Nilesh Patra pushed to branch master at Debian Med / prottest
Commits: fa47ffe0 by Nilesh Patra at 2021-10-29T18:05:12+05:30 Add patch to fix autopkgtests (Closes: #997886) - - - - - 7c4fb987 by Nilesh Patra at 2021-10-29T18:06:59+05:30 d/t/run-unit-tests: Remove un-necessary template - - - - - 37b0d72e by Nilesh Patra at 2021-10-29T18:06:59+05:30 Upload to unstable - - - - - 4 changed files: - debian/changelog - + debian/patches/read-stats-file.patch - debian/patches/series - debian/tests/run-unit-test Changes: ===================================== debian/changelog ===================================== @@ -1,3 +1,10 @@ +prottest (3.4.2+dfsg-7) unstable; urgency=medium + + * Team Upload. + * Add patch to fix autopkgtests (Closes: #997886) + + -- Nilesh Patra <[email protected]> Fri, 29 Oct 2021 18:05:16 +0530 + prottest (3.4.2+dfsg-6) unstable; urgency=medium * Re-activate real test suggested by Tassia ===================================== debian/patches/read-stats-file.patch ===================================== @@ -0,0 +1,24 @@ +Description: properly resolve stats and tree files, add missing dot +Author: Nilesh Patra <[email protected]> +Bug-Debian: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=997886 +Last-Update: 2021-10-29 +--- a/src/main/java/es/uvigo/darwin/prottest/exe/PhyMLv3AminoAcidRunEstimator.java ++++ b/src/main/java/es/uvigo/darwin/prottest/exe/PhyMLv3AminoAcidRunEstimator.java +@@ -378,7 +378,7 @@ + if (!(statsFile.exists() && statsFile.canRead())) + { + /* try with txt suffix */ +- statsFile = new File(workAlignment + STATS_FILE_SUFFIX + "txt"); ++ statsFile = new File(workAlignment + STATS_FILE_SUFFIX + ".txt"); + if (!(statsFile.exists() && statsFile.canRead())) + throw new StatsFileFormatException("PhyML", + "Stats file does not exist. Please check if PhyML is working."); +@@ -389,7 +389,7 @@ + if (!(treeFile.exists() && treeFile.canRead())) + { + /* try with txt suffix */ +- treeFile = new File(workAlignment + TREE_FILE_SUFFIX + "txt"); ++ treeFile = new File(workAlignment + TREE_FILE_SUFFIX + ".txt"); + if (!(treeFile.exists() && treeFile.canRead())) + throw new TreeFormatException( + "Tree file does not exist. Please check if PhyML is working correctly."); ===================================== debian/patches/series ===================================== @@ -1,3 +1,4 @@ use_debian_packaged_phyml.patch build.patch alter-import.patch +read-stats-file.patch ===================================== debian/tests/run-unit-test ===================================== @@ -20,21 +20,6 @@ cd $AUTOPKGTEST_TMP cp -a /usr/share/doc/${pkg}/examples/* . -# Run simulations with demo models -# Unfortunately there are issues with the Debian packaged phyml as described here -# https://github.com/ddarriba/prottest3/issues/12 -# -# 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 : Sun Feb 21 14:44:46 UTC 2021 -# Runtime: 0h:02:29 -# -# -# Lk not initialized - prottest -i COX2_PF0016/alignment -t COX2_PF0016/tree -S 0 -all-distributions -F -AIC -BIC -tc 0.5 prottest -i Ribosomal_L5_PF00673/alignment -t Ribosomal_L5_PF00673/tree -S 0 -all-distributions -F -AIC -BIC -tc 0.5 View it on GitLab: https://salsa.debian.org/med-team/prottest/-/compare/0078b6b6f9c161ca9fe2089b128794001ca1cc6b...37b0d72eff823911de381fc822af716e07dd9ad3 -- View it on GitLab: https://salsa.debian.org/med-team/prottest/-/compare/0078b6b6f9c161ca9fe2089b128794001ca1cc6b...37b0d72eff823911de381fc822af716e07dd9ad3 You're receiving this email because of your account on salsa.debian.org.
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