Finalize 6.1.20090809-2 for upload to unstable

(with the release team's blessing, per #596733).

diff --git a/.gitignore b/.gitignore
new file mode 100644 (file)
index 0000000..460a322
--- /dev/null
+++ b/.gitignore
@@ -0,0 +1,6 @@
+bin
+build
+include
+lib
+shlib
+*-stamp

diff --git a/debian/.gitignore b/debian/.gitignore
new file mode 100644 (file)
index 0000000..5180eb4
--- /dev/null
+++ b/debian/.gitignore
@@ -0,0 +1,18 @@
+*.xpm
+*.debhelper
+*.debhelper.log
+*.menu
+*.substvars
+blast2
+files
+libncbi6
+libvibrant6a
+lib*-dbg
+lib*-dev
+ncbi-data
+ncbi-tools-bin
+ncbi-tools-x11
+ncbi-tools6
+tmp
+vibrant6
+ncbi-rrna-data

diff --git a/debian/changelog b/debian/changelog
index 7b8233e..998eff7 100644 (file)
--- a/debian/changelog
+++ b/debian/changelog
@@ -1,3 +1,23 @@
+ncbi-tools6 (6.1.20090809-2) unstable; urgency=low
+
+  * debian/rules
+    - Clean up compilation settings; in particular, use dpkg-buildflags rather
+      than relying on dpkg-buildpackage to have set CFLAGS appropriately.
+    - (clean): restore expected empty directories if necessary,
+      for compatibility with VCSes (notably git) that don't track them.
+    - (VIB): add asndisc, as upstream takes care to publish binaries thereof.
+  * debian/ncbi-tools6.install: likewise add asndisc.
+  * (debian/).gitignore: Ignore content generated during build.
+  * make/makenet.unx: don't link asndisc against extraneous libraries.
+  * doc/man/asndisc.1: throw together a man page for asndisc.
+  * doc/man/cleanasn.1: fix SEE ALSO formatting.
+  * debian/control:
+    - bump dpkg-dev build-dep to >= 1.15.7 for dpkg-buildflags.
+    - Standards-Version: 3.9.1 (already compliant).
+    - note switch to git-mediated Debian-Med team maintenance.
+
+ -- Aaron M. Ucko <ucko@debian.org>  Wed, 13 Oct 2010 20:23:37 -0400
+
 ncbi-tools6 (6.1.20090809-1) unstable; urgency=low
 
   * New upstream release.

diff --git a/debian/control b/debian/control
index 66016e2..d2b82f3 100644 (file)
--- a/debian/control
+++ b/debian/control
@@ -1,11 +1,14 @@
 Source: ncbi-tools6
 Section: libdevel
 Priority: optional
-Maintainer: Aaron M. Ucko <ucko@debian.org>
-Build-Depends: csh | c-shell, debhelper (>= 7), dpkg-dev (>= 1.14.17), lesstif2-dev, libglu1-mesa-dev | libglu-dev, libpcre3-dev, libpng12-dev | libpng-dev, libxmu-dev
+Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
+Uploaders: Aaron M. Ucko <ucko@debian.org>
+Build-Depends: csh | c-shell, debhelper (>= 7), dpkg-dev (>= 1.15.7), lesstif2-dev, libglu1-mesa-dev | libglu-dev, libpcre3-dev, libpng12-dev | libpng-dev, libxmu-dev
 Build-Depends-Indep: icoutils, imagemagick
-Standards-Version: 3.8.2
+Standards-Version: 3.9.1
 Homepage: http://www.ncbi.nlm.nih.gov/IEB/ToolBox/
+Vcs-Browser: http://git.debian.org/?p=debian-med/ncbi-tools6.git
+Vcs-Git: git://git.debian.org/debian-med/ncbi-tools6.git
 
 Package: libncbi6
 Architecture: any

diff --git a/debian/ncbi-tools-bin.install b/debian/ncbi-tools-bin.install
index bfddd1d..611c906 100644 (file)
--- a/debian/ncbi-tools-bin.install
+++ b/debian/ncbi-tools-bin.install
@@ -6,6 +6,7 @@ usr/bin/asn2gb
 usr/bin/asn2idx
 usr/bin/asn2xml
 usr/bin/asndhuff
+usr/bin/asndisc
 usr/bin/asnval
 usr/bin/checksub
 usr/bin/cleanasn

diff --git a/debian/rules b/debian/rules
index 6ff0e7f..c16493b 100755 (executable)
--- a/debian/rules
+++ b/debian/rules
@@ -18,7 +18,7 @@ testversions:
 
 # Set these here, rather than using the csh hackage that passes for an
 # upstream build system.  Mostly taken from ../platform/{ppc,}linux.ncbi.mk.
-# CC = gcc -pipe
+CC = gcc # -pipe
 VIBFLAG = -DWIN_MOTIF
 VIBLIBS = -lXm -lXmu -lXt -lX11 # -lXext # -lXp
 OTHERLIBS = -lm
@@ -32,7 +32,7 @@ THREAD_OBJ =
 endif
 NETENTREZVERSION = 2.02c2ASN1SPEC6
 
-CFLAGS += -Wall
+CFLAGS := $(shell dpkg-buildflags --get CFLAGS) -Wall
 ifeq ($(DEB_HOST_ARCH),alpha)
 CFLAGS += -mieee
 endif
@@ -44,7 +44,7 @@ OGLLIBS = -lGLU -lGL
 PNG_INCLUDE = -D_PNG
 PNG_LIBS = -lpng # -lz
 
-USESHLIB = NCBI_LINKINGLIBDIR="../shlib -L../lib" # Kludge.
+USESHLIB = NCBI_LINKINGLIBDIR="../shlib"
 MAKESHLIB = $(USESHLIB) NCBI_SHLIBS=shlib
 # Controls how shared libraries are built; appropriate for ELF w/GNU tools.
 
@@ -62,8 +62,9 @@ MTAPPS = blast blastall blastall_old blastpgp seedtop megablast rpsblast \
          blastclust
 
 VIB = Psequin sbtedit udv ddv blastcl3 taxblast idfetch bl2seq asn2gb tbl2asn \
-      gene2xml entrez2 gbseqget asn2all asn2asn asn2fsa asn2xml asnval \
-      cleanasn insdseqget nps2gps spidey trna2sap trna2tbl $(OGL_TARGETS)
+      gene2xml entrez2 gbseqget asn2all asn2asn asn2fsa asn2xml asndisc \
+      asnval cleanasn insdseqget nps2gps spidey trna2sap trna2tbl \
+      $(OGL_TARGETS)
 
 #OTHERS = others
 OTHERS = libncbimla.a libnetblast.a libncbitxc2.a libncbiid1.a shlib
@@ -119,6 +120,7 @@ endif
 clean:
        dh clean
        -rm -rf build/* bin/* include/* lib/* shlib
+       mkdir -p build bin include lib
        -rm -f debian/*.menu $(ICONS)
 
 install-common: install-common-stamp

diff --git a/doc/man/asndisc.1 b/doc/man/asndisc.1
new file mode 100644 (file)
index 0000000..f1b9254
--- /dev/null
+++ b/doc/man/asndisc.1
@@ -0,0 +1,188 @@
+.TH ASNDISC 1 2010-09-02 NCBI "NCBI Tools User's Manual"
+.SH NAME
+asndisc \- check ASN.1 biological sequence records for discrepancies
+.SH SYNOPSIS
+.B asndisc
+[\|\fB\-\fP\|]
+[\|\fB\-B\fP\|]
+[\|\fB\-C\fP\ \fIN\fP\|]
+[\|\fB\-I\fP\ \fIpath\fP\|]
+[\|\fB\-N\fP\ \fIfilename\fP\|]
+[\|\fB\-R\fP\|]
+[\|\fB\-S\fP\|]
+[\|\fB\-T\fP\|]
+[\|\fB\-X\fP\ \fItests\fP\|]
+[\|\fB\-Z\fP\|]
+[\|\fB\-a\fP\ \fIstr\fP\|]
+[\|\fB\-b\fP\|]
+[\|\fB\-c\fP\|]
+[\|\fB\-d\fP\ \fItests\fP\|]
+[\|\fB\-e\fP\ \fItests\fP\|]
+[\|\fB\-f\fP\|]
+[\|\fB\-i\fP\ \fIfilename\fP\|]
+[\|\fB\-k\fP\|]
+[\|\fB\-l\fP\|]
+[\|\fB\-o\fP\ \fIfilename\fP\|]
+[\|\fB\-p\fP\ \fIpath\fP\|]
+[\|\fB\-r\fP\ \fIdir\fP\|]
+[\|\fB\-s\fP\ \fIext\fP\|]
+[\|\fB\-u\fP\|]
+[\|\fB\-x\fP\ \fIstr\fP\|]
+.SH DESCRIPTION
+\fBasndisc\fP is a command-line tool to check ASN.1-format biological
+sequence records for discrepancies.
+.SH OPTIONS
+A summary of options is included below.
+.TP
+\fB\-\fP
+Print usage message
+.TP
+\fB\-B\fP
+Big sequence report
+.TP
+\fB\-C\fP\ \fIN\fP
+Max count
+.TP
+\fB\-I\fP\ \fIpath\fP
+Path to Indexed binary ASN.1 data
+.TP
+\fB\-N\fP\ \fIfilename\fP
+File with list of product names to check
+.TP
+\fB\-R\fP
+Remote fetching from ID
+.TP
+\fB\-S\fP
+Summary report
+.TP
+\fB\-T\fP
+Use threads
+.TP
+\fB\-X\fP\ \fItests\fP
+EXpand report categories (comma-delimited list of test names as listed
+below or ALL).
+.TP
+\fB\-Z\fP
+Remote CDS Product Fetch
+.TP
+\fB\-a\fP\ \fIstr\fP
+.RS
+.PD 0
+.IP a
+Any (default)
+.IP e
+seq-Entry
+.IP b
+Bioseq
+.IP s
+bioseq-Set
+.IP m
+seq-subMit
+.IP t
+baTch bioseq-set
+.IP u
+batch seq-sUbmit
+.PD
+.RE
+.TP
+\fB\-b\fP
+Batch file is Binary
+.TP
+\fB\-c\fP
+Batch file is Compressed
+.TP
+\fB\-d\fP\ \fIstr\fP
+Disable tests (comma-delimited list of test names as listed below).
+.TP
+\fB\-e\fP\ \fIstr\fP
+Enable tests (comma-delimited list of test names as listed below).
+.TP
+\fB\-f\fP
+Use Feature table output format
+.TP
+\fB\-i\fP\ \fIfilename\fP
+Single input file (standard input by default)
+.TP
+\fB\-k\fP
+Local fetching
+.TP
+\fB\-l\fP
+Load components in advance
+.TP
+\fB\-o\fP\ \fIfilename\fP
+Single output file
+.TP
+\fB\-p\fP\ \fIpath\fP
+Path to ASN.1 files
+.TP
+\fB\-r\fP\ \fIdir\fP
+Output directory
+.TP
+\fB\-s\fP\ \fIext\fP
+Output file Suffix (\fB.dr\fP by default)
+.TP
+\fB\-u\fP
+Recurse
+.TP
+\fB\-x\fP\ \fIstr\fP
+File selection substring (\fB.sqn\fP by default)
+.SS AVAILABLE TESTS
+.P
+.ad l
+.nh
+MISSING_GENES, EXTRA_GENES, MISSING_LOCUS_TAGS, DUPLICATE_LOCUS_TAGS,
+BAD_LOCUS_TAG_FORMAT, INCONSISTENT_LOCUS_TAG_PREFIX, NON_GENE_LOCUS_TAG,
+DISC_COUNT_NUCLEOTIDES, MISSING_PROTEIN_ID, INCONSISTENT_PROTEIN_ID,
+FEATURE_LOCATION_CONFLICT, GENE_PRODUCT_CONFLICT, DUPLICATE_GENE_LOCUS,
+EC_NUMBER_NOTE, PSEUDO_MISMATCH, JOINED_FEATURES, OVERLAPPING_GENES,
+OVERLAPPING_CDS, CONTAINED_CDS, RNA_CDS_OVERLAP, SHORT_CONTIG,
+INCONSISTENT_BIOSOURCE, SUSPECT_PRODUCT_NAMES, INCONSISTENT_SOURCE_DEFLINE,
+PARTIAL_CDS_COMPLETE_SEQUENCE, EC_NUMBER_ON_UNKNOWN_PROTEIN,
+TAX_LOOKUP_MISSING, TAX_LOOKUP_MISMATCH, SHORT_SEQUENCES, SUSPECT_PHRASES,
+DISC_SUSPICIOUS_NOTE_TEXT, COUNT_TRNAS, FIND_DUP_TRNAS, FIND_BADLEN_TRNAS,
+FIND_STRAND_TRNAS, COUNT_RRNAS, FIND_DUP_RRNAS, RNA_NO_PRODUCT,
+TRANSL_NO_NOTE, NOTE_NO_TRANSL, TRANSL_TOO_LONG, CDS_TRNA_OVERLAP,
+COUNT_PROTEINS, DISC_FEAT_OVERLAP_SRCFEAT, MISSING_GENPRODSET_PROTEIN,
+DUP_GENPRODSET_PROTEIN, MISSING_GENPRODSET_TRANSCRIPT_ID,
+DISC_DUP_GENPRODSET_TRANSCRIPT_ID, DISC_PERCENT_N, N_RUNS, ZERO_BASECOUNT,
+ADJACENT_PSEUDOGENES, NO_ANNOTATION, DISC_INFLUENZA_DATE_MISMATCH,
+DISC_SHORT_INTRON, DISC_MISSING_VIRAL_QUALS, DISC_SRC_QUAL_PROBLEM,
+DISC_MISSING_SRC_QUAL, DISC_DUP_SRC_QUAL, DISC_DUP_SRC_QUAL_DATA,
+DISC_HAPLOTYPE_MISMATCH, DISC_FEATURE_MOLTYPE_MISMATCH,
+DISC_CDS_WITHOUT_MRNA, DISC_EXON_INTRON_CONFLICT, DISC_FEATURE_COUNT,
+DISC_SPECVOUCHER_TAXNAME_MISMATCH, DISC_GENE_PARTIAL_CONFLICT,
+DISC_FLATFILE_FIND_ONCALLER, DISC_CDS_PRODUCT_FIND, DISC_DUP_DEFLINE,
+DUP_DISC_ATCC_CULTURE_CONFLICT, DISC_USA_STATE, DISC_INCONSISTENT_MOLTYPES,
+DISC_SUBMITBLOCK_CONFLICT, DISC_POSSIBLE_LINKER,
+DISC_TITLE_AUTHOR_CONFLICT, DISC_BAD_GENE_STRAND,
+DISC_MAP_CHROMOSOME_CONFLICT, DISC_RBS_WITHOUT_GENE,
+DISC_CITSUBAFFIL_CONFLICT, DISC_REQUIRED_CLONE, DISC_SOURCE_QUALS_ASNDISC,
+DISC_mRNA_ON_WRONG_SEQUENCE_TYPE, DISC_RETROVIRIDAE_DNA,
+DISC_CHECK_AUTH_CAPS, DISC_CHECK_RNA_PRODUCTS_AND_COMMENTS,
+DISC_MICROSATELLITE_REPEAT_TYPE, DISC_MITOCHONDRION_REQUIRED,
+DISC_UNPUB_PUB_WITHOUT_TITLE, DISC_QUALITY_SCORES,
+DISC_INTERNAL_TRANSCRIBED_SPACER_RRNA, DISC_PARTIAL_PROBLEMS,
+DISC_BACTERIAL_PARTIAL_NONEXTENDABLE_PROBLEMS,
+DISC_BACTERIAL_PARTIAL_NONEXTENDABLE_EXCEPTION, DISC_SUSPECT_RRNA_PRODUCTS,
+DISC_SUSPECT_MISC_FEATURES, DISC_BACTERIA_MISSING_STRAIN,
+DISC_MISSING_DEFLINES, DISC_MISSING_AFFIL,
+DISC_BACTERIA_SHOULD_NOT_HAVE_ISOLATE, DISC_BACTERIA_SHOULD_NOT_HAVE_MRNA,
+DISC_CDS_HAS_NEW_EXCEPTION, DISC_TRINOMIAL_SHOULD_HAVE_QUALIFIER,
+DISC_METAGENOMIC, DISC_METAGENOME_SOURCE, ONCALLER_GENE_MISSING,
+ONCALLER_SUPERFLUOUS_GENE, DISC_SHORT_RRNA, ONCALLER_CHECK_AUTHORITY,
+ONCALLER_CONSORTIUM, ONCALLER_STRAIN_CULTURE_COLLECTION_MISMATCH,
+ONCALLER_MULTISRC, ONCALLER_MULTIPLE_CULTURE_COLLECTION,
+DISC_SEGSETS_PRESENT, DISC_NONWGS_SETS_PRESENT, DISC_FEATURE_LIST,
+DISC_CATEGORY_HEADER, DISC_MISMATCHED_COMMENTS,
+DISC_STRAIN_TAXNAME_MISMATCH, DISC_HUMAN_HOST,
+DISC_BAD_BACTERIAL_GENE_NAME, ONCALLER_ORDERED_LOCATION,
+ONCALLER_COMMENT_PRESENT, ONCALLER_DEFLINE_ON_SET,
+ONCALLER_HIV_RNA_INCONSISTENT, SHORT_PROT_SEQUENCES, TEST_EXON_ON_MRNA,
+TEST_HAS_PROJECT_ID
+.hy
+.ad b
+.SH AUTHOR
+The National Center for Biotechnology Information.
+.SH SEE ALSO
+.BR asnval (1),
+.BR cleanasn (1).

diff --git a/doc/man/asnval.1 b/doc/man/asnval.1
index 2398029..bfa5b82 100644 (file)
--- a/doc/man/asnval.1
+++ b/doc/man/asnval.1
@@ -1,4 +1,4 @@
-.TH ASNVAL 1 2009-07-31 NCBI "NCBI Tools User's Manual"
+.TH ASNVAL 1 2010-09-02 NCBI "NCBI Tools User's Manual"
 .SH NAME
 asnval \- validate ASN.1 biological sequence records
 .SH SYNOPSIS
@@ -189,5 +189,6 @@ File selection substring (\fB.ent\fP by default)
 .SH AUTHOR
 The National Center for Biotechnology Information.
 .SH SEE ALSO
+.BR asndisc (1),
 .BR cleanasn (1),
 .BR sequin (1).

diff --git a/doc/man/cleanasn.1 b/doc/man/cleanasn.1
index 403e34e..8ec0cc3 100644 (file)
--- a/doc/man/cleanasn.1
+++ b/doc/man/cleanasn.1
@@ -1,4 +1,4 @@
-.TH CLEANASN 1 2009-07-31 NCBI "NCBI Tools User's Manual"
+.TH CLEANASN 1 2010-09-02 NCBI "NCBI Tools User's Manual"
 .SH NAME
 cleanasn \- clean up irregularities in NCBI ASN.1 objects
 .SH SYNOPSIS
@@ -205,5 +205,6 @@ File selection suffix for use with \fB\-p\fP (defaults to \fB.ent\fP)
 .SH AUTHOR
 The National Center for Biotechnology Information.
 .SH SEE ALSO
-asnval (1),
-sequin (1).
+.BR asndisc (1),
+.BR asnval (1),
+.BR sequin (1).

diff --git a/make/makenet.unx b/make/makenet.unx
index b4ed36a..33ef257 100644 (file)
--- a/make/makenet.unx
+++ b/make/makenet.unx
@@ -1048,8 +1048,7 @@ asnval_dbx_psf :  asnval.c
 # asndisc program (asndisc)
 asndisc :      asndisc.c
        $(CC) -g -o asndisc $(LDFLAGS) asndisc.c $(THREAD_OBJ) $(LIB41) \
-               $(NETCLILIB) $(LIB23) $(LIBCOMPADJ) $(LIB2) $(LIB1) \
-               $(OTHERLIBS) $(THREAD_OTHERLIBS)
+               $(LIB23) $(LIB2) $(LIB1) $(THREAD_OTHERLIBS)
 
 # asndisc_psf, uses PUBSEQBioseqFetchEnable instead of PubSeqFetchEnable
 # should be used only internally within NCBI.