Andreas Tille pushed to branch master at Debian Med / prottest
Commits: fbbbfaa8 by Andreas Tille at 2021-02-21T15:52:35+01:00 Unfortunately we can only do a superficial for the moment - - - - - 4fb1f613 by Andreas Tille at 2021-02-21T15:58:15+01:00 Upload to unstable - - - - - 3 changed files: - debian/changelog - debian/tests/control - debian/tests/run-unit-test Changes: ===================================== debian/changelog ===================================== @@ -1,4 +1,4 @@ -prottest (3.4.2+dfsg-5) UNRELEASED; urgency=medium +prottest (3.4.2+dfsg-5) unstable; urgency=medium * Team upload @@ -8,6 +8,9 @@ prottest (3.4.2+dfsg-5) UNRELEASED; urgency=medium [ Tassia Camoes Araujo ] * Add functional test + Unfortunately we can only do a superficial for the moment until there + will be a way to run with phyml provided in Debian (see + https://github.com/ddarriba/prottest3/issues/12 ) [ Pierre Gruet ] * Adding libbetter-appframework-java in runtime dependencies and its ===================================== debian/tests/control ===================================== @@ -1,3 +1,3 @@ Tests: run-unit-test Depends: @ -Restrictions: allow-stderr +Restrictions: allow-stderr, superficial ===================================== debian/tests/run-unit-test ===================================== @@ -21,7 +21,22 @@ cd $AUTOPKGTEST_TMP cp -a /usr/share/doc/${pkg}/examples/* . # Run simulations with demo models -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 +# 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 + +# For the moment we'll leave the trivial test +#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 echo "PASS" View it on GitLab: https://salsa.debian.org/med-team/prottest/-/compare/006ef64028fe70f877338d448b31d83bd46581ed...4fb1f6138726ee947b043fac7f156cd005d5f582 -- View it on GitLab: https://salsa.debian.org/med-team/prottest/-/compare/006ef64028fe70f877338d448b31d83bd46581ed...4fb1f6138726ee947b043fac7f156cd005d5f582 You're receiving this email because of your account on salsa.debian.org.
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