[med-svn] [sra-sdk] branch master updated (be7b56c -> 61da137)
Andreas Tille
tille at debian.org
Tue Dec 24 07:59:15 UTC 2013
This is an automated email from the git hooks/post-receive script.
tille pushed a change to branch master
in repository sra-sdk.
from be7b56c Standards-Version: 3.9.5 (no changes needed)
new f14de0e Imported Upstream version 2.3.4-2+dfsg
new 2f5856f Merge tag 'upstream/2.3.4-2+dfsg'
new 91c9d19 Adapt patch to new upstream version
new e2b6d9d New upstream version
new 3b9e1e3 Some patches for symbols file (somehow not every hunk applies)
new 4a5be73 Finally fix symbols file
new 61da137 Upload to unstable
The 7 revisions listed above as "new" are entirely new to this
repository and will be described in separate emails. The revisions
listed as "adds" were already present in the repository and have only
been added to this reference.
Summary of changes:
build/Makefile.env | 10 +-
build/Makefile.mac | 4 +
build/ld.linux.exe.sh | 7 +-
build/ld.mac.exe.sh | 7 +-
build/win-cc.sh | 33 +-
configuration-assistant.perl | 19 +-
debian/changelog | 4 +-
debian/patches/build-with-system-libbz2-libz.patch | 10 +-
debian/patches/hardening.patch | 10 +-
debian/sra-toolkit-libs0.symbols | 12186 ++++++++++---------
interfaces/kfg/kart.h | 3 +
interfaces/kfg/keystore.h | 2 -
interfaces/kfg/kfg-priv.h | 35 +-
interfaces/kfs/kfs-priv.h | 8 +
interfaces/klib/refcount.h | 9 +-
interfaces/klib/report.h | 5 +
interfaces/klib/{time.h => sra-release-version.h} | 81 +-
interfaces/kns/KCurlRequest.h | 4 +
interfaces/kns/ascp.h | 9 +-
.../{cc/gcc/i386/strtol.h => kns/manager-ext.h} | 34 +-
interfaces/kns/manager.h | 13 +
interfaces/kns/socket.h | 67 +-
interfaces/krypto/extern.h | 33 +-
interfaces/ktst/unit_test_suite.hpp | 11 +-
interfaces/ncbi/wgs-contig.h | 25 +-
interfaces/ncbi/wgs-contig.vschema | 71 +-
interfaces/os/mac/os-native.h | 2 +-
interfaces/vdb/vdb-priv.h | 5 +
interfaces/vfs/manager-priv.h | 5 -
interfaces/vfs/path.h | 11 +
libs/align/Makefile | 30 +-
libs/align/bam.c | 21 +-
libs/align/libalign-access.vers | 1 -
libs/align/libalign-reader.vers | 1 -
libs/align/libncbi-bam.vers | 1 -
libs/align/reference.c | 26 +-
libs/align/writer-reference.c | 14 +-
libs/align/writer-refseq.c | 5 +-
libs/ascp/ascp.c | 71 +-
libs/ascp/win/ascp-path.c | 4 +-
libs/ascp/win/connect.c | 23 +-
libs/axf/libaxf.vers | 1 -
libs/axf/libwaxf.vers | 1 -
libs/ext/Makefile | 55 -
libs/ext/bzip2/Makefile | 143 -
libs/ext/curl/Makefile | 103 -
libs/ext/zlib/Makefile | 150 -
libs/kapp/args.c | 2 +-
libs/kapp/libkapp.vers | 1 -
libs/kapp/libload.vers | 1 -
libs/kapp/loader-file.c | 10 +-
libs/kapp/progressbar.c | 2 +-
libs/kapp/tokenizer.c | 4 +-
libs/kapp/unix/sysmain.c | 6 +
libs/kapp/win/sysmain.c | 1 +
libs/kdb/btree.c | 42 +-
libs/kdb/column-cc.c | 2 +-
libs/kdb/database.c | 4 +-
libs/kdb/libkdb.vers | 1 -
libs/kdb/libwkdb.vers | 1 -
libs/kdb/trieidx-v2.c | 70 +-
libs/kfg/Makefile | 10 +-
libs/kfg/config-grammar.c | 109 +-
libs/kfg/config-lex.c | 128 +-
libs/kfg/config-tokens.h | 4 +-
libs/kfg/config.c | 416 +-
libs/kfg/kart.c | 131 +-
libs/kfg/keystore.c | 14 +-
libs/kfg/libkfg.vers | 1 -
libs/kfg/report-kfg.c | 9 +-
libs/kfg/repository.c | 10 +-
libs/kfs/bzip.c | 6 +-
libs/kfs/cacheteefile.c | 2 +-
libs/kfs/gzip.c | 6 +-
libs/kfs/libkdl.vers | 1 -
libs/kfs/libkff.vers | 1 -
libs/kfs/libkfs.vers | 1 -
libs/kfs/quickmount.c | 6 +-
libs/kfs/tocentry.c | 2 +-
libs/kfs/win/lnk_tools.c | 4 +-
libs/kfs/win/sysdir-priv.h | 7 -
libs/kfs/win/sysdir.c | 6 +-
libs/kfs/win/sysdll.c | 2 +-
libs/kfs/win/sysfile.c | 15 +-
libs/klib/Makefile | 3 +-
libs/klib/libkascii.vers | 1 -
libs/klib/libklib.vers | 1 -
libs/klib/libktlog.vers | 1 -
libs/klib/libkutf8.vers | 1 -
libs/klib/log.c | 4 +-
libs/klib/maybeswap.h | 34 +-
libs/klib/pbstree-impl.c | 198 +-
libs/klib/printf.c | 27 +-
libs/klib/refcount.c | 29 +-
.../cc/vc++/stdbool.h => libs/klib/release-vers.h | 29 +-
libs/klib/report.c | 45 +-
libs/klib/sra-release-version.c | 328 +
libs/klib/win/syserrcode.c | 2 +-
libs/klib/win/systime.c | 1 -
libs/klib/win/syswriter.c | 6 +-
libs/kns/KCurlFile.c | 4 +-
libs/kns/Makefile | 1 +
libs/kns/http-priv.h | 2 +-
libs/kns/http-test.c | 8 +-
libs/kns/http.c | 131 +-
libs/kns/kns_manager-ext.c | 140 +
libs/kns/kns_manager.c | 29 +-
libs/kns/kns_mgr_priv.h | 10 +-
libs/kns/libkns.vers | 1 -
libs/kns/libkurl.vers | 1 -
libs/kns/unix/sysendpoint.c | 87 +-
libs/kns/unix/syssock.c | 160 +-
libs/kns/win/sysendpoint.c | 101 +-
libs/kns/win/syssock.c | 105 +-
libs/kproc/libkproc.vers | 1 -
libs/kproc/libkq.vers | 1 -
libs/kproc/libksproc.vers | 1 -
libs/kproc/unix/systimeout.c | 4 +-
libs/kproc/win/syscond.c | 4 +-
libs/krypto/Makefile | 29 +-
libs/krypto/cipher-byte.c | 2 +-
libs/krypto/cipher.c | 4 +-
libs/krypto/encfile-priv.h | 2 +-
libs/krypto/encfile.c | 4 +-
libs/krypto/encfilev2.c | 2 +-
libs/krypto/libkrypto.vers | 1 -
libs/krypto/libkryptotest.vers | 1 -
libs/krypto/reencfile.c | 2 +-
libs/krypto/wgaencrypt.c | 10 +-
libs/kxml/libkxfs.vers | 1 -
libs/kxml/libkxml.vers | 1 -
libs/kxml/xtoc.c | 4 +-
libs/loader/common-writer.c | 8 +-
libs/ncbi-vdb/Makefile | 4 +-
libs/ncbi-vdb/libncbi-vdb.vers | 2 +-
libs/ncbi-vdb/libncbi-wvdb.vers | 2 +-
libs/search/libksrch.vers | 1 -
libs/search/libnucstrstr.vers | 1 -
libs/search/search.c | 18 +-
libs/sra/libsra-schema.vers | 1 -
libs/sra/libsradb.vers | 1 -
libs/sra/libsrareader.vers | 1 -
libs/sra/libsraschema.vers | 1 -
libs/sra/libwsra-schema.vers | 1 -
libs/sra/libwsradb.vers | 1 -
libs/sra/libwsraschema.vers | 1 -
libs/sra/sracache.c | 2 +-
libs/sraxf/libsraxf.vers | 1 -
libs/sraxf/libwsraxf.vers | 1 -
libs/vdb/column-priv.h | 3 +-
libs/vdb/cursor-cmn.c | 63 +-
libs/vdb/cursor-priv.h | 9 +-
libs/vdb/cursor.c | 2 +-
libs/vdb/database-cmn.c | 12 +
libs/vdb/libvdb.vers | 1 -
libs/vdb/libwvdb.vers | 1 -
libs/vdb/page-map.h | 4 +-
libs/vdb/prod-cmn.c | 32 +-
libs/vdb/prod-expr.c | 6 +-
libs/vdb/prod-expr.h | 3 +
libs/vdb/prod-func.c | 235 +-
libs/vdb/prod.c | 2 +-
libs/vdb/schema-eval.c | 80 +-
libs/vdb/schema-expr.c | 14 +-
libs/vdb/schema-expr.h | 6 +-
libs/vdb/schema-func.c | 437 +-
libs/vdb/schema-parse.h | 8 +-
libs/vdb/schema-priv.h | 42 +-
libs/vdb/schema-prod.c | 16 +-
libs/vdb/schema-type.c | 21 +-
libs/vdb/schema.c | 1 +
libs/vdb/wcolumn.c | 6 +-
libs/vdb/wcursor.c | 23 +-
libs/vdb/wprod.c | 8 +-
libs/vfs/Makefile | 3 +-
libs/vfs/keyring.c | 189 +-
libs/vfs/libsrapath.vers | 1 -
libs/vfs/libvfs.vers | 1 -
libs/vfs/manager.c | 91 +-
libs/vfs/path-priv.h | 4 +-
libs/vfs/path.c | 6 +-
libs/vfs/resolver.c | 512 +-
libs/vfs/unix/syspath.c | 2 +-
libs/vfs/win/syspath.c | 5 +-
libs/vxf/libvxf.vers | 1 -
libs/vxf/libwvxf.vers | 1 -
libs/vxf/simple-sub-select.c | 170 +-
libs/wgsxf/libwgsxf.vers | 1 -
libs/wgsxf/libwwgsxf.vers | 1 -
tools/Makefile | 12 -
tools/align-info/align-info.vers | 2 +-
tools/bam-loader/bam-load.3.vers | 1 +
tools/bam-loader/bam-load.vers | 2 +-
tools/bam-loader/loader-imp.c | 27 +-
tools/cache-mgr/Makefile | 23 +-
tools/cache-mgr/cache-mgr.c | 8 +-
tools/cache-mgr/cache-mgr.vers | 2 +-
tools/cg-load/Makefile | 19 +-
tools/cg-load/cg-load.c | 132 +-
tools/cg-load/cg-load.vers | 2 +-
tools/cg-load/defs.h | 4 +
tools/cg-load/f1_5.c | 10 +-
tools/cg-load/f2_0.c | 9 +-
tools/cg-load/f2_2.c | 9 +-
tools/cg-load/factory-cmn.h | 2 +-
tools/cg-load/factory-evidence-dnbs.c | 2 +
tools/cg-load/factory-evidence-intervals.c | 2 +
tools/cg-load/factory-mappings.c | 2 +
tools/cg-load/factory-reads.c | 1 +
tools/cg-load/file-version-factory.c | 1 +
tools/cg-load/file.c | 16 +
tools/cg-load/file.h | 3 +
tools/fastq-loader/Makefile | 8 -
tools/fastq-loader/fastq-lex.c | 56 +-
tools/fastq-loader/latf-load.vers | 2 +-
tools/kar/Makefile | 28 +-
tools/kar/kar.c | 60 +-
tools/kar/kar.vers | 2 +-
tools/kar/sra-kar.vers | 2 +-
tools/nenctool/nenctest.vers | 2 +-
tools/nenctool/nenctool.vers | 2 +-
tools/nencvalid/Makefile | 10 -
tools/nencvalid/nencvalid.vers | 2 +-
tools/prefetch/prefetch.c | 2634 ++--
tools/prefetch/prefetch.vers | 2 +-
tools/sam-dump/sam-dump.c | 2 +-
tools/sra-dbcc/Makefile | 15 +-
tools/sra-dbcc/sra-dbcc.vers | 2 +-
tools/sra-dump/Makefile | 19 -
tools/sra-dump/abi-dump.vers | 2 +-
tools/sra-dump/core.c | 83 +-
tools/sra-dump/fastq-dump.vers | 2 +-
tools/sra-dump/illumina-dump.vers | 2 +-
tools/sra-dump/sff-dump.vers | 2 +-
tools/sra-dump/sra-dump.vers | 2 +-
tools/sra-load/Makefile | 8 -
tools/sra-load/abi-load.vers | 2 +-
tools/sra-load/fastq-load.vers | 2 +-
tools/sra-load/helicos-load.vers | 2 +-
tools/sra-load/illumina-load.vers | 2 +-
tools/sra-load/pacbio-loadxml.vers | 1 +
tools/sra-load/sff-load.vers | 2 +-
tools/sra-load/srf-load.vers | 2 +-
tools/sra-pileup/Makefile | 2 +
tools/sra-pileup/cmdline_cmn.c | 382 +-
tools/sra-pileup/cmdline_cmn.h | 27 +-
tools/sra-pileup/ref_regions.c | 491 +
.../sra-pileup/ref_regions.h | 75 +-
tools/sra-pileup/ref_walker.c | 997 ++
tools/sra-pileup/ref_walker.h | 128 +
tools/sra-pileup/reref.c | 22 +-
tools/sra-pileup/reref.h | 5 -
tools/sra-pileup/sam-aligned.c | 244 +-
tools/sra-pileup/sam-dump-opts.c | 10 +-
tools/sra-pileup/sam-dump-opts.h | 6 +-
tools/sra-pileup/sam-dump.c | 2 +-
tools/sra-pileup/sam-dump.vers | 2 +-
tools/sra-pileup/sam-dump3.c | 99 +-
tools/sra-pileup/sam-hdr.c | 8 +-
tools/sra-pileup/sam-unaligned.c | 4 +-
tools/sra-pileup/sra-pileup.c | 315 +-
tools/sra-pileup/sra-pileup.vers | 2 +-
tools/sra-sort/sra-sort.vers | 2 +-
tools/sra-stat/sra-stat.vers | 2 +-
tools/srapath/Makefile | 8 +-
tools/srapath/srapath.vers | 2 +-
tools/util/Makefile | 20 +-
tools/util/kdbmeta.c | 47 +-
tools/util/kdbmeta.vers | 2 +-
tools/util/md5cp.vers | 1 +
tools/util/rcexplain.vers | 2 +-
tools/util/rowwritetest.vers | 2 +-
tools/util/schema-replace.vers | 1 +
tools/util/{syspass-priv.h => test-sra-priv.h} | 12 +-
tools/util/test-sra.c | 977 +-
tools/util/test-sra.vers | 2 +-
tools/util/testld.vers | 2 +-
tools/util/txt2kdb.vers | 2 +-
tools/util/unix/{syspass.c => PrintOS.c} | 52 +-
tools/util/vdb-lock.vers | 2 +-
tools/util/vdb-passwd.vers | 2 +-
tools/util/vdb-unlock.vers | 2 +-
tools/util/{unix/syspass.c => win/PrintOS.c} | 52 +-
tools/vdb-config/Makefile | 10 -
tools/vdb-config/vdb-config.c | 27 +-
tools/vdb-config/vdb-config.vers | 2 +-
tools/vdb-copy/vdb-copy.vers | 2 +-
tools/vdb-decrypt/Makefile | 16 +-
tools/vdb-decrypt/vdb-decrypt.c | 2 +-
tools/vdb-decrypt/vdb-decrypt.vers | 2 +-
tools/vdb-decrypt/vdb-encrypt.vers | 2 +-
tools/vdb-dump/Makefile | 2 +
tools/vdb-dump/vdb-dump-context.c | 89 +-
tools/vdb-dump/vdb-dump-context.h | 25 +-
tools/vdb-dump/vdb-dump-fastq.c | 498 +
.../reref.h => vdb-dump/vdb-dump-fastq.h} | 21 +-
.../out_redir.c => vdb-dump/vdb-dump-redir.c} | 4 +-
.../out_redir.h => vdb-dump/vdb-dump-redir.h} | 6 +-
tools/vdb-dump/vdb-dump.c | 274 +-
tools/vdb-dump/vdb-dump.vers | 2 +-
tools/vdb-validate/vdb-validate.vers | 2 +-
301 files changed, 15938 insertions(+), 10361 deletions(-)
copy interfaces/klib/{time.h => sra-release-version.h} (50%)
copy interfaces/{cc/gcc/i386/strtol.h => kns/manager-ext.h} (75%)
delete mode 100644 libs/align/libalign-access.vers
delete mode 100644 libs/align/libalign-reader.vers
delete mode 100644 libs/align/libncbi-bam.vers
delete mode 100644 libs/axf/libaxf.vers
delete mode 100644 libs/axf/libwaxf.vers
delete mode 100644 libs/ext/Makefile
delete mode 100644 libs/ext/bzip2/Makefile
delete mode 100644 libs/ext/curl/Makefile
delete mode 100644 libs/ext/zlib/Makefile
delete mode 100644 libs/kapp/libkapp.vers
delete mode 100644 libs/kapp/libload.vers
delete mode 100644 libs/kdb/libkdb.vers
delete mode 100644 libs/kdb/libwkdb.vers
delete mode 100644 libs/kfg/libkfg.vers
delete mode 100644 libs/kfs/libkdl.vers
delete mode 100644 libs/kfs/libkff.vers
delete mode 100644 libs/kfs/libkfs.vers
delete mode 100644 libs/klib/libkascii.vers
delete mode 100644 libs/klib/libklib.vers
delete mode 100644 libs/klib/libktlog.vers
delete mode 100644 libs/klib/libkutf8.vers
copy interfaces/cc/vc++/stdbool.h => libs/klib/release-vers.h (76%)
create mode 100644 libs/klib/sra-release-version.c
create mode 100644 libs/kns/kns_manager-ext.c
delete mode 100644 libs/kns/libkns.vers
delete mode 100644 libs/kns/libkurl.vers
delete mode 100644 libs/kproc/libkproc.vers
delete mode 100644 libs/kproc/libkq.vers
delete mode 100644 libs/kproc/libksproc.vers
delete mode 100644 libs/krypto/libkrypto.vers
delete mode 100644 libs/krypto/libkryptotest.vers
delete mode 100644 libs/kxml/libkxfs.vers
delete mode 100644 libs/kxml/libkxml.vers
delete mode 100644 libs/search/libksrch.vers
delete mode 100644 libs/search/libnucstrstr.vers
delete mode 100644 libs/sra/libsra-schema.vers
delete mode 100644 libs/sra/libsradb.vers
delete mode 100644 libs/sra/libsrareader.vers
delete mode 100644 libs/sra/libsraschema.vers
delete mode 100644 libs/sra/libwsra-schema.vers
delete mode 100644 libs/sra/libwsradb.vers
delete mode 100644 libs/sra/libwsraschema.vers
delete mode 100644 libs/sraxf/libsraxf.vers
delete mode 100644 libs/sraxf/libwsraxf.vers
delete mode 100644 libs/vdb/libvdb.vers
delete mode 100644 libs/vdb/libwvdb.vers
delete mode 100644 libs/vfs/libsrapath.vers
delete mode 100644 libs/vfs/libvfs.vers
delete mode 100644 libs/vxf/libvxf.vers
delete mode 100644 libs/vxf/libwvxf.vers
delete mode 100644 libs/wgsxf/libwgsxf.vers
delete mode 100644 libs/wgsxf/libwwgsxf.vers
create mode 100644 tools/bam-loader/bam-load.3.vers
create mode 100644 tools/sra-load/pacbio-loadxml.vers
create mode 100644 tools/sra-pileup/ref_regions.c
copy libs/kdb/wdatabase-priv.h => tools/sra-pileup/ref_regions.h (54%)
create mode 100644 tools/sra-pileup/ref_walker.c
create mode 100644 tools/sra-pileup/ref_walker.h
create mode 100644 tools/util/md5cp.vers
create mode 100644 tools/util/schema-replace.vers
copy tools/util/{syspass-priv.h => test-sra-priv.h} (88%)
copy tools/util/unix/{syspass.c => PrintOS.c} (58%)
copy tools/util/{unix/syspass.c => win/PrintOS.c} (55%)
create mode 100644 tools/vdb-dump/vdb-dump-fastq.c
copy tools/{sra-pileup/reref.h => vdb-dump/vdb-dump-fastq.h} (85%)
copy tools/{sra-pileup/out_redir.c => vdb-dump/vdb-dump-redir.c} (96%)
copy tools/{sra-pileup/out_redir.h => vdb-dump/vdb-dump-redir.h} (91%)
--
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