088bf0000) => /lib64/ (0x00007f20889cf000)
	/lib64/ (0x00007f208c6d8000) => /usr/lib64/ (0x00007f20887cb000) => /usr/lib64/ (0x00007f20885c5000) => /lib64/ (0x00007f20883be000) => /usr/lib64/ (0x00007f20881a5000) => /lib64/ (0x00007f2087f9d000)
Comment 3 Martin Mokrejš 2019-03-28 11:15:56 UTC
The jpeg/png libs come from -lXm , probably is OK then.

$ ldd /usr/lib64/ (0x00007fff047fb000) => /usr/lib64/ (0x00007f06a3f0f000) => /usr/lib64/ (0x00007f06a3ca6000) => /usr/lib64/ (0x00007f06a3a94000) => /usr/lib64/ (0x00007f06a3754000) => /usr/lib64/ (0x00007f06a34ca000) => /usr/lib64/ (0x00007f06a3290000) => /lib64/ (0x00007f06a2ebf000) => /usr/lib64/ (0x00007f06a2cb7000) => /usr/lib64/ (0x00007f06a2a9b000) => /usr/lib64/ (0x00007f06a2872000) => /lib64/ (0x00007f06a266e000) => /lib64/ (0x00007f06a2456000) => /lib64/ (0x00007f06a20d6000)
	/lib64/ (0x00007f06a45fb000) => /lib64/ (0x00007f06a1ecf000) => /usr/lib64/ (0x00007f06a1cb6000) => /usr/lib64/ (0x00007f06a1ab2000) => /usr/lib64/ (0x00007f06a18ac000) => /lib64/ (0x00007f06a16a4000) => /lib64/ (0x00007f06a1483000)
Comment 4 Larry the Git Cow gentoo-dev 2019-04-06 19:01:48 UTC
The bug has been closed via the following commit(s):

commit 3230f4fae4d914eabb4683d57f27d0633d3adc6b
Author:     David Seifert <>
AuthorDate: 2019-04-06 19:01:08 +0000
Commit:     David Seifert <>
CommitDate: 2019-04-06 19:01:08 +0000

    sci-biology/consed: Fix building under GCC 7+
    consed (and MOTIF programs in general) is very sensitive
    to link order:
    Package-Manager: Portage-2.3.62, Repoman-2.3.12
    Signed-off-by: David Seifert <>

 .../consed/files/consed-29-fix-build-system.patch     |  2 +-
 sci-biology/consed/files/consed-29-fix-qa.patch       | 19 +++++++++++++++++++
 2 files changed, 20 insertions(+), 1 deletion(-)