Dmitry Roshchin
8dc23cce8d
- Update to version 3.3.2
* Fixed a recently introduced bug that could cause hmmsearch
(and presumably hmmscan) to segfault on rare comparisons
involving highly biased sequences.
* ./configure –enable-PIC wasn’t setting -fPIC option in
impl-sse, impl-vmx Makefiles.
* fixed an uninitialized ptr in makehmmerdb, in the fm_data
structure, which could cause makehmmerdb to crash.
OBS-URL: https://build.opensuse.org/request/show/1036523
OBS-URL: https://build.opensuse.org/package/show/science/hmmer3?expand=0&rev=6
193 lines
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193 lines
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-------------------------------------------------------------------
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Thu Nov 17 06:16:16 UTC 2022 - Stefan Brüns <stefan.bruens@rwth-aachen.de>
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- Update to version 3.3.2
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* Fixed a recently introduced bug that could cause hmmsearch
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(and presumably hmmscan) to segfault on rare comparisons
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involving highly biased sequences.
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* ./configure –enable-PIC wasn’t setting -fPIC option in
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impl-sse, impl-vmx Makefiles.
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* fixed an uninitialized ptr in makehmmerdb, in the fm_data
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structure, which could cause makehmmerdb to crash.
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-------------------------------------------------------------------
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Thu Nov 21 12:11:17 UTC 2019 - Luigi Baldoni <aloisio@gmx.com>
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- Update to version 3.3
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most important changes:
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* We improved the `hmmpgmd` search daemon. (`hmmpgmd` is the
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compute server used at EBI to support their HMMER web
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servers.) Now `hmmpgmd` handles large target sequence
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databases more efficiently by using "sharding". Instead of
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loading the entire target sequence database into memory on
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every node, a target database can be sharded across multiple
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nodes. The `hmmpgmd` daemon also now has its own user guide.
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* We improved how we calculate our default sequence weights
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(Henikoff position-based weights), especially on deep
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alignments of 10-100K+ sequences. Now we calculate PB weights
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only on consensus columns, not all columns. This avoids some
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cases of artifactually extreme weights on very gappy
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alignments. We also changed to a better rule for defining
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sequence fragments. These changes give a small improvement
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in sensitivity/specificity benchmarking of HMMER/Pfam
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searches, and substantial speed improvements in building
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profiles on deep alignments. Because of these changes,
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profile HMMs built with version 3.3 give slightly different
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scores compared to previous HMMER3 versions.
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* Fixed a bug in the `hmmstat` "compKL" (composition KL
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divergence) calculation, which was off by a constant. Now it
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is reported as a standard KL divergence in bits.
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bug fixes:
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* fixed a bug where in some rare and complicated situations,
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`nhmmer` could report overlapping envelopes on reverse
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strand. [iss#159]
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* Several bugs were fixed in MPI mode, including iss#157
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(`hmmsim --mpi` was always segfaulting, even on simple
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examples) and iss#154 (problems in `hmmscan` that were
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corrupting output data).
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* Fixed some 32-bit integer overflow bugs in `hmmpgmd`.
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* Fixed a bug in the `hmmstat` "compKL" (composition KL
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divergence) calculation, which was off by a constant. Now it
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is reported as a standard KL divergence in bits.
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* Fixed a bug where `hmmconvert --outfmt` wasn't recognizing
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`3/f` as a format.
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Smaller changes:
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* Our fasta format parser now detects aligned FASTA format
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(.afa files) more robustly, and will not attempt to read a
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.afa file as an unaligned sequence file. [iss#153]
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* Our `make check` tests depend on Python >= 3.5. Added checks
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in `./configure` and `make` to fail gracefully if python3
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isn't available.
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* `./configure` now always calls `AC_PROG_CC_STDC` to add
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compiler flags for C99 (even with icc).
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* Removed undocumented `--{tmm,tmi,tmd,tim,tii,tdm,tdd}`
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options from hmmbuild.
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* Data serialization routines (used in `hmmpgmd`) were
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rewritten and improved.
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- Spec cleanup
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-------------------------------------------------------------------
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Fri Jun 15 08:34:00 UTC 2018 - aloisio@gmx.com
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- Update to version 3.2.1
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* iss #142: compilation fails ungracefully on unsupported
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ppc64le
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* iss #140: jackhmmer --fast segfault. Removes --fast
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and --symfrac options from jackhmmer and its documentation.
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* iss #141, #120: compilation failures on i586, ppc64be.
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* iss #132: hmmbuild miscounts transitions in final node.
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-------------------------------------------------------------------
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Fri Jun 8 17:05:33 UTC 2018 - aloisio@gmx.com
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- Update to version 3.2
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Larger changes:
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* HMMER is now distributed under the BSD license, instead of
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the GPL.
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* The 'make install' has been streamlined. Now we install only
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programs and man pages, for 18 HMMER programs and 22 Easel
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miniapps. We don't install development .h headers or .a
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libraries.
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* We changed our default policy on the number of threads/cores
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that the search programs use. Previously multithreaded
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programs would use all available cores by default; now we use
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two worker threads by default (~2 cores), if multiple cores
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are available. HMMER3 search programs do not scale much beyond
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2 cores anyway, due to input saturation and memory use.
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* H3 now strictly requires either SSE2 or Altivec/VMX vector
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support. The portable 'dummy' implementation has been removed.
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This was an non-vectorized portable pure C implementation,
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much slower than HMMER3 on x86 and PowerPC platforms with SSE2
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or Altivec/VMX vector instructions. We had included it because
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we could -- HMMER3 implements "generic" non-vectorized versions
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of its core algorithms for unit testing purposes anyway. We
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thought maybe it'd be useful. As far as I can tell, it was
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never useful, but several packagers on non-x86, non-PowerPC
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platforms packaged and distributed it, ignoring the prominent
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health warnings we put on it.
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Smaller new features include:
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* improved documentation of --mxfile and score matrix file
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format
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* adds support for EBI's "uncheck all hits" on jackhmmer web
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site
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* removed experimental hmmbuild --seq_weights_r and
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--seq_weights_e options
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* appeased new gcc6 --Wmisleading-indentation warning
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* SSI indexing is now robust against duplicate keys
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* autoconf now robust against someone running gnu `autoheader`
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* improved autoconf of SIMD vector support
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* improved autoconf of DAZ,FTZ support on x86 processors
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* improved autodetection of phylip interleaved vs sequential
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format
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* improved autodetection of A2M vs. aligned FASTA format
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* clarified A2M format parse error when file contains 'O'
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residue
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* improved portability to Intel/Solaris
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* FASTA parser now ignores description line after a ctrl-A
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* MSAs output with -A option now include name, acc, desc,
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author markup.
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* In Easel miniapps, esl-translate replaces previous (buggy)
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esl-stranslate.
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* Easel miniapps include esl-alirev, reverse complementing
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RNA/DNA alignment
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* nhmmer/nhmmscan now allow alignments as target dbs
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* target relentropy for DNA models changed from 0.45 to 0.62
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* updated the User Guide
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Fixed bugs include:
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* nhmmscan faulted on old model files because it expected MAXL
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field
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* --cut-ga wasn't checking that GA line was actually present
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in model
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* GA thresholds weren't being captured from DNA/RNA Stockholm
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alignments
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* A2M alignment parsing was corrupted on lines ending in
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insertions
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* alphabet-guessing failed for FASTA seq >4096 bytes and <4000
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residues
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* genbank to fasta format conversion was leaving extra \n in
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accession
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* NCBI db format: multithreaded nhmmer was failing to read
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* NCBI db format: 1st database sequence was skipped for second
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query (#e6)
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* unit test failures in esl_normal, esl_random due to floating
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point math
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* nhmmer was corrupted by * symbols in input sequence (iss#118)
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* hmmsearch -A crashed if top-ranked hit has no domains
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(iss#131)
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* new variety of "backconverted subseq" hmmsearch crash on *'s
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(iss#135)
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* qsort() callbacks now return -1/0/1 as they should.
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(Infernal iss#11)
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* esl_buffer hangs when input ends with \r (Easel iss#23)
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- Dropped hmmer-bufferoverflowstrncat.patch (merged upstream)
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- Dropped devel subpackage (easel no longer installs header files
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and static library)
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-------------------------------------------------------------------
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Wed Oct 19 08:13:27 UTC 2016 - aloisio@gmx.com
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- Update to 3.1b2 (see release-notes for changelog)
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- Spec cleanup
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- Fixed ppc64/ppc64le build
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- Backported hmmer3-bufferoverflowstrncat.patch from trunk
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to avoid buffer overflow errors.
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- Added devel subpackage
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-------------------------------------------------------------------
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Sun Mar 20 08:49:09 UTC 2016 - mailaender@opensuse.org
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- Adapted for openSUSE science:
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* spec file cleanup
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* use source urls
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* fix rpmlint warnings
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* don't strip binaries manually
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-------------------------------------------------------------------
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Fri Sep 10 11:48:55 UTC 2010 - kai.blin@biotech.uni-tuebingen.de
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- Initial spec file heavily based on Dominik Borowski's version
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o Fixed a couple of rpmlint warnings
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