Summary: | sci-biology/rmblast-1.2: boost incompatibility, introduce boost USE flag | ||
---|---|---|---|
Product: | Gentoo Linux | Reporter: | Martin Mokrejš <mmokrejs> |
Component: | New packages | Assignee: | Gentoo Science Biology related packages <sci-biology> |
Status: | RESOLVED FIXED | ||
Severity: | normal | CC: | sci-biology |
Priority: | High | ||
Version: | unspecified | ||
Hardware: | All | ||
OS: | Linux | ||
Whiteboard: | |||
Package list: | Runtime testing required: | --- | |
Bug Depends on: | |||
Bug Blocks: | 457936 | ||
Attachments: |
build.log
build.log_1.41__vs__1.42_current_ebuild.txt build.log_1.42__vs__1.42_current_ebuild_with-boost-usr-include-boost.txt build.log |
Description
Martin Mokrejš
2011-02-24 16:59:12 UTC
Starting with the obvious: does '--with-boost=/usr/include/boost' work ? What about a build log ? Or is this for the moment just a configure failure ? config.log then. Created attachment 263707 [details]
build.log
build.log with the current ebuild ignoring USE=boost
Hmm, I tried the '--with-boost=/usr/include/boost' manually as well but that did not help. But, 'eselect boost list' told me I have 1.42 select as current. I selected 1.35 from the list and I am compiling some cove well after the problematic-one. Could emerge switch the profile for me automatically? @comment 3: that looks like an incorrect solution. Could you attach build log of the failure in case of '--with-boost=/usr/include/boost' ? First of all, manually selecting using eselect either 1.35 or 1.41 I can compile using current ebuild quite ok (gcc-4.4.4). Second, I will attach these files: diff -u rmblast-1.2__boost-1.41/temp/build.log rmblast-1.2__boost-1.42/temp/build.log > build.log_1.41__vs__1.42_current_ebuild.txt diff -u rmblast-1.2__boost-1.42/temp/build.log rmblast-1.2__boost-1.42-with-boost-usr-include-boost/temp/build.log > build.log_1.42__vs__1.42_current_ebuild_with-boost-usr-include-boost.txt rmblast-1.2__boost-1.42-with-boost-usr-include-boost/temp/build.log (the file you have asked for) ;) Created attachment 263777 [details]
build.log_1.41__vs__1.42_current_ebuild.txt
Trimmed down since the region where compilation fails.
Created attachment 263779 [details]
build.log_1.42__vs__1.42_current_ebuild_with-boost-usr-include-boost.txt
Created attachment 263781 [details]
build.log
Generate with '--with-boost=/usr/include/boost', otherwise un-modified current ebuild, gcc-4.4.4, and
# eselect boost list
Available boost versions:
[1] boost-1.35/default
[2] boost-1.41/default
[3] boost-1.42/default *
#
OK, I finally took a look at the source tarball - it's both trivial and complicated. Basically, it's the same as in ncbi-tools++ - the constructor has changed. The catch is that if I read boost docs correctly, boost_exception was not meant to be used the way these two packages use it. On unrelated note: that build log suggests you should look at 'eselect wxwidgets'. And on a related note: ncbi-tools++ 2.2.24 has a few changes with '#if BOOST_VERSION >= 104200' - perhaps similar will help here too. +*rmblast-1.2-r1 (18 Feb 2013) + + 18 Feb 2013; Justin Lecher <jlec@gentoo.org> rmblast-1.2.ebuild, + +rmblast-1.2-r1.ebuild, +files/rmblast-1.2-gcc47.patch, metadata.xml: + Bug fixes: Build against any boost, #356315; build with gcc-4.7, #442266 + |