Sorry no testsuite, only runtime
Requires sci-chemistry/ccp4-apps. Which target should we stabilize?
Could you try and go for sci-chemistry/ccp4-apps-6.1.3-r8. In case this pulls many other deps, please report back. I will then delay this one and recheck all the deps separately.
Delayed
Please go ahead now.
amd64: AOK
amd64 >=sci-libs/ccp4-libs-6.1.3-r8 should be added as a dependency to the ebuild or else you'll have a circular dependency block like the following: [blocks B ] <sci-libs/ccp4-libs-6.1.3-r10 ("<sci-libs/ccp4-libs-6.1.3-r10" is blocking sci-libs/ssm-1.1) [blocks B ] sci-libs/ssm ("sci-libs/ssm" is blocking sci-libs/ccp4-libs-6.1.3-r8)
THere was a twist in the versioning.
We need to change version. in 1.5.* there is a serious internal scrambling of the data between input and output.
==== Summary There is a serious error in all the 1.5.x versions of Pointless for certain cases, fixed now in version 1.6.1 available now from our ftp site. The wrong 1.5.x versions have been distributed by CCP4 in releases 6.1.24 and the recent 6.2.0, but earlier CCP4 releases (6.1.13 and before) contained earlier versions of Pointless (eg 1.4.x versions) which do not suffer from this bug. However I know that people have installed 1.5.x versions from our ftp site. I would like to apologise for problems caused by this error mea culpa Phil Evans === Corrected versions ftp://ftp.mrc-lmb.cam.ac.uk/pub/pre pointless-1.6.1.linux linux executable pointless-1.6.1.osx10.6 osx 10.6 executable pointless-1.6.1.tar.gz source pointless.html doc === What cases does the bug affect? The bug may scramble the order of symmetry operators relative to the ISYM flags on each observation (see below, technicalities), leading to an incorrect reconstruction of the original hkl indices in Scala or Aimless. This happens for MTZ input files (usually from Mosflm) integrated is the highest point group in higher symmetry lattices, specifically tetragonal 422, hexagonal 622, rhombohedral R32 and cubic 432, when the output file is also in the same point group. In these cases, the output file will be wrong even if Pointless is just copying from input to output ("-c" or COPY options) The bug does NOT affect: 1) lower symmetry lattices (triclinic, monoclinic, orthorhombic) 2) data input or output in lower than maximum point group symmetry within the same Laue class (eg 4, 3, 321, 23, R3) 3) XDS or other non-MTZ input === How serious is it? Files with scrambled symmetry operators will lead to wrong reconstruction of the original indices which are used in Scala or Aimless to generate beam directions for the SECONDARY absorption correction. Thus the error will have the biggest effect on long wavelength data with substantial absorption, and have much less effect on typical short wavelength data. High multiplicity will also tend to average out the errors. === Technicalities Unmerged MTZ files store for each observation the hkl indices reduced to the asymmetric unit and a flag ISYM which is the index into the list of space group symmetry operators stored in the file. This information can then be used to reconstruct the original hkl indices measured. This bug caused to order of the symmetry operators to be changed without changing the ISYM flags, leading to a wrong reconstruction of original hkl in Scala/Aimless, and hence wrong secondary beam directions for the absorption correction.
This and all the sci-* packages are not ready to go stable ( Too much bug dependencies floating around. ). Maybe you should consider removing arches for now?
(In reply to comment #10) > This and all the sci-* packages are not ready to go stable ( Too much bug > dependencies floating around. ). Maybe you should consider removing arches for > now? I don't see any bugs in deps. Which are you referring to?
amd64 ok, you can mark stable at same time the following list: =sci-chemistry/xia2-0.3.3.1 =sci-chemistry/mrbump-0.4.4 =sci-chemistry/oasis-4.0-r2 =sci-chemistry/ccp4-apps-6.1.3-r10 =sci-chemistry/pointless-1.6.2 there are no blocks for me merging this list at same time.
+ 06 Oct 2011; Tony Vroon <chainsaw@gentoo.org> pointless-1.6.2.ebuild: + Marked stable on AMD64 based on arch testing by Agostino "ago" Sarubbo in bug + #351753.
No can do, we don't have usable tkimg in tree, required by ccp4-apps
X86 please go ahead
x86 stabilized with bug 375917. Thanks, closing!
