[med-svn] [Git][med-team/ncbi-blastplus][master] 4 commits: Start work on ncbi-blast+ 2.10.0-2, primarily for #969608.
Aaron M. Ucko
gitlab at salsa.debian.org
Mon Sep 7 04:16:08 BST 2020
Aaron M. Ucko pushed to branch master at Debian Med / ncbi-blastplus
Commits:
9932cfe5 by Aaron M. Ucko at 2020-09-06T22:48:22-04:00
Start work on ncbi-blast+ 2.10.0-2, primarily for #969608.
- - - - -
569b721d by Aaron M. Ucko at 2020-09-06T22:57:36-04:00
d/p/support_gcc10: Additionally avoid narrowing errors on e.g. i386.
Tweak ncbifile.cpp to avoid narrowing errors on some platforms.
- - - - -
ac5160f5 by Aaron M. Ucko at 2020-09-06T23:04:32-04:00
tune_32bit_lmdb_defaults (new): Conditionalize dflt map sz (#969608).
Patch to avoid allocation failures on 32-bit platforms.
- - - - -
83841e9a by Aaron M. Ucko at 2020-09-06T23:07:37-04:00
Finalize ncbi-blast+ 2.10.0-2 for unstable, urgency high per #969608.
- - - - -
4 changed files:
- debian/changelog
- debian/patches/series
- debian/patches/support_gcc10
- + debian/patches/tune_32bit_lmdb_defaults
Changes:
=====================================
debian/changelog
=====================================
@@ -1,3 +1,13 @@
+ncbi-blast+ (2.10.0-2) unstable; urgency=high
+
+ * debian/patches/support_gcc10: Additionally tweak ncbifile.cpp to avoid
+ narrowing errors on some platforms (i386, for one).
+ * debian/patches/tune_32bit_lmdb_defaults (new): Conditionalize default
+ map size to avoid allocation failures on 32-bit platforms.
+ (Closes: #969608.)
+
+ -- Aaron M. Ucko <ucko at debian.org> Sun, 06 Sep 2020 23:07:37 -0400
+
ncbi-blast+ (2.10.0-1) unstable; urgency=medium
* New upstream release.
=====================================
debian/patches/series
=====================================
@@ -15,3 +15,4 @@ reprobuild
spelling
support_gcc10
run_perl_directly
+tune_32bit_lmdb_defaults
=====================================
debian/patches/support_gcc10
=====================================
@@ -1,19 +1,26 @@
Author: Aaron M. Ucko <ucko at debian.org>
-Date: Sun Apr 26 11:20:45 2020 -0400
+Date: Sun Sep 06 22:57:35 2020 -0400
Description: Support GCC 10+.
Debian-Bug: 957581.
-Formally recognize GCC 10 and up, even if (as in Debian) -dumpversion
-reports only one or two components of the version number. Corresponds to
+* build system: Formally recognize GCC 10 and up, even if (as in
+ Debian) -dumpversion reports only one or two components of the
+ version number. These patches correspond to merges of
-https://www.ncbi.nlm.nih.gov/viewvc/v1?view=revision&revision=88985
-https://www.ncbi.nlm.nih.gov/viewvc/v1?view=revision&revision=88988
-https://www.ncbi.nlm.nih.gov/viewvc/v1?view=revision&revision=88989
-https://www.ncbi.nlm.nih.gov/viewvc/v1?view=revision&revision=89711
+ https://www.ncbi.nlm.nih.gov/viewvc/v1?view=revision&revision=88985
+ https://www.ncbi.nlm.nih.gov/viewvc/v1?view=revision&revision=88988
+ https://www.ncbi.nlm.nih.gov/viewvc/v1?view=revision&revision=88989
+ https://www.ncbi.nlm.nih.gov/viewvc/v1?view=revision&revision=89711
-though the last of those doesn't apply cleanly without some
-intervening changes for better Clang support.
+ though the last of those doesn't apply cleanly without some
+ intervening changes for better Clang support.
+* ncbifile.cpp (s_GetFileSystemInfo): Formally cast st.f_type to avoid
+ narrowing errors for cases with the high bit set when that field is
+ a 32-bit signed integer (as on i386).
+
+Index: b/c++/src/build-system/config.h.in
+===================================================================
--- a/c++/src/build-system/config.h.in
+++ b/c++/src/build-system/config.h.in
@@ -966,7 +966,7 @@
@@ -25,6 +32,8 @@ intervening changes for better Clang support.
#undef NCBI_COMPILER_VERSION
/* Compiler name */
+Index: b/c++/src/build-system/configure
+===================================================================
--- a/c++/src/build-system/configure
+++ b/c++/src/build-system/configure
@@ -8233,9 +8233,10 @@ fi
@@ -201,6 +210,8 @@ intervening changes for better Clang support.
-*gcc|-il ) boost_comp_vers=`echo $compiler_version | cut -c1-2` ;;
* ) boost_comp_vers='' ;;
esac
+Index: b/c++/src/build-system/configure.ac
+===================================================================
--- a/c++/src/build-system/configure.ac
+++ b/c++/src/build-system/configure.ac
@@ -1257,9 +1257,10 @@ changequote(, )dnl
@@ -386,3 +397,16 @@ intervening changes for better Clang support.
-*gcc|-il ) boost_comp_vers=`echo $compiler_version | cut -c1-2` ;;
* ) boost_comp_vers='' ;;
esac
+Index: b/c++/src/corelib/ncbifile.cpp
+===================================================================
+--- a/c++/src/corelib/ncbifile.cpp
++++ b/c++/src/corelib/ncbifile.cpp
+@@ -5129,7 +5129,7 @@ void s_GetFileSystemInfo(const string&
+
+ GET_STATFS_INFO;
+ if (flags & (fFSI_Type | fFSI_DiskSpace)) {
+- switch (st.f_type) {
++ switch (static_cast<Uint4>(st.f_type)) {
+ case 0xADF5: info->fs_type = CFileUtil::eADFS; break;
+ case 0xADFF: info->fs_type = CFileUtil::eAFFS; break;
+ case 0x5346414F: info->fs_type = CFileUtil::eAFS; break;
=====================================
debian/patches/tune_32bit_lmdb_defaults
=====================================
@@ -0,0 +1,36 @@
+Index: b/c++/include/objtools/blast/seqdb_writer/writedb_lmdb.hpp
+===================================================================
+--- a/c++/include/objtools/blast/seqdb_writer/writedb_lmdb.hpp
++++ b/c++/include/objtools/blast/seqdb_writer/writedb_lmdb.hpp
+@@ -48,6 +48,11 @@ USING_SCOPE(objects);
+
+ BEGIN_NCBI_SCOPE
+
++#if NCBI_PLATFORM_BITS >= 64
++# define NCBI_WRITEDB_DEFAULT_MAP_SIZE 300 * 1000 * 1000 * 1000
++#else
++# define NCBI_WRITEDB_DEFAULT_MAP_SIZE 1000 * 1000 * 1000
++#endif
+
+ /// This class supports creation of a string accession to integer OID
+ /// lmdb database
+@@ -59,7 +64,8 @@ public:
+
+ /// Constructor for LMDB write access
+ /// @param dbname Database name
+- CWriteDB_LMDB(const string& dbname, Uint8 map_size = 300000000000, Uint8 capacity = 500000);
++ CWriteDB_LMDB(const string& dbname, Uint8 map_size = NCBI_WRITEDB_DEFAULT_MAP_SIZE,
++ Uint8 capacity = 500000);
+
+ // Destructor
+ ~CWriteDB_LMDB();
+@@ -130,7 +136,8 @@ public:
+
+ /// Constructor for LMDB write access
+ /// @param dbname Database name
+- CWriteDB_TaxID(const string& dbname, Uint8 map_size = 300000000000, Uint8 capacity = 500000);
++ CWriteDB_TaxID(const string& dbname, Uint8 map_size = NCBI_WRITEDB_DEFAULT_MAP_SIZE,
++ Uint8 capacity = 500000);
+
+ // Destructor
+ ~CWriteDB_TaxID();
View it on GitLab: https://salsa.debian.org/med-team/ncbi-blastplus/-/compare/ea0764c2e03c42daa0fc5fc7e78d5c31256f6b6f...83841e9a65c44737a343454eb0dc110a5e3627f7
--
View it on GitLab: https://salsa.debian.org/med-team/ncbi-blastplus/-/compare/ea0764c2e03c42daa0fc5fc7e78d5c31256f6b6f...83841e9a65c44737a343454eb0dc110a5e3627f7
You're receiving this email because of your account on salsa.debian.org.
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://alioth-lists.debian.net/pipermail/debian-med-commit/attachments/20200907/9c751257/attachment-0001.html>
More information about the debian-med-commit
mailing list