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Bug 346801 - sci-biology/consed-20.0: attribute error: open with O_CREAT in second argument needs 3 arguments
Summary: sci-biology/consed-20.0: attribute error: open with O_CREAT in second argumen...
Status: RESOLVED TEST-REQUEST
Alias: None
Product: Gentoo Linux
Classification: Unclassified
Component: Current packages (show other bugs)
Hardware: All Linux
: High enhancement (vote)
Assignee: Gentoo Science Biology related packages
URL:
Whiteboard:
Keywords:
Depends on:
Blocks:
 
Reported: 2010-11-25 21:45 UTC by Martin Mokrejš
Modified: 2014-10-26 16:15 UTC (History)
1 user (show)

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


Attachments
consed-20.ebuild (consed-20.ebuild,2.20 KB, text/plain)
2010-11-25 21:46 UTC, Martin Mokrejš
Details
nextPhredPipeline.cpp.patch (nextPhredPipeline.cpp.patch,439 bytes, patch)
2011-01-08 20:20 UTC, Martin Mokrejš
Details | Diff

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Description Martin Mokrejš 2010-11-25 21:45:30 UTC
This is a almost working ebuild but needs some not yet existing patch to get the thing compiled, at least for me on ~x86. The ebuild contains the fix from bug #312893#c1 for expansion of the EPREFIX variable.

g++   -w -DINLINE_RWTPTRORDEREDVECTOR -DINLINE_RWTVALORDEREDVECTOR -DINLINE_MBTVALVECTOR -DLINUX_COMPILE -DSOCKLEN_T_DEFINED -D__BOOL_DEFINED -DANSI_C -DOFSTREAM_OPEN_WITHOUT_PERMISSIONS -fpermissive -DNO_POUND_POUND_MACROS -DUSE_USING_IN_PUBLIC_TEMPLATE_CLASSES -DINT_CHAR_OPERATOR -D_FILE_OFFSET_BITS=64 -O -I/usr/X11R6/include -c nextPhredPipeline.cpp
In file included from /usr/include/fcntl.h:264,
                from /usr/include/sys/file.h:25,
                from nextPhredPipeline.cpp:51:
In function ‘int open(const char*, int, ...)’,
   inlined from ‘void nextPhredPipeline::openAndLockControlFile()’ at nextPhredPipeline.cpp:479:
/usr/include/bits/fcntl2.h:51: error: call to ‘__open_missing_mode’ declared with attribute error: open with O_CREAT in second argument needs 3 arguments
make: *** [nextPhredPipeline.o] Error 1


Is this an issue with one of the headers or with nextPhredPipeline.cpp of consed-20.0? I have: gcc-4.4.5, glibc-2.12.1-r3, 2.6.27.54, i686.
Comment 1 Martin Mokrejš 2010-11-25 21:46:10 UTC
Created attachment 255439 [details]
consed-20.ebuild
Comment 2 Martin Mokrejš 2011-01-08 15:53:44 UTC
> Is this an issue with one of the headers or with nextPhredPipeline.cpp of
> consed-20.0? I have: gcc-4.4.5, glibc-2.12.1-r3, 2.6.27.54, i686.

Upstrream answered:

"nextPhredPipeline is not needed--I will probably remove those modules
in the next release"
Comment 3 Rafał Mużyło 2011-01-08 17:47:49 UTC
See 'man 3p open'.
There were several such problems, back when _FORTIFY_SOURCE on -O2 was introduced.
Comment 4 Martin Mokrejš 2011-01-08 20:20:27 UTC
Created attachment 259314 [details, diff]
nextPhredPipeline.cpp.patch

Thanks to the tip from galtgendo I made a patch. ;-) Will commit the fixed ebuild with the patch to science overlay.
Comment 5 Justin Lecher (RETIRED) gentoo-dev 2014-10-26 16:15:01 UTC
Please try with consed-27 and reopen if still exists