This is an automated email from the git hooks/post-receive script. tille pushed a commit to branch master in repository psortb.
commit accaccd8861fee14f49dcc04013134f501f60d85 Author: Andreas Tille <[email protected]> Date: Wed Apr 12 21:00:37 2017 +0200 Adapt to hmmer2 interface --- debian/control | 2 +- debian/patches/fix_hmmer_interface.patch | 20 ++++++++++++++++++++ debian/patches/series | 1 + 3 files changed, 22 insertions(+), 1 deletion(-) diff --git a/debian/control b/debian/control index 923a885..0398ed8 100644 --- a/debian/control +++ b/debian/control @@ -6,7 +6,7 @@ Priority: optional Build-Depends: debhelper (>= 10), bioperl, ncbi-blast+-legacy, - libsquid-dev, + libsquid-dev (>= 1.9g+cvs20050121-9~), libhmmer2-dev, pkg-config Standards-Version: 3.9.8 diff --git a/debian/patches/fix_hmmer_interface.patch b/debian/patches/fix_hmmer_interface.patch new file mode 100644 index 0000000..6b65eb7 --- /dev/null +++ b/debian/patches/fix_hmmer_interface.patch @@ -0,0 +1,20 @@ +--- a/algorithm-hmm/hmm-binding.cpp ++++ b/algorithm-hmm/hmm-binding.cpp +@@ -71,7 +71,7 @@ int HMM::load(char *filename) { + if(strlen(filename) == 0) return -1; + + // Load the model from the specified file. +- if((hmmfp = HMMFileOpen(filename, "HMMERDB")) == NULL) return -1; ++ if((hmmfp = HMMFileOpen(filename, (char *)"HMMERDB")) == NULL) return -1; + + if(! HMMFileRead(hmmfp, &tmp_model)) { + HMMFileClose(hmmfp); +@@ -107,7 +107,7 @@ HMMReport *HMM::search(char *seq) { + if((model == NULL) ||(seq == NULL) || (!(seqlen = strlen(seq)))) return NULL; + + // Convert the sequence to the format the HMMER library expects. +- dseq = DigitizeSequence(seq, seqlen); ++ dseq = DigitizeSequence((char *)seq, seqlen); + + // Calculate the raw scores for the sequence. + if (P7ViterbiSize(seqlen, model->M) <= RAMLIMIT) diff --git a/debian/patches/series b/debian/patches/series index e334345..86dc063 100644 --- a/debian/patches/series +++ b/debian/patches/series @@ -1 +1,2 @@ biosquid_includes.patch +fix_hmmer_interface.patch -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/psortb.git _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
