Created attachment 365990 [details] emerge --info On my system 'emerge -c' fails due to the following error: * Dependencies could not be completely resolved due to * the following required packages not being installed: * * sci-libs/hdf5:0/1.8.11= pulled in by: * dev-python/pytables-3.0.0 Manually downgrading hdf5 to version 1.8.11 temporarily resolves this, but upon 'emerge -uD @world' it gets upgraded to version 1.8.12 again. I'll try to give the relevant info, but tell me if I miss something. Output of 'emerge -vcp hdf5': Calculating dependencies... done! sci-libs/hdf5-1.8.12 pulled in by: dev-python/pytables-3.0.0 requires sci-libs/hdf5:= media-libs/vigra-1.9.0 requires sci-libs/hdf5 sci-libs/flann-1.8.4 requires sci-libs/hdf5 pytables is ultimately pulled in by sci-mathematics/sage on my system (although sage is not in main tree, the ebuilds for hdf5 and pytables are from the main tree).
What's the output of "emerge -cp" when hdf-1.8.11 is installed? Please attach the debug.log created by "emerge -uD @world --pretend --debug &>debug.log" when hdf-1.8.11 is installed.
(In reply to Sebastian Luther (few) from comment #1) > What's the output of "emerge -cp" when hdf-1.8.11 is installed? It says everything is fine and nothing needs to be removed. > Please attach the debug.log created by > "emerge -uD @world --pretend --debug &>debug.log" > when hdf-1.8.11 is installed. In the works.
Created attachment 366000 [details] requested output of emerge --debug (xzipped) HTH, it's rather large ...
Please attach the depclean_debug.log created by "emerge -cpv --debug &> depclean_debug.log". According to your debug.log dev-python/pytables isn't a deep dependency of @world. This explains why its dependency on hdf5 is ignored with -uD. I would expect it to be removed by "emerge -c". Lets find out why it isn't.
Created attachment 366052 [details] requested output of emerge --depclean --debug (xzipped) I manually pieced together the following dependency chain: sci-libs/hdf5:0/1.8.11= dev-python/pytables-3.0.0 dev-python/pandas-0.12.0 dev-python/rpy-2.3.8 sci-mathematics/sage-5.12 and I took a close look at my world file and sage is listed normally like every other atom.
This seems to be a duplicate of bug 493374. The problem is that the dependency between rpy and pandas is only build time. This leads emerge to ignore it during -uD world, but consider it during -c. As a workaround use either --with-bdeps=y for -uD or --with-bdeps=n for -c.
*** This bug has been marked as a duplicate of bug 493374 ***
I changed my mind. The issue is different and may be fixed in a different way.
17 Feb 2015; Justin Lecher <jlec@gentoo.org> -pytables-3.0.0.ebuild, -pytables-3.1.0.ebuild, -pytables-3.1.1.ebuild: Drop old
(In reply to Sebastian Luther (few) from comment #6) > This seems to be a duplicate of bug 493374. > > The problem is that the dependency between rpy and pandas is only build time. > This leads emerge to ignore it during -uD world, but consider it during -c. > > As a workaround use either --with-bdeps=y for -uD or --with-bdeps=n for -c. Unfortunately, there's no way do avoid inconsistencies like this when you have an option like --with-bdeps=n, so I recommend to put --with-bdeps=y in EMERGE_DEFAULT_OPTS if it bothers you.
