[med-svn] [Git][med-team/prime-phylo][master] 5 commits: gcc-14.patch: fix improper use of close(2) by using fclose(3).
Étienne Mollier (@emollier)
gitlab at salsa.debian.org
Wed Aug 7 15:57:11 BST 2024
Étienne Mollier pushed to branch master at Debian Med / prime-phylo
Commits:
ac2e6e0e by Étienne Mollier at 2024-08-07T16:43:16+02:00
gcc-14.patch: fix improper use of close(2) by using fclose(3).
Closes: #1075397
- - - - -
19e672ac by Étienne Mollier at 2024-08-07T16:50:10+02:00
typos.patch: new: fix multiple typos caught by lintian.
- - - - -
2a86e8ad by Étienne Mollier at 2024-08-07T16:51:01+02:00
d/control: declare compliance to standards version 4.7.0.
- - - - -
4fa83607 by Étienne Mollier at 2024-08-07T16:55:17+02:00
d/lintian-overrides: new: flag false positive typos.
- - - - -
53e0510b by Étienne Mollier at 2024-08-07T16:55:59+02:00
d/control: add myself to uploaders.
- - - - -
5 changed files:
- debian/control
- + debian/lintian-overrides
- + debian/patches/gcc-14.patch
- debian/patches/series
- + debian/patches/typos.patch
Changes:
=====================================
debian/control
=====================================
@@ -1,7 +1,8 @@
Source: prime-phylo
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
Uploaders: Erik Sjolund <erik.sjolund at gmail.com>,
- Andreas Tille <tille at debian.org>
+ Andreas Tille <tille at debian.org>,
+ Étienne Mollier <emollier at debian.org>
Section: science
Priority: optional
Build-Depends: debhelper-compat (= 13),
@@ -18,7 +19,7 @@ Build-Depends: debhelper-compat (= 13),
libboost-mpi-dev,
libboost-serialization-dev,
zlib1g-dev
-Standards-Version: 4.5.1
+Standards-Version: 4.7.0
Vcs-Browser: https://salsa.debian.org/med-team/prime-phylo
Vcs-Git: https://salsa.debian.org/med-team/prime-phylo.git
Homepage: http://prime.sbc.su.se
=====================================
debian/lintian-overrides
=====================================
@@ -0,0 +1,6 @@
+# These spelling errors seem to stem from mangled strings within object
+# files and are not reflected in any way in the source code, so are most
+# likely false positives.
+spelling-error-in-binary WIh With [usr/lib/prime-phylo/libprime-phylo.so]
+spelling-error-in-binary defaul default [usr/bin/primeDTLSR]
+spelling-error-in-binary ofthe of the [usr/bin/chainsaw]
=====================================
debian/patches/gcc-14.patch
=====================================
@@ -0,0 +1,23 @@
+Description: fix file closure.
+ The initial code attempts to close a FILE pointer using close(2) which
+ is the bare system call expecting a file descriptor. The correct
+ function to call on such variable would be glibc's fclose(3). This was
+ caught by the gcc bump to version 14.
+
+Author: Étienne Mollier <emollier at debian.org>
+Bug-Debian: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1075397
+Forwarded: no
+Last-Update: 2024-08-07
+---
+This patch header follows DEP-3: http://dep.debian.net/deps/dep3/
+--- prime-phylo.orig/src/cxx/libraries/prime/NHXparse.y
++++ prime-phylo/src/cxx/libraries/prime/NHXparse.y
+@@ -351,7 +351,7 @@
+
+ /* Cleanup */
+ if (f != NULL) {
+- close(f);
++ fclose(f);
+ yytree_in = stdin;
+ }
+
=====================================
debian/patches/series
=====================================
@@ -4,3 +4,5 @@ fix-gcc-8.patch
0003-Fix-build-with-Boost-1.67.patch
0004-fix-gcc10-build.patch
fix-ftbfs-with-gcc13.patch
+gcc-14.patch
+typos.patch
=====================================
debian/patches/typos.patch
=====================================
@@ -0,0 +1,99 @@
+Description: fix multiple typos caught by lintian.
+Author: Étienne Mollier <emollier at debian.org>
+Forwarded: no
+Last-Update: 2024-08-07
+---
+This patch header follows DEP-3: http://dep.debian.net/deps/dep3/
+--- prime-phylo.orig/src/cxx/applications/primeCT/primect.cc
++++ prime-phylo/src/cxx/applications/primeCT/primect.cc
+@@ -858,7 +858,7 @@
+ * @param vertices A set of virtual vertices to sift. Assumes count has already been calculated.
+ * @param hp_vertices Storage for the found vertices upon return.
+ * @param threshold_count Posterior threshold. Note that this is a number reperesenting a count
+- * of states a vertex must have occured in to qualify as a high posterior
++ * of states a vertex must have occurred in to qualify as a high posterior
+ * vertex. It is NOT a probability.
+ */
+ void
+--- prime-phylo.orig/src/cxx/applications/primeRecon/primeRecon.cc
++++ prime-phylo/src/cxx/applications/primeRecon/primeRecon.cc
+@@ -883,7 +883,7 @@
+ * @param vertices A set of virtual vertices to sift. Assumes count has already been calculated.
+ * @param hp_vertices Storage for the found vertices upon return.
+ * @param threshold_count Posterior threshold. Note that this is a number reperesenting a count
+- * of states a vertex must have occured in to qualify as a high posterior
++ * of states a vertex must have occurred in to qualify as a high posterior
+ * vertex. It is NOT a probability.
+ */
+ void
+@@ -1544,4 +1544,4 @@
+ mvvs.push_back(max);
+ }
+ }
+-}
+\ No newline at end of file
++}
+--- prime-phylo.orig/src/cxx/libraries/prime/Beep.cc
++++ prime-phylo/src/cxx/libraries/prime/Beep.cc
+@@ -153,7 +153,7 @@
+ else
+ {
+ std::cerr << "typeid " + t +
+- " not recogized by typeid2typstring\n";
++ " not recognized by typeid2typstring\n";
+ throw bad_typeid();
+ return "Error";
+ }
+--- prime-phylo.orig/src/cxx/libraries/prime/LambdaMap.cc
++++ prime-phylo/src/cxx/libraries/prime/LambdaMap.cc
+@@ -176,7 +176,7 @@
+ }
+ catch (AnError& e)
+ {
+- cerr << "An error occured when trying to map genes to species.\n"
++ cerr << "An error occurred when trying to map genes to species.\n"
+ << "Please verify that gene and species names are correct\n"
+ << "and complete!\n\n";
+ e.action();
+--- prime-phylo.orig/src/cxx/libraries/prime/ReconciliationTimeModel.cc
++++ prime-phylo/src/cxx/libraries/prime/ReconciliationTimeModel.cc
+@@ -299,7 +299,7 @@
+ << "G (gene tree):\n"
+ //here should be added a G->tree4os statement when this becomes available
+ << "\n"
+- << "gamma (reconciliation betweeen S and G):\n"
++ << "gamma (reconciliation between S and G):\n"
+ //here should be added a gamma->gamma4os statement when this becomes available
+ << gamma
+ << "\n"
+--- prime-phylo.orig/src/cxx/libraries/prime/ReconciliationTimeSampler.cc
++++ prime-phylo/src/cxx/libraries/prime/ReconciliationTimeSampler.cc
+@@ -399,7 +399,7 @@
+ << "G (gene tree):\n"
+ //here should be added a G->tree4os statement when this becomes available
+ << "\n"
+- << "gamma (reconciliation betweeen S and G):\n"
++ << "gamma (reconciliation between S and G):\n"
+ //here should be added a gamma->gamma4os statement when this becomes available
+ << gamma
+ << "\n"
+--- prime-phylo.orig/src/cxx/libraries/sfile/seqreader.l
++++ prime-phylo/src/cxx/libraries/sfile/seqreader.l
+@@ -294,7 +294,7 @@
+ *ndone = seq_entry_list_length(sf->entry_list);
+ return sf->entry_list;
+ } else {
+- WARNING("Progamming error: Tried to read from NULL sequence-file.");
++ WARNING("Programming error: Tried to read from NULL sequence-file.");
+ return NULL;
+ }
+ } else {
+@@ -355,7 +355,7 @@
+ }
+ return sf->entry_list;
+ } else {
+- WARNING("Progamming error: Tried to read from NULL sequence-file.");
++ WARNING("Programming error: Tried to read from NULL sequence-file.");
+ return NULL;
+ }
+ } else {
View it on GitLab: https://salsa.debian.org/med-team/prime-phylo/-/compare/e409ac424018ba7e07705669e131407e7c74576f...53e0510baf5b97c8e653383a2414ec7d38a23c81
--
View it on GitLab: https://salsa.debian.org/med-team/prime-phylo/-/compare/e409ac424018ba7e07705669e131407e7c74576f...53e0510baf5b97c8e653383a2414ec7d38a23c81
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