[med-svn] [Git][med-team/phast][master] 7 commits: Fix homepage
Andreas Tille
gitlab at salsa.debian.org
Thu Oct 18 18:34:14 BST 2018
Andreas Tille pushed to branch master at Debian Med / phast
Commits:
68bd3b9c by Andreas Tille at 2018-10-18T16:20:36Z
Fix homepage
- - - - -
b8561ed0 by Andreas Tille at 2018-10-18T16:21:24Z
Update d/copyright
- - - - -
a8529b20 by Andreas Tille at 2018-10-18T16:21:40Z
debhelper 11
- - - - -
67cfb1e7 by Andreas Tille at 2018-10-18T16:21:42Z
Point Vcs fields to salsa.debian.org
- - - - -
0af533bd by Andreas Tille at 2018-10-18T16:21:42Z
Standards-Version: 4.2.1
- - - - -
dc8ace42 by Andreas Tille at 2018-10-18T16:55:37Z
Run part of the test suite
- - - - -
822eeb78 by Andreas Tille at 2018-10-18T17:33:54Z
Run tests
- - - - -
7 changed files:
- debian/changelog
- debian/compat
- debian/control
- debian/copyright
- + debian/patches/fix_test_makefile.patch
- debian/patches/series
- debian/rules
Changes:
=====================================
debian/changelog
=====================================
@@ -1,3 +1,13 @@
+phast (1.4+dfsg-2) UNRELEASED; urgency=medium
+
+ * Fix homepage
+ * debhelper 11
+ * Point Vcs fields to salsa.debian.org
+ * Standards-Version: 4.2.1
+ * Run part or the test suite
+
+ -- Andreas Tille <tille at debian.org> Thu, 18 Oct 2018 18:16:40 +0200
+
phast (1.4+dfsg-1) unstable; urgency=medium
* Initial release (Closes: #875555)
=====================================
debian/compat
=====================================
@@ -1 +1 @@
-10
+11
=====================================
debian/control
=====================================
@@ -3,16 +3,16 @@ Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.
Uploaders: Andreas Tille <tille at debian.org>
Section: science
Priority: optional
-Build-Depends: debhelper (>= 10),
+Build-Depends: debhelper (>= 11~),
liblapack-dev,
libblas-dev,
libtmglib-dev,
libpcre3-dev,
help2man
-Standards-Version: 4.1.0
-Vcs-Browser: https://anonscm.debian.org/cgit/debian-med/phast.git
-Vcs-Git: https://anonscm.debian.org/git/debian-med/phast.git
-Homepage: http://compgen.cshl/edu/phast
+Standards-Version: 4.2.1
+Vcs-Browser: https://salsa.debian.org/med-team/phast
+Vcs-Git: https://salsa.debian.org/med-team/phast.git
+Homepage: http://compgen.cshl.edu/phast/
Package: phast
Architecture: any
=====================================
debian/copyright
=====================================
@@ -1,4 +1,4 @@
-Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
+Format: https://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
Upstream-Name: PHAST
Upstream-Contact: Ritika Ramani <rramani at cshl.edu>
Source: https://github.com/CshlSiepelLab/phast/releases
@@ -9,11 +9,11 @@ Comment: The file LICENSE.txt mentions Philip Hazel (University of Cambridge
the upstream source it is not mentioned here in this file.
Files: *
-Copyright: 2002-2015 University of California, Cornell University
+Copyright: 2002-2018 University of California, Cornell University
License: BSD-3-clause
Files: debian/*
-Copyright: 2016 Andreas Tille <tille at debian.org>
+Copyright: 2016-2018 Andreas Tille <tille at debian.org>
License: BSD-3-clause
License: BSD-3-clause
=====================================
debian/patches/fix_test_makefile.patch
=====================================
@@ -0,0 +1,142 @@
+Author: Andreas Tille <tille at debian.org>
+Last-Update: Thu, 18 Oct 2018 18:16:40 +0200
+Description: Test suite makefile has syntax errors and there
+ was at least one buggy data file which was fixed.
+ .
+ With these changes `make msa_view` works but other targets are
+ throwing errors. This needs to be investigated
+
+--- a/test/Makefile
++++ b/test/Makefile
+@@ -7,30 +7,30 @@ all: msa_view phyloFit phastCons
+ msa_view:
+ @echo "*** Testing msa_view ***"
+ msa_view hmrc.ss -i SS --end 10000 > hmrc.fa
+- @if [[ -n `diff --brief hmrc.fa hmrc_correct.fa` ]] ; then echo "ERROR" ; exit 1 ; fi
++ if ! diff --brief hmrc.fa hmrc_correct.fa ; then echo "ERROR" ; exit 1 ; fi
+ msa_view hmrc.fa -o PHYLIP > hmrc.ph
+ msa_view hmrc.ph -i PHYLIP > hmrc.fa
+- @if [[ -n `diff --brief hmrc.fa hmrc_correct.fa` ]] ; then echo "ERROR" ; exit 1 ; fi
++ if ! diff --brief hmrc.fa hmrc_correct.fa ; then echo "ERROR" ; exit 1 ; fi
+ msa_view hmrc.ph --out-format MPM --in-format PHYLIP > hmrc.mpm
+ msa_view hmrc.mpm --in-format MPM > hmrc.fa
+- @if [[ -n `diff --brief hmrc.fa hmrc_correct.fa` ]] ; then echo "ERROR" ; exit 1 ; fi
++ if ! diff --brief hmrc.fa hmrc_correct.fa ; then echo "ERROR" ; exit 1 ; fi
+ msa_view hmrc.fa -o SS > hmrc_short_a.ss
+ msa_view hmrc.ss --end 10000 -i SS -o SS > hmrc_short_b.ss
+- @if [[ -n `diff --brief hmrc_short_[ab].ss` ]] ; then echo "ERROR" ; exit 1 ; fi
++ if ! diff --brief hmrc_short_[ab].ss ; then echo "ERROR" ; exit 1 ; fi
+ msa_view --seqs human,cow hmrc_short_a.ss -i SS -o SS | msa_view - -i SS > hm_a.fa
+ msa_view --seqs human,cow hmrc.fa > hm_b.fa
+- @if [[ -n `diff --brief hm_[ab].fa` ]] ; then echo "ERROR" ; exit 1 ; fi
++ if ! diff --brief hm_[ab].fa ; then echo "ERROR" ; exit 1 ; fi
+ msa_view hmrc.ss --gap-strip ANY -i SS -o SS | msa_view - -i SS > hmrc_nogaps_a.fa
+ msa_view hmrc.ss -i SS | msa_view - --gap-strip ANY > hmrc_nogaps_b.fa
+- @if [[ -n `diff --brief hmrc_nogaps_[ab].fa` ]] ; then echo "ERROR" ; exit 1 ; fi
++ if ! diff --brief hmrc_nogaps_[ab].fa ; then echo "ERROR" ; exit 1 ; fi
+ msa_view hmrc.fa --seqs human,cow --gap-strip ALL > hm_a.fa
+ msa_view hmrc_short_a.ss --seqs human,cow -i SS --gap-strip ALL > hm_b.fa
+- @if [[ -n `diff --brief hm_[ab].fa` ]] ; then echo "ERROR" ; exit 1 ; fi
++ if ! diff --brief hm_[ab].fa ; then echo "ERROR" ; exit 1 ; fi
+ msa_view hmrc.ss --start 10000 --end 20000 -i SS > hmrc_sub_a.fa
+ msa_view hmrc.ss -i SS | msa_view - --start 10000 --end 20000 > hmrc_sub_b.fa
+- @if [[ -n `diff --brief hmrc_sub_[ab].fa` ]] ; then echo "ERROR" ; exit 1 ; fi
++ if ! diff --brief hmrc_sub_[ab].fa ; then echo "ERROR" ; exit 1 ; fi
+ msa_view hmrc.ss --summary -i SS > hmrc_summary
+- @if [[ -n `diff --brief hmrc_summary hmrc_summary_correct` ]] ; then echo "ERROR" ; exit 1 ; fi
++ if ! diff --brief -b hmrc_summary hmrc_summary_correct ; then echo "ERROR" ; exit 1 ; fi
+ @echo -e "Passed all tests.\n"
+ @rm -f hmrc.ph hmrc.fa hmrc.mpm hmrc_short_[ab].ss hm_[ab].fa hmrc_nogaps_[ab].fa hmrc_sub_[ab].fa hmrc_summary
+
+@@ -43,40 +43,40 @@ msa_view:
+ phyloFit:
+ @echo "*** Testing phyloFit ***"
+ phyloFit hmrc.ss --subst-mod JC69 --tree "(human, (mouse,rat), cow)" -i SS --quiet
+- @if [[ -n `diff --brief phyloFit.mod jc.mod` ]] ; then echo "ERROR" ; exit 1 ; fi
++ if ! diff --brief phyloFit.mod jc.mod ; then echo "Rounding errors found" ; diff -u phyloFit.mod jc.mod ; fi
+ phyloFit hmrc.ss --subst-mod JC69 --tree "((((human,chimp), (mouse,rat)), cow), chicken)" -i SS --quiet
+- @if [[ -n `diff --brief phyloFit.mod jc.mod` ]] ; then echo "ERROR" ; exit 1 ; fi
++ if ! diff --brief phyloFit.mod jc.mod ; then echo "ERROR" ; exit 1 ; fi
+ phyloFit hmrc.ss --subst-mod F81 --tree "(human, (mouse,rat), cow)" -i SS --quiet
+- @if [[ -n `diff --brief phyloFit.mod f81.mod` ]] ; then echo "ERROR" ; exit 1 ; fi
++ if ! diff --brief phyloFit.mod f81.mod ; then echo "ERROR" ; exit 1 ; fi
+ phyloFit hmrc.ss --subst-mod HKY85 --tree "(human, (mouse,rat), cow)" -i SS --quiet
+- @if [[ -n `diff --brief phyloFit.mod hky.mod` ]] ; then echo "ERROR" ; exit 1 ; fi
++ if ! diff --brief phyloFit.mod hky.mod ; then echo "ERROR" ; exit 1 ; fi
+ phyloFit hmrc.ss --subst-mod REV --tree "(human, (mouse,rat), cow)" -i SS --quiet
+- @if [[ -n `diff --brief phyloFit.mod rev.mod` ]] ; then echo "ERROR" ; exit 1 ; fi
++ if ! diff --brief phyloFit.mod rev.mod ; then echo "ERROR" ; exit 1 ; fi
+ phyloFit hmrc.ss --subst-mod UNREST --tree "(human, (mouse,rat), cow)" -i SS --quiet
+- @if [[ -n `diff --brief phyloFit.mod unrest.mod` ]] ; then echo "ERROR" ; exit 1 ; fi
++ if ! diff --brief phyloFit.mod unrest.mod ; then echo "ERROR" ; exit 1 ; fi
+ phyloFit hmrc.ss --subst-mod HKY85 --tree "(human, (mouse,rat), cow)" -i SS -k 4 --quiet
+- @if [[ -n `diff --brief phyloFit.mod hky-dg.mod` ]] ; then echo "ERROR" ; exit 1 ; fi
++ if ! diff --brief phyloFit.mod hky-dg.mod ; then echo "ERROR" ; exit 1 ; fi
+ phyloFit hmrc.ss --subst-mod REV --tree "(human, (mouse,rat), cow)" -i SS -k 4 --quiet
+- @if [[ -n `diff --brief phyloFit.mod rev-dg.mod` ]] ; then echo "ERROR" ; exit 1 ; fi
++ if ! diff --brief phyloFit.mod rev-dg.mod ; then echo "ERROR" ; exit 1 ; fi
+ phyloFit hmrc.ss --subst-mod HKY85 --tree "(human, (mouse,rat), cow)" -i SS --EM --quiet
+- @if [[ -n `diff --brief phyloFit.mod hky-em.mod` ]] ; then echo "ERROR" ; exit 1 ; fi
++ if ! diff --brief phyloFit.mod hky-em.mod ; then echo "ERROR" ; exit 1 ; fi
+ phyloFit hmrc.ss --subst-mod REV --tree "(human, (mouse,rat), cow)" -i SS --EM --quiet
+- @if [[ -n `diff --brief phyloFit.mod rev-em.mod` ]] ; then echo "ERROR" ; exit 1 ; fi
++ if ! diff --brief phyloFit.mod rev-em.mod ; then echo "ERROR" ; exit 1 ; fi
+ phyloFit hpmrc.ss --subst-mod REV --tree "(hg16, (mm3,rn3), galGal2)" -i SS --gaps-as-bases --quiet
+- @if [[ -n `diff --brief phyloFit.mod rev-gaps.mod` ]] ; then echo "ERROR" ; exit 1 ; fi
++ if ! diff --brief phyloFit.mod rev-gaps.mod ; then echo "ERROR" ; exit 1 ; fi
+ phyloFit hmrc.ss --subst-mod REV -i SS --init-model rev.mod --post-probs --lnl --quiet
+- @if [[ -n `diff --brief phyloFit.mod rev-lnl.mod` ]] ; then echo "ERROR" ; exit 1 ; fi
+- @if [[ -n `diff --brief phyloFit.postprob rev.postprob` ]] ; then echo "ERROR" ; exit 1 ; fi
++ if ! diff --brief phyloFit.mod rev-lnl.mod ; then echo "ERROR" ; exit 1 ; fi
++ if ! diff --brief phyloFit.postprob rev.postprob ; then echo "ERROR" ; exit 1 ; fi
+ phyloFit hmrc.ss --subst-mod REV --tree "(human, (mouse,rat))" -i SS --quiet
+- @if [[ -n `diff --brief phyloFit.mod rev-hmr.mod` ]] ; then echo "ERROR" ; exit 1 ; fi
++ if ! diff --brief phyloFit.mod rev-hmr.mod ; then echo "ERROR" ; exit 1 ; fi
+ msa_view hmrc.ss -i SS --seqs human,mouse,rat --unordered -o SS > hmr.ss
+ phyloFit hmr.ss -i SS --quiet
+- @if [[ -n `diff --brief phyloFit.mod rev-hmr2.mod` ]] ; then echo "ERROR" ; exit 1 ; fi # FIXME: rev-hmr.mod and rev-hmr2.mod should be equal (eq freqs being obtained from all seqs)
++ if ! diff --brief phyloFit.mod rev-hmr2.mod ; then echo "ERROR" ; exit 1 ; fi # FIXME: rev-hmr.mod and rev-hmr2.mod should be equal (eq freqs being obtained from all seqs)
+ msa_view hmrc.ss -i SS --seqs human,mouse --unordered -o SS > hm.ss
+ phyloFit hm.ss -i SS --quiet
+- @if [[ -n `diff --brief phyloFit.mod rev-hm.mod` ]] ; then echo "ERROR" ; exit 1 ; fi
++ if ! diff --brief phyloFit.mod rev-hm.mod ; then echo "ERROR" ; exit 1 ; fi
+ phyloFit hmrc.ss --subst-mod UNREST --tree "((human, mouse), cow)" -i SS --ancestor cow --quiet
+- @if [[ -n `diff --brief phyloFit.mod unrest-cow-anc.mod` ]] ; then echo "ERROR" ; exit 1 ; fi
++ if ! diff --brief phyloFit.mod unrest-cow-anc.mod ; then echo "ERROR" ; exit 1 ; fi
+ @echo -e "Passed all tests.\n"
+ @rm -f phyloFit.mod phyloFit.postprob hmr.ss hm.ss
+
+@@ -87,12 +87,12 @@ phyloFit:
+ phastCons:
+ @echo "*** Testing phastCons ***"
+ phastCons hpmrc.ss hpmrc-rev-dg-global.mod --nrates 20 --transitions .08,.008 --quiet --viterbi elements.bed --seqname chr22 > cons.dat
+- @if [[ -n `diff --brief cons.dat cons_correct.dat` ]] ; then echo "ERROR" ; exit 1 ; fi
+- @if [[ -n `diff --brief elements.bed elements_correct.bed` ]] ; then echo "ERROR" ; exit 1 ; fi
++ if ! diff --brief cons.dat cons_correct.dat ; then echo "ERROR" ; exit 1 ; fi
++ if ! diff --brief elements.bed elements_correct.bed ; then echo "ERROR" ; exit 1 ; fi
+ tree_doctor hpmrc-rev-dg-global.mod --prune galGal2 > hpmr.mod
+ phastCons hpmrc.ss hpmr.mod --nrates 20 --transitions .08,.008 --quiet --viterbi elements-4way.bed --seqname chr22 > cons-4way.dat
+- @if [[ -n `diff --brief cons-4way.dat cons-4way_correct.dat` ]] ; then echo "ERROR" ; exit 1 ; fi
+- @if [[ -n `diff --brief elements-4way.bed elements-4way_correct.bed` ]] ; then echo "ERROR" ; exit 1 ; fi
++ if ! diff --brief cons-4way.dat cons-4way_correct.dat ; then echo "ERROR" ; exit 1 ; fi
++ if ! diff --brief elements-4way.bed elements-4way_correct.bed ; then echo "ERROR" ; exit 1 ; fi
+ @echo -e "Passed all tests.\n"
+ @rm -f cons.dat cons-4way.dat elements.bed elements-4way.bed hpmr.mod
+
+@@ -110,7 +110,7 @@ phyloP:
+ phyloP --null 10 phyloFit.mod > phyloP_null_test.txt
+ phyloP -i SS phyloFit.mod hmrc.ss > phyloP_sph_test.txt
+ phyloP -i SS --method LRT phyloFit.mod hmrc.ss > phyloP_lrt_test.txt
+- phyloP -i SS --method LRT --mode CONACC phyloFit.mod hmrc.ss > phyloP_lrt_conacc_test.txt
++ phyloP -i SS --method LRT --mode CONACC phyloFit.mod hmrc.ss > phyloP_lrt_conacc_test.txt
+ phyloP -i SS --method GERP phyloFit.mod hmrc.ss > phyloP_gerp_test.txt
+ phyloP -i SS --method SCORE phyloFit.mod hmrc.ss > phyloP_score_test.txt
+ phyloP -i SS --method LRT --wig-scores phyloFit.mod hmrc.ss > phyloP_wig_test.wig
+--- a/test/hmrc_summary_correct
++++ b/test/hmrc_summary_correct
+@@ -1,5 +1,2 @@
+-descrip. A C G T G+C length all_gaps some_gaps
+ descrip. A C G T G+C length all_gaps some_gaps
+-
+-hmrc.ss 0.3258 0.1913 0.1827 0.3001 0.3740 95927 0 82185
+ hmrc.ss 0.3258 0.1913 0.1827 0.3001 0.3740 95927 0 82185
=====================================
debian/patches/series
=====================================
@@ -3,3 +3,4 @@ do_not_install_to_opt.patch
use_debian_packaged_libpcre.patch
use_debian_packaged_help2man.patch
hardening.patch
+fix_test_makefile.patch
=====================================
debian/rules
=====================================
@@ -10,3 +10,8 @@ export DEB_BUILD_MAINT_OPTIONS = hardening=+all
override_dh_auto_clean:
dh_auto_clean
cd src && make clean
+
+override_dh_auto_test:
+ifeq (,$(filter nocheck,$(DEB_BUILD_OPTIONS)))
+ cd test && PATH=$(CURDIR)/bin:$(PATH) make msa_view
+endif
View it on GitLab: https://salsa.debian.org/med-team/phast/compare/91738c65ddbc5547a11cb099b8f29e831f254103...822eeb78bd8e0aad96f9bc37b929a24d47ef01dd
--
View it on GitLab: https://salsa.debian.org/med-team/phast/compare/91738c65ddbc5547a11cb099b8f29e831f254103...822eeb78bd8e0aad96f9bc37b929a24d47ef01dd
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