Andreas Tille pushed to branch master at Debian Med / mapdamage
Commits: 4ae67b6e by Andreas Tille at 2018-12-08T21:38:12Z New upstream version 2.0.9+dfsg - - - - - a80a5d97 by Andreas Tille at 2018-12-08T21:38:12Z Update upstream source from tag 'upstream/2.0.9+dfsg' Update to upstream version '2.0.9+dfsg' with Debian dir b6a5d94ab06db27eb4838fb7bae3b676cb1aade7 - - - - - d58d9605 by Andreas Tille at 2018-12-08T21:38:12Z New upstream version - - - - - 3c964fc6 by Andreas Tille at 2018-12-08T21:38:50Z Remove trailing whitespace in debian/changelog - - - - - 805f45f8 by Andreas Tille at 2018-12-08T21:38:50Z Remove trailing whitespace in debian/rules - - - - - 3c484663 by Andreas Tille at 2018-12-08T21:41:57Z Upload to unstable - - - - - 4 changed files: - debian/changelog - debian/rules - mapdamage/Rscripts/stats/function.R - mapdamage/seq.py Changes: ===================================== debian/changelog ===================================== @@ -1,3 +1,11 @@ +mapdamage (2.0.9+dfsg-1) unstable; urgency=medium + + * New upstream version + * Remove trailing whitespace in debian/changelog + * Remove trailing whitespace in debian/rules + + -- Andreas Tille <[email protected]> Sat, 08 Dec 2018 22:38:50 +0100 + mapdamage (2.0.8+dfsg-2) unstable; urgency=medium [ Steffen Moeller ] @@ -39,7 +47,7 @@ mapdamage (2.0.6+dfsg-2) unstable; urgency=medium r-cran-rcppgsl package * Edit path to seqtk in composition.py Closes: #859090 - * Fix typo in tests/control + * Fix typo in tests/control * Add patch to fix quantile call to remove NA and NaNs * Add dependency providing liblapack.so and libblas.so Closes: #859091 @@ -47,7 +55,7 @@ mapdamage (2.0.6+dfsg-2) unstable; urgency=medium * Add information how to check R libraries and what to do in case of errors to README.test * Provide tests for examples from documentation - Closes: #848326 + Closes: #848326 * Fixed typo in README.test -- Nadiya Sitdykova <[email protected]> Thu, 23 Mar 2017 21:34:41 -0700 ===================================== debian/rules ===================================== @@ -17,4 +17,4 @@ override_dh_install: dh_install mv `find debian -name rescale_test.py` $(TESTDIR) sed -i 's/^import rescale/from mapdamage &/' $(TESTDIR)/rescale_test.py - + ===================================== mapdamage/Rscripts/stats/function.R ===================================== @@ -145,7 +145,7 @@ seqProbVecLambda <- function(lambda,lambda_disp,m,fo_only=NA,re_only=NA){ #The following is an MC simulation code to mimic the #nick frequency part in the model from Philip -seqProbVecNuWithLengths<- cxxfunction( signature( +seqProbVecNuWithLengths<- cxxfunction(methods::signature( I_la="numeric", I_la_disp="numeric", I_nu="numeric", @@ -270,7 +270,7 @@ logLikFunOneBaseSlow <- function(Gen,S,Theta,deltad,deltas,laVec,nuVec,m,lin){ #The same logic as in logLikFunOneBaseSlow except using a compiled code #to do the hard work -logLikFunOneBaseFast <- cxxfunction(signature( +logLikFunOneBaseFast <- cxxfunction(methods::signature( I_Gen="numeric", I_S="numeric", I_Theta="numeric", ===================================== mapdamage/seq.py ===================================== @@ -63,6 +63,12 @@ def read_fasta_index(filename): print_err("Column 2 in FASTA index did not contain a number, found '%s':" % ref[1], filename, line) return None + if not fai: + sys.stderr.write("Error: Index for %r does contain any sequences.\n" % (filename,)) + sys.stderr.write(" Please ensure that FASTA file is valid, and\n") + sys.stderr.write(" re-index file using 'samtool faidx'.\n") + return None + return fai View it on GitLab: https://salsa.debian.org/med-team/mapdamage/compare/8ad2d6e981d61f0a84c0889c57caf2c414d79978...3c484663e67fa5595048daa173d0ec1e88269a11 -- View it on GitLab: https://salsa.debian.org/med-team/mapdamage/compare/8ad2d6e981d61f0a84c0889c57caf2c414d79978...3c484663e67fa5595048daa173d0ec1e88269a11 You're receiving this email because of your account on salsa.debian.org.
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