Your message dated Fri, 29 Oct 2021 13:34:07 +0000 with message-id <e1mgs1h-0009s3...@fasolo.debian.org> and subject line Bug#997886: fixed in prottest 3.4.2+dfsg-7 has caused the Debian Bug report #997886, regarding prottest: autopkgtest regression: Stats file does not exist to be marked as done.
This means that you claim that the problem has been dealt with. If this is not the case it is now your responsibility to reopen the Bug report if necessary, and/or fix the problem forthwith. (NB: If you are a system administrator and have no idea what this message is talking about, this may indicate a serious mail system misconfiguration somewhere. Please contact ow...@bugs.debian.org immediately.) -- 997886: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=997886 Debian Bug Tracking System Contact ow...@bugs.debian.org with problems
--- Begin Message ---Source: prottest Version: 3.4.2+dfsg-6 X-Debbugs-CC: debian...@lists.debian.org Severity: serious User: debian...@lists.debian.org Usertags: regression Dear maintainer(s), With a recent upload of prottest the autopkgtest of prottest fails in testing when that autopkgtest is run with the binary packages of prottest from unstable. It passes when run with only packages from testing. In tabular form: pass fail prottest from testing 3.4.2+dfsg-6 all others from testing from testing I copied some of the output at the bottom of this report. Currently this regression is blocking the migration to testing [1]. Can you please investigate the situation and fix it? More information about this bug and the reason for filing it can be found on https://wiki.debian.org/ContinuousIntegration/RegressionEmailInformation Paul [1] https://qa.debian.org/excuses.php?package=prottest https://ci.debian.net/data/autopkgtest/testing/amd64/p/prottest/16225046/log.gz ------------------------------------------------------------------------------------------------- Basic usage: - Sequential version: java -jar prottest-3.4.2.jar -i align_file [OPTIONS] ./prottest3 -i align_file [OPTIONS] - Parallel version: mpjrun.sh -wdir $PWD/ -np [NUM_PROCS] -jar prottest-3.4.2.jar -i align_file [OPTIONS] OPTIONS: -i alignment_filename Alignment input file (required) -t tree_filename Tree file (optional) [default: NJ tree] -o output_filename Output file (optional) [default: standard output] -log enabled/disabled Enables / Disables PhyML logging into log directory (see prottest.properties) -[matrix] Include matrix (Amino-acid) = JTT LG DCMut MtREV MtMam MtArt Dayhoff WAG RtREV CpREV Blosum62 VT HIVb HIVw FLU If you don't specify any matrix, all matrices displayed above will be included. -I Include models with a proportion of invariable sites -G Include models with rate variation among sites and number of categories -IG include models with both +I and +G properties -all-distributions Include models with rate variation among sites, number of categories and both -ncat number_of_categories Define number of categories for +G and +I+G models [default: 4] -F Include models with empirical frequency estimation -AIC Display models sorted by Akaike Information Criterion (AIC) -BIC Display models sorted by Bayesian Information Criterion (BIC) -AICC Display models sorted by Corrected Akaike Information Criterion (AICc) -DT Display models sorted by Decision Theory Criterion -all Displays a 7-framework comparison table -S optimization_strategy Optimization strategy mode: [default: 0] 0: Fixed BIONJ JTT 1: BIONJ Tree 2: Maximum Likelihood tree 3: User defined topology -s moves Tree search operation for ML search: NNI (fastest), SPR (slowest), BEST (best of NNI and SPR) [default: NNI] -t1 Display best-model's newick tree [default: false] -t2 Display best-model's ASCII tree [default: false] -tc consensus_threshold Display consensus tree with the specified threshold, between 0.5 and 1.0 [0.5 = majority rule consensus ; 1.0 = strict consensus] -threads number_or_threads Number of threads requested to compute (only if MPJ is not used) [default: 1] -verbose Verbose mode [default: false] ------------------------------------------------------------------------------------------------- Example: - Sequential version: java -jar prottest-3.4.2.jar -i align_file -t tree_file -S 0 -all-distributions -F -AIC -BIC -tc 0.5 > output - Parallel version: mpjrun.sh -wdir $PWD/ -np 2 -jar prottest-3.4.2.jar -i align_file -t tree_file -S 0 -all-distributions -F -AIC -BIC -tc 0.5 PHYLIP format detected.MSA read in PHYLIP format (Taxa = 28, Length = 149).MSA successfully converted to PHYLIP format! No such file or directory ---------------------------------------------------------------------------------------------- ProtTest 3.4.2 Fast selection of the best-fit models of protein evolution (c) 2009-2016 Diego Darriba (1,2), Guillermo Taboada (2), Ramón Doallo (2), David Posada (1) (1) Facultad de Biologia, Universidad de Vigo, 36200 Vigo, Spain (2) Facultade de Informática, Universidade da Coruña, 15071 A Coruña, Spain ---------------------------------------------------------------------------------------------- Manual: http://darwin.uvigo.es/download/prottest_manual.pdf Homepage: http://github.com/ddarriba/prottest3 Discussion group: https://groups.google.com/group/prottest Contact: ddarr...@h-its.org, dpos...@uvigo.es ---------------------------------------------------------------------------------------------- Version: 3.4.2 : 8th May 2016 Date: Tue Oct 26 10:11:23 UTC 2021 OS: Linux (4.19.0-18-amd64) Arch: amd64 Java: 11.0.12 (Debian) PhyML: /usr/bin/phyml Citation: Darriba D, Taboada GL, Doallo R, Posada D. ProtTest 3: fast selection of best-fit models of protein evolution. Bioinformatics, 27:1164-1165, 2011 ProtTest options ---------------- Alignment file........... : COX2_PF0016/alignment Tree..................... : COX2_PF0016/tree StrategyMode............. : User defined topology Candidate models......... : Matrices............... : JTT LG DCMut MtREV MtMam MtArt Dayhoff WAG RtREV CpREV Blosum62 VT HIVb HIVw FLU Distributions.......... : Uniform +G +I +I+G Observed frequencies... : true Statistical framework Sort models according to....: AIC BIC Sample size.................: 149.0 Other options: Display best tree in ASCII..: false Display best tree in Newick.: false Display consensus tree......: true Consensus threshold.........: 0.5 Verbose.....................: false ********************************************************** Observed number of invariant sites: 13 Observed aminoacid frequencies: A: 0.044 C: 0.018 D: 0.054 E: 0.056 F: 0.049 G: 0.057 H: 0.026 I: 0.086 K: 0.032 L: 0.086 M: 0.039 N: 0.055 P: 0.051 Q: 0.034 R: 0.036 S: 0.086 T: 0.050 V: 0.068 W: 0.028 Y: 0.044 ********************************************************** Model optimization exception: there was an error while executing there was an error parsing PhyML stats file: Stats file does not exist. Please check if PhyML is working. Model................................ : JTT Number of parameters............... : 53 (0 + 53 branch length estimates) Model optimization exception: there was an error while executing there was an error parsing PhyML stats file: Stats file does not exist. Please check if PhyML is working. Model................................ : JTT+F Number of parameters............... : 72 (19 + 53 branch length estimates) Model optimization exception: there was an error while executing there was an error parsing PhyML stats file: Stats file does not exist. Please check if PhyML is working. Model................................ : JTT+I Number of parameters............... : 54 (1 + 53 branch length estimates) Model optimization exception: there was an error while executing there was an error parsing PhyML stats file: Stats file does not exist. Please check if PhyML is working. Model................................ : JTT+I+F Number of parameters............... : 73 (20 + 53 branch length estimates) Model optimization exception: there was an error while executing there was an error parsing PhyML stats file: Stats file does not exist. Please check if PhyML is working. Model................................ : JTT+G Number of parameters............... : 54 (1 + 53 branch length estimates) Model optimization exception: there was an error while executing there was an error parsing PhyML stats file: Stats file does not exist. Please check if PhyML is working. Model................................ : JTT+G+F Number of parameters............... : 73 (20 + 53 branch length estimates) Model optimization exception: there was an error while executing there was an error parsing PhyML stats file: Stats file does not exist. Please check if PhyML is working. Model................................ : JTT+I+G Number of parameters............... : 55 (2 + 53 branch length estimates) Model optimization exception: there was an error while executing there was an error parsing PhyML stats file: Stats file does not exist. Please check if PhyML is working. Model................................ : JTT+I+G+F Number of parameters............... : 74 (21 + 53 branch length estimates) Model optimization exception: there was an error while executing there was an error parsing PhyML stats file: Stats file does not exist. Please check if PhyML is working. Model................................ : LG Number of parameters............... : 53 (0 + 53 branch length estimates) Model optimization exception: there was an error while executing there was an error parsing PhyML stats file: Stats file does not exist. Please check if PhyML is working. Model................................ : LG+F Number of parameters............... : 72 (19 + 53 branch length estimates) Model optimization exception: there was an error while executing there was an error parsing PhyML stats file: Stats file does not exist. Please check if PhyML is working. Model................................ : LG+I Number of parameters............... : 54 (1 + 53 branch length estimates) Model optimization exception: there was an error while executing there was an error parsing PhyML stats file: Stats file does not exist. Please check if PhyML is working. Model................................ : LG+I+F Number of parameters............... : 73 (20 + 53 branch length estimates) Model optimization exception: there was an error while executing there was an error parsing PhyML stats file: Stats file does not exist. Please check if PhyML is working. Model................................ : LG+G Number of parameters............... : 54 (1 + 53 branch length estimates) Model optimization exception: there was an error while executing there was an error parsing PhyML stats file: Stats file does not exist. Please check if PhyML is working. Model................................ : LG+G+F Number of parameters............... : 73 (20 + 53 branch length estimates) Model optimization exception: there was an error while executing there was an error parsing PhyML stats file: Stats file does not exist. Please check if PhyML is working. Model................................ : LG+I+G Number of parameters............... : 55 (2 + 53 branch length estimates) Model optimization exception: there was an error while executing there was an error parsing PhyML stats file: Stats file does not exist. Please check if PhyML is working. Model................................ : LG+I+G+F Number of parameters............... : 74 (21 + 53 branch length estimates) Model optimization exception: there was an error while executing there was an error parsing PhyML stats file: Stats file does not exist. Please check if PhyML is working. Model................................ : DCMut Number of parameters............... : 53 (0 + 53 branch length estimates) Model optimization exception: there was an error while executing there was an error parsing PhyML stats file: Stats file does not exist. Please check if PhyML is working. Model................................ : DCMut+F Number of parameters............... : 72 (19 + 53 branch length estimates) Model optimization exception: there was an error while executing there was an error parsing PhyML stats file: Stats file does not exist. Please check if PhyML is working. Model................................ : DCMut+I Number of parameters............... : 54 (1 + 53 branch length estimates) Model optimization exception: there was an error while executing there was an error parsing PhyML stats file: Stats file does not exist. Please check if PhyML is working. Model................................ : DCMut+I+F Number of parameters............... : 73 (20 + 53 branch length estimates) Model optimization exception: there was an error while executing there was an error parsing PhyML stats file: Stats file does not exist. Please check if PhyML is working. Model................................ : DCMut+G Number of parameters............... : 54 (1 + 53 branch length estimates) Model optimization exception: there was an error while executing there was an error parsing PhyML stats file: Stats file does not exist. Please check if PhyML is working. Model................................ : DCMut+G+F Number of parameters............... : 73 (20 + 53 branch length estimates) Model optimization exception: there was an error while executing there was an error parsing PhyML stats file: Stats file does not exist. Please check if PhyML is working. Model................................ : DCMut+I+G Number of parameters............... : 55 (2 + 53 branch length estimates) Model optimization exception: there was an error while executing there was an error parsing PhyML stats file: Stats file does not exist. Please check if PhyML is working. Model................................ : DCMut+I+G+F Number of parameters............... : 74 (21 + 53 branch length estimates) Model optimization exception: there was an error while executing there was an error parsing PhyML stats file: Stats file does not exist. Please check if PhyML is working. Model................................ : MtREV Number of parameters............... : 53 (0 + 53 branch length estimates) Model optimization exception: there was an error while executing there was an error parsing PhyML stats file: Stats file does not exist. Please check if PhyML is working. Model................................ : MtREV+F Number of parameters............... : 72 (19 + 53 branch length estimates) Model optimization exception: there was an error while executing there was an error parsing PhyML stats file: Stats file does not exist. Please check if PhyML is working. Model................................ : MtREV+I Number of parameters............... : 54 (1 + 53 branch length estimates) Model optimization exception: there was an error while executing there was an error parsing PhyML stats file: Stats file does not exist. Please check if PhyML is working. Model................................ : MtREV+I+F Number of parameters............... : 73 (20 + 53 branch length estimates) Model optimization exception: there was an error while executing there was an error parsing PhyML stats file: Stats file does not exist. Please check if PhyML is working. Model................................ : MtREV+G Number of parameters............... : 54 (1 + 53 branch length estimates) Model optimization exception: there was an error while executing there was an error parsing PhyML stats file: Stats file does not exist. Please check if PhyML is working. Model................................ : MtREV+G+F Number of parameters............... : 73 (20 + 53 branch length estimates) Model optimization exception: there was an error while executing there was an error parsing PhyML stats file: Stats file does not exist. Please check if PhyML is working. Model................................ : MtREV+I+G Number of parameters............... : 55 (2 + 53 branch length estimates) Model optimization exception: there was an error while executing there was an error parsing PhyML stats file: Stats file does not exist. Please check if PhyML is working. Model................................ : MtREV+I+G+F Number of parameters............... : 74 (21 + 53 branch length estimates) Model optimization exception: there was an error while executing there was an error parsing PhyML stats file: Stats file does not exist. Please check if PhyML is working. Model................................ : MtMam Number of parameters............... : 53 (0 + 53 branch length estimates) Model optimization exception: there was an error while executing there was an error parsing PhyML stats file: Stats file does not exist. Please check if PhyML is working. Model................................ : MtMam+F Number of parameters............... : 72 (19 + 53 branch length estimates) Model optimization exception: there was an error while executing there was an error parsing PhyML stats file: Stats file does not exist. Please check if PhyML is working. Model................................ : MtMam+I Number of parameters............... : 54 (1 + 53 branch length estimates) Model optimization exception: there was an error while executing there was an error parsing PhyML stats file: Stats file does not exist. Please check if PhyML is working. Model................................ : MtMam+I+F Number of parameters............... : 73 (20 + 53 branch length estimates) Model optimization exception: there was an error while executing there was an error parsing PhyML stats file: Stats file does not exist. Please check if PhyML is working. Model................................ : MtMam+G Number of parameters............... : 54 (1 + 53 branch length estimates) Model optimization exception: there was an error while executing there was an error parsing PhyML stats file: Stats file does not exist. Please check if PhyML is working. Model................................ : MtMam+G+F Number of parameters............... : 73 (20 + 53 branch length estimates) Model optimization exception: there was an error while executing there was an error parsing PhyML stats file: Stats file does not exist. Please check if PhyML is working. Model................................ : MtMam+I+G Number of parameters............... : 55 (2 + 53 branch length estimates) Model optimization exception: there was an error while executing there was an error parsing PhyML stats file: Stats file does not exist. Please check if PhyML is working. Model................................ : MtMam+I+G+F Number of parameters............... : 74 (21 + 53 branch length estimates) Model optimization exception: there was an error while executing there was an error parsing PhyML stats file: Stats file does not exist. Please check if PhyML is working. Model................................ : MtArt Number of parameters............... : 53 (0 + 53 branch length estimates) Model optimization exception: there was an error while executing there was an error parsing PhyML stats file: Stats file does not exist. Please check if PhyML is working. Model................................ : MtArt+F Number of parameters............... : 72 (19 + 53 branch length estimates) Model optimization exception: there was an error while executing there was an error parsing PhyML stats file: Stats file does not exist. Please check if PhyML is working. Model................................ : MtArt+I Number of parameters............... : 54 (1 + 53 branch length estimates) Model optimization exception: there was an error while executing there was an error parsing PhyML stats file: Stats file does not exist. Please check if PhyML is working. Model................................ : MtArt+I+F Number of parameters............... : 73 (20 + 53 branch length estimates) Model optimization exception: there was an error while executing there was an error parsing PhyML stats file: Stats file does not exist. Please check if PhyML is working. Model................................ : MtArt+G Number of parameters............... : 54 (1 + 53 branch length estimates) Model optimization exception: there was an error while executing there was an error parsing PhyML stats file: Stats file does not exist. Please check if PhyML is working. Model................................ : MtArt+G+F Number of parameters............... : 73 (20 + 53 branch length estimates) Model optimization exception: there was an error while executing there was an error parsing PhyML stats file: Stats file does not exist. Please check if PhyML is working. Model................................ : MtArt+I+G Number of parameters............... : 55 (2 + 53 branch length estimates) Model optimization exception: there was an error while executing there was an error parsing PhyML stats file: Stats file does not exist. Please check if PhyML is working. Model................................ : MtArt+I+G+F Number of parameters............... : 74 (21 + 53 branch length estimates) Model optimization exception: there was an error while executing there was an error parsing PhyML stats file: Stats file does not exist. Please check if PhyML is working. Model................................ : Dayhoff Number of parameters............... : 53 (0 + 53 branch length estimates) Model optimization exception: there was an error while executing there was an error parsing PhyML stats file: Stats file does not exist. Please check if PhyML is working. Model................................ : Dayhoff+F Number of parameters............... : 72 (19 + 53 branch length estimates) Model optimization exception: there was an error while executing there was an error parsing PhyML stats file: Stats file does not exist. Please check if PhyML is working. Model................................ : Dayhoff+I Number of parameters............... : 54 (1 + 53 branch length estimates) Model optimization exception: there was an error while executing there was an error parsing PhyML stats file: Stats file does not exist. Please check if PhyML is working. Model................................ : Dayhoff+I+F Number of parameters............... : 73 (20 + 53 branch length estimates) Model optimization exception: there was an error while executing there was an error parsing PhyML stats file: Stats file does not exist. Please check if PhyML is working. Model................................ : Dayhoff+G Number of parameters............... : 54 (1 + 53 branch length estimates) Model optimization exception: there was an error while executing there was an error parsing PhyML stats file: Stats file does not exist. Please check if PhyML is working. Model................................ : Dayhoff+G+F Number of parameters............... : 73 (20 + 53 branch length estimates) Model optimization exception: there was an error while executing there was an error parsing PhyML stats file: Stats file does not exist. Please check if PhyML is working. Model................................ : Dayhoff+I+G Number of parameters............... : 55 (2 + 53 branch length estimates) Model optimization exception: there was an error while executing there was an error parsing PhyML stats file: Stats file does not exist. Please check if PhyML is working. Model................................ : Dayhoff+I+G+F Number of parameters............... : 74 (21 + 53 branch length estimates) Model optimization exception: there was an error while executing there was an error parsing PhyML stats file: Stats file does not exist. Please check if PhyML is working. Model................................ : WAG Number of parameters............... : 53 (0 + 53 branch length estimates) Model optimization exception: there was an error while executing there was an error parsing PhyML stats file: Stats file does not exist. Please check if PhyML is working. Model................................ : WAG+F Number of parameters............... : 72 (19 + 53 branch length estimates) Model optimization exception: there was an error while executing there was an error parsing PhyML stats file: Stats file does not exist. Please check if PhyML is working. Model................................ : WAG+I Number of parameters............... : 54 (1 + 53 branch length estimates) Model optimization exception: there was an error while executing there was an error parsing PhyML stats file: Stats file does not exist. Please check if PhyML is working. Model................................ : WAG+I+F Number of parameters............... : 73 (20 + 53 branch length estimates) Model optimization exception: there was an error while executing there was an error parsing PhyML stats file: Stats file does not exist. Please check if PhyML is working. Model................................ : WAG+G Number of parameters............... : 54 (1 + 53 branch length estimates) Model optimization exception: there was an error while executing there was an error parsing PhyML stats file: Stats file does not exist. Please check if PhyML is working. Model................................ : WAG+G+F Number of parameters............... : 73 (20 + 53 branch length estimates) Model optimization exception: there was an error while executing there was an error parsing PhyML stats file: Stats file does not exist. Please check if PhyML is working. Model................................ : WAG+I+G Number of parameters............... : 55 (2 + 53 branch length estimates) Model optimization exception: there was an error while executing there was an error parsing PhyML stats file: Stats file does not exist. Please check if PhyML is working. Model................................ : WAG+I+G+F Number of parameters............... : 74 (21 + 53 branch length estimates) Model optimization exception: there was an error while executing there was an error parsing PhyML stats file: Stats file does not exist. Please check if PhyML is working. Model................................ : RtREV Number of parameters............... : 53 (0 + 53 branch length estimates) Model optimization exception: there was an error while executing there was an error parsing PhyML stats file: Stats file does not exist. Please check if PhyML is working. Model................................ : RtREV+F Number of parameters............... : 72 (19 + 53 branch length estimates) Model optimization exception: there was an error while executing there was an error parsing PhyML stats file: Stats file does not exist. Please check if PhyML is working. Model................................ : RtREV+I Number of parameters............... : 54 (1 + 53 branch length estimates) Model optimization exception: there was an error while executing there was an error parsing PhyML stats file: Stats file does not exist. Please check if PhyML is working. Model................................ : RtREV+I+F Number of parameters............... : 73 (20 + 53 branch length estimates) Model optimization exception: there was an error while executing there was an error parsing PhyML stats file: Stats file does not exist. Please check if PhyML is working. Model................................ : RtREV+G Number of parameters............... : 54 (1 + 53 branch length estimates) Model optimization exception: there was an error while executing there was an error parsing PhyML stats file: Stats file does not exist. Please check if PhyML is working. Model................................ : RtREV+G+F Number of parameters............... : 73 (20 + 53 branch length estimates) Model optimization exception: there was an error while executing there was an error parsing PhyML stats file: Stats file does not exist. Please check if PhyML is working. Model................................ : RtREV+I+G Number of parameters............... : 55 (2 + 53 branch length estimates) Model optimization exception: there was an error while executing there was an error parsing PhyML stats file: Stats file does not exist. Please check if PhyML is working. Model................................ : RtREV+I+G+F Number of parameters............... : 74 (21 + 53 branch length estimates) Model optimization exception: there was an error while executing there was an error parsing PhyML stats file: Stats file does not exist. Please check if PhyML is working. Model................................ : CpREV Number of parameters............... : 53 (0 + 53 branch length estimates) Model optimization exception: there was an error while executing there was an error parsing PhyML stats file: Stats file does not exist. Please check if PhyML is working. Model................................ : CpREV+F Number of parameters............... : 72 (19 + 53 branch length estimates) Model optimization exception: there was an error while executing there was an error parsing PhyML stats file: Stats file does not exist. Please check if PhyML is working. Model................................ : CpREV+I Number of parameters............... : 54 (1 + 53 branch length estimates) Model optimization exception: there was an error while executing there was an error parsing PhyML stats file: Stats file does not exist. Please check if PhyML is working. Model................................ : CpREV+I+F Number of parameters............... : 73 (20 + 53 branch length estimates) Model optimization exception: there was an error while executing there was an error parsing PhyML stats file: Stats file does not exist. Please check if PhyML is working. Model................................ : CpREV+G Number of parameters............... : 54 (1 + 53 branch length estimates) Model optimization exception: there was an error while executing there was an error parsing PhyML stats file: Stats file does not exist. Please check if PhyML is working. Model................................ : CpREV+G+F Number of parameters............... : 73 (20 + 53 branch length estimates) Model optimization exception: there was an error while executing there was an error parsing PhyML stats file: Stats file does not exist. Please check if PhyML is working. Model................................ : CpREV+I+G Number of parameters............... : 55 (2 + 53 branch length estimates) Model optimization exception: there was an error while executing there was an error parsing PhyML stats file: Stats file does not exist. Please check if PhyML is working. Model................................ : CpREV+I+G+F Number of parameters............... : 74 (21 + 53 branch length estimates) Model optimization exception: there was an error while executing there was an error parsing PhyML stats file: Stats file does not exist. Please check if PhyML is working. Model................................ : Blosum62 Number of parameters............... : 53 (0 + 53 branch length estimates) Model optimization exception: there was an error while executing there was an error parsing PhyML stats file: Stats file does not exist. Please check if PhyML is working. Model................................ : Blosum62+F Number of parameters............... : 72 (19 + 53 branch length estimates) Model optimization exception: there was an error while executing there was an error parsing PhyML stats file: Stats file does not exist. Please check if PhyML is working. Model................................ : Blosum62+I Number of parameters............... : 54 (1 + 53 branch length estimates) Model optimization exception: there was an error while executing there was an error parsing PhyML stats file: Stats file does not exist. Please check if PhyML is working. Model................................ : Blosum62+I+F Number of parameters............... : 73 (20 + 53 branch length estimates) Model optimization exception: there was an error while executing there was an error parsing PhyML stats file: Stats file does not exist. Please check if PhyML is working. Model................................ : Blosum62+G Number of parameters............... : 54 (1 + 53 branch length estimates) Model optimization exception: there was an error while executing there was an error parsing PhyML stats file: Stats file does not exist. Please check if PhyML is working. Model................................ : Blosum62+G+F Number of parameters............... : 73 (20 + 53 branch length estimates) Model optimization exception: there was an error while executing there was an error parsing PhyML stats file: Stats file does not exist. Please check if PhyML is working. Model................................ : Blosum62+I+G Number of parameters............... : 55 (2 + 53 branch length estimates) Model optimization exception: there was an error while executing there was an error parsing PhyML stats file: Stats file does not exist. Please check if PhyML is working. Model................................ : Blosum62+I+G+F Number of parameters............... : 74 (21 + 53 branch length estimates) Model optimization exception: there was an error while executing there was an error parsing PhyML stats file: Stats file does not exist. Please check if PhyML is working. Model................................ : VT Number of parameters............... : 53 (0 + 53 branch length estimates) Model optimization exception: there was an error while executing there was an error parsing PhyML stats file: Stats file does not exist. Please check if PhyML is working. Model................................ : VT+F Number of parameters............... : 72 (19 + 53 branch length estimates) Model optimization exception: there was an error while executing there was an error parsing PhyML stats file: Stats file does not exist. Please check if PhyML is working. Model................................ : VT+I Number of parameters............... : 54 (1 + 53 branch length estimates) Model optimization exception: there was an error while executing there was an error parsing PhyML stats file: Stats file does not exist. Please check if PhyML is working. Model................................ : VT+I+F Number of parameters............... : 73 (20 + 53 branch length estimates) Model optimization exception: there was an error while executing there was an error parsing PhyML stats file: Stats file does not exist. Please check if PhyML is working. Model................................ : VT+G Number of parameters............... : 54 (1 + 53 branch length estimates) Model optimization exception: there was an error while executing there was an error parsing PhyML stats file: Stats file does not exist. Please check if PhyML is working. Model................................ : VT+G+F Number of parameters............... : 73 (20 + 53 branch length estimates) Model optimization exception: there was an error while executing there was an error parsing PhyML stats file: Stats file does not exist. Please check if PhyML is working. Model................................ : VT+I+G Number of parameters............... : 55 (2 + 53 branch length estimates) Model optimization exception: there was an error while executing there was an error parsing PhyML stats file: Stats file does not exist. Please check if PhyML is working. Model................................ : VT+I+G+F Number of parameters............... : 74 (21 + 53 branch length estimates) Model optimization exception: there was an error while executing there was an error parsing PhyML stats file: Stats file does not exist. Please check if PhyML is working. Model................................ : HIVb Number of parameters............... : 53 (0 + 53 branch length estimates) Model optimization exception: there was an error while executing there was an error parsing PhyML stats file: Stats file does not exist. Please check if PhyML is working. Model................................ : HIVb+F Number of parameters............... : 72 (19 + 53 branch length estimates) Model optimization exception: there was an error while executing there was an error parsing PhyML stats file: Stats file does not exist. Please check if PhyML is working. Model................................ : HIVb+I Number of parameters............... : 54 (1 + 53 branch length estimates) Model optimization exception: there was an error while executing there was an error parsing PhyML stats file: Stats file does not exist. Please check if PhyML is working. Model................................ : HIVb+I+F Number of parameters............... : 73 (20 + 53 branch length estimates) Model optimization exception: there was an error while executing there was an error parsing PhyML stats file: Stats file does not exist. Please check if PhyML is working. Model................................ : HIVb+G Number of parameters............... : 54 (1 + 53 branch length estimates) Model optimization exception: there was an error while executing there was an error parsing PhyML stats file: Stats file does not exist. Please check if PhyML is working. Model................................ : HIVb+G+F Number of parameters............... : 73 (20 + 53 branch length estimates) Model optimization exception: there was an error while executing there was an error parsing PhyML stats file: Stats file does not exist. Please check if PhyML is working. Model................................ : HIVb+I+G Number of parameters............... : 55 (2 + 53 branch length estimates) Model optimization exception: there was an error while executing there was an error parsing PhyML stats file: Stats file does not exist. Please check if PhyML is working. Model................................ : HIVb+I+G+F Number of parameters............... : 74 (21 + 53 branch length estimates) Model optimization exception: there was an error while executing there was an error parsing PhyML stats file: Stats file does not exist. Please check if PhyML is working. Model................................ : HIVw Number of parameters............... : 53 (0 + 53 branch length estimates) Model optimization exception: there was an error while executing there was an error parsing PhyML stats file: Stats file does not exist. Please check if PhyML is working. Model................................ : HIVw+F Number of parameters............... : 72 (19 + 53 branch length estimates) Model optimization exception: there was an error while executing there was an error parsing PhyML stats file: Stats file does not exist. Please check if PhyML is working. Model................................ : HIVw+I Number of parameters............... : 54 (1 + 53 branch length estimates) Model optimization exception: there was an error while executing there was an error parsing PhyML stats file: Stats file does not exist. Please check if PhyML is working. Model................................ : HIVw+I+F Number of parameters............... : 73 (20 + 53 branch length estimates) Model optimization exception: there was an error while executing there was an error parsing PhyML stats file: Stats file does not exist. Please check if PhyML is working. Model................................ : HIVw+G Number of parameters............... : 54 (1 + 53 branch length estimates) Model optimization exception: there was an error while executing there was an error parsing PhyML stats file: Stats file does not exist. Please check if PhyML is working. Model................................ : HIVw+G+F Number of parameters............... : 73 (20 + 53 branch length estimates) Model optimization exception: there was an error while executing there was an error parsing PhyML stats file: Stats file does not exist. Please check if PhyML is working. Model................................ : HIVw+I+G Number of parameters............... : 55 (2 + 53 branch length estimates) Model optimization exception: there was an error while executing there was an error parsing PhyML stats file: Stats file does not exist. Please check if PhyML is working. Model................................ : HIVw+I+G+F Number of parameters............... : 74 (21 + 53 branch length estimates) Model optimization exception: there was an error while executing there was an error parsing PhyML stats file: Stats file does not exist. Please check if PhyML is working. Model................................ : FLU Number of parameters............... : 53 (0 + 53 branch length estimates) Model optimization exception: there was an error while executing there was an error parsing PhyML stats file: Stats file does not exist. Please check if PhyML is working. Model................................ : FLU+F Number of parameters............... : 72 (19 + 53 branch length estimates) Model optimization exception: there was an error while executing there was an error parsing PhyML stats file: Stats file does not exist. Please check if PhyML is working. Model................................ : FLU+I Number of parameters............... : 54 (1 + 53 branch length estimates) Model optimization exception: there was an error while executing there was an error parsing PhyML stats file: Stats file does not exist. Please check if PhyML is working. Model................................ : FLU+I+F Number of parameters............... : 73 (20 + 53 branch length estimates) Model optimization exception: there was an error while executing there was an error parsing PhyML stats file: Stats file does not exist. Please check if PhyML is working. Model................................ : FLU+G Number of parameters............... : 54 (1 + 53 branch length estimates) Model optimization exception: there was an error while executing there was an error parsing PhyML stats file: Stats file does not exist. Please check if PhyML is working. Model................................ : FLU+G+F Number of parameters............... : 73 (20 + 53 branch length estimates) Model optimization exception: there was an error while executing there was an error parsing PhyML stats file: Stats file does not exist. Please check if PhyML is working. Model................................ : FLU+I+G Number of parameters............... : 55 (2 + 53 branch length estimates) Model optimization exception: there was an error while executing there was an error parsing PhyML stats file: Stats file does not exist. Please check if PhyML is working. Model................................ : FLU+I+G+F Number of parameters............... : 74 (21 + 53 branch length estimates) ************************************************************ Date : Tue Oct 26 10:14:30 UTC 2021 Runtime: 0h:03:07 Lk not initialized autopkgtest [10:14:30]: test run-unit-test
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--- Begin Message ---Source: prottest Source-Version: 3.4.2+dfsg-7 Done: Nilesh Patra <nil...@debian.org> We believe that the bug you reported is fixed in the latest version of prottest, which is due to be installed in the Debian FTP archive. A summary of the changes between this version and the previous one is attached. Thank you for reporting the bug, which will now be closed. If you have further comments please address them to 997...@bugs.debian.org, and the maintainer will reopen the bug report if appropriate. Debian distribution maintenance software pp. Nilesh Patra <nil...@debian.org> (supplier of updated prottest package) (This message was generated automatically at their request; if you believe that there is a problem with it please contact the archive administrators by mailing ftpmas...@ftp-master.debian.org) -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 1.8 Date: Fri, 29 Oct 2021 18:05:16 +0530 Source: prottest Architecture: source Version: 3.4.2+dfsg-7 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team <debian-med-packag...@lists.alioth.debian.org> Changed-By: Nilesh Patra <nil...@debian.org> Closes: 997886 Changes: prottest (3.4.2+dfsg-7) unstable; urgency=medium . * Team Upload. * Add patch to fix autopkgtests (Closes: #997886) Checksums-Sha1: d3ffb8c67474858dd0ba88445541b5f235d0d27a 2108 prottest_3.4.2+dfsg-7.dsc d2897f2af4e750f88e16638f295738656d166cd2 7104 prottest_3.4.2+dfsg-7.debian.tar.xz 8e3b79d8c9de8c3140e8da638393b1038ab8303c 10789 prottest_3.4.2+dfsg-7_amd64.buildinfo Checksums-Sha256: f5a206a1f71caf1c8f6563b537d0e7db55dac2419d6ab7458ea4870e578b5e60 2108 prottest_3.4.2+dfsg-7.dsc c0f569d65cd6230ca6208337e65716821f119a3ab6f3f1f13498f2f922c1f02b 7104 prottest_3.4.2+dfsg-7.debian.tar.xz 3d125c145f97bee66b963e5c15eb05123424c74e002ce6e9f835fe11faaa3c61 10789 prottest_3.4.2+dfsg-7_amd64.buildinfo Files: f4d05f38249ad121922e66ad65f02ea9 2108 science optional prottest_3.4.2+dfsg-7.dsc 401e709230e319ebaf83bb6e4a244fc2 7104 science optional prottest_3.4.2+dfsg-7.debian.tar.xz 20f77b1202a83c6bb172b6b9c25632de 10789 science optional prottest_3.4.2+dfsg-7_amd64.buildinfo -----BEGIN PGP SIGNATURE----- iQJGBAEBCgAwFiEEPpmlJvXcwMu/HO6mALrnSzQzafEFAmF79rISHG5pbGVzaEBk ZWJpYW4ub3JnAAoJEAC650s0M2nxw70P/0qJaJOIHQWugtPbVxxnc9IPsL1RzohH aBBHkvro7pGDMPFqIBSSwtPuJS3A3CtxFlvA/012SNPCnq7mwRIc0sUgLdD95jgU hzZtfJP1Fv09sONicFZ6S3wm9JnCULESQSRzwrR6QvUp1lG4sB/yFhqbWuoGehNH eh4EpN/YFBf7Sv5h1hLKa2cGvC2qpGQL7kd8vTEvznC7VqlOUAqFAlsnQkreaDLI ym+JAFffl7KFwT0lLyzVVSx2j6Oi/ktpDRkC0q5yhdzwqxBrfpk/S+tY41E5eqiW 27s2a9ibH0CoKJZ3iS0BWbWAf82Kb9sTlkUX/DZX6GcJGABmhtDWPVYKrKX+WNjw sIEwF8daAbBmwuv69ifEOI5rC1I8tzSlGMEqtGa+M1hLFcovddy0stHi98MNhLlw 97OjewKKG94Zq0Kh21hTzqdiwULLsAr6bzqOMxK2qcvK0cugZv9wHHu4rifFe44X tvMEd2bJi+BneOv8bgS5fO+giKMuinShSIfPHI7xxhhSeSEDRDhxCvFUdlGUtsV1 CD4Z1kcG9HOJF+KaLKEfS1D0uByickrRowcpzkbtUG7dln2+R7QyD+Q4b+jAHhbi 1USAIwd/Wh1DHl9sWuxjZucJja+56H5JfknAjbUMkkUzsuX1QiyExA12BSvgfHeK J7IpltZFAqFN =JbGm -----END PGP SIGNATURE-----
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