[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
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