[med-svn] [Git][med-team/anfo][master] 5 commits: Adapt to gcc 12 (Thanks to Aaron Ucko for the hint)
Andreas Tille (@tille)
gitlab at salsa.debian.org
Thu Sep 29 07:38:39 BST 2022
Andreas Tille pushed to branch master at Debian Med / anfo
Commits:
b37ea9fe by Andreas Tille at 2022-09-29T08:13:27+02:00
Adapt to gcc 12 (Thanks to Aaron Ucko for the hint)
- - - - -
310893bb by Andreas Tille at 2022-09-29T08:14:00+02:00
routine-update: Standards-Version: 4.6.1
- - - - -
af708548 by Andreas Tille at 2022-09-29T08:14:09+02:00
Set upstream metadata fields: Bug-Database, Bug-Submit, Repository.
Changes-By: lintian-brush
Fixes: lintian: upstream-metadata-missing-bug-tracking
See-also: https://lintian.debian.org/tags/upstream-metadata-missing-bug-tracking.html
Fixes: lintian: upstream-metadata-missing-repository
See-also: https://lintian.debian.org/tags/upstream-metadata-missing-repository.html
- - - - -
adfab868 by Andreas Tille at 2022-09-29T08:26:52+02:00
Replace more auto_ptr instances
- - - - -
24384abb by Andreas Tille at 2022-09-29T08:36:07+02:00
unique_ptr should be std:unique_ptr
- - - - -
5 changed files:
- debian/changelog
- debian/control
- + debian/patches/06-gcc12.patch
- debian/patches/series
- debian/upstream/metadata
Changes:
=====================================
debian/changelog
=====================================
@@ -1,3 +1,12 @@
+anfo (0.98-10) UNRELEASED; urgency=medium
+
+ * Adapt to gcc 12
+ Closes: #1012893
+ * Standards-Version: 4.6.1 (routine-update)
+ * Set upstream metadata fields: Bug-Database, Bug-Submit, Repository.
+
+ -- Andreas Tille <tille at debian.org> Thu, 29 Sep 2022 08:11:16 +0200
+
anfo (0.98-9) unstable; urgency=medium
* uscan can't fetch latest upstream since https certificate became invalid
=====================================
debian/control
=====================================
@@ -13,7 +13,7 @@ Build-Depends: debhelper-compat (= 13),
pkg-config,
protobuf-compiler,
d-shlibs
-Standards-Version: 4.6.0
+Standards-Version: 4.6.1
Vcs-Browser: https://salsa.debian.org/med-team/anfo
Vcs-Git: https://salsa.debian.org/med-team/anfo.git
Homepage: https://bioinf.eva.mpg.de/anfo/
=====================================
debian/patches/06-gcc12.patch
=====================================
@@ -0,0 +1,376 @@
+Description: Adapt to gcc 12
+Bug-Debian: https://bugs.debian.org/1012893
+Author: Andreas Tille <tille at debian.org>
+Last-Upadte: Thu, 29 Sep 2022 08:11:16 +0200
+
+--- a/src/compress_stream.h
++++ b/src/compress_stream.h
+@@ -31,7 +31,7 @@
+ class InflateStream : public google::protobuf::io::ZeroCopyInputStream
+ {
+ private:
+- std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ;
++ std::unique_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ;
+
+ z_stream zs_ ;
+ const Bytef *next_undelivered_ ;
+@@ -94,7 +94,7 @@ class InflateStream : public google::pro
+ }
+
+ public:
+- InflateStream( std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is ) : is_( is ), total_( 0 )
++ InflateStream( std::unique_ptr< google::protobuf::io::ZeroCopyInputStream > is ) : is_( is ), total_( 0 )
+ {
+ zs_.avail_in = 0 ;
+
+@@ -222,7 +222,7 @@ struct BzipError : public Exception {
+ class BunzipStream : public google::protobuf::io::ZeroCopyInputStream
+ {
+ private:
+- std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ;
++ std::unique_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ;
+
+ bz_stream zs_ ;
+ char *next_undelivered_ ;
+@@ -275,7 +275,7 @@ class BunzipStream : public google::prot
+ }
+
+ public:
+- BunzipStream( std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is ) : is_( is )
++ BunzipStream( std::unique_ptr< google::protobuf::io::ZeroCopyInputStream > is ) : is_( is )
+ {
+ zs_.avail_in = 0 ;
+
+@@ -392,7 +392,7 @@ class BzipStream : public google::protob
+
+ inline google::protobuf::io::FileOutputStream *make_output_stream( const char *name )
+ {
+- std::auto_ptr< google::protobuf::io::FileOutputStream > fos(
++ std::unique_ptr< google::protobuf::io::FileOutputStream > fos(
+ new google::protobuf::io::FileOutputStream(
+ !name || 0 == strcmp( name, "-" ) ? dup( 1 ) :
+ throw_errno_if_minus1( open( name, O_WRONLY | O_CREAT, 0666 ),
+--- a/src/ducttape.h
++++ b/src/ducttape.h
+@@ -136,7 +136,7 @@ class GlzWriter : public Stream
+ class ThreeAlnWriter : public Stream
+ {
+ private:
+- std::auto_ptr< std::ostream > out_ ;
++ std::unique_ptr< std::ostream > out_ ;
+ std::string name_ ;
+ Chan chan_ ;
+
+--- a/src/output_streams.h
++++ b/src/output_streams.h
+@@ -42,7 +42,7 @@ namespace streams {
+ class TextWriter : public Stream
+ {
+ private:
+- auto_ptr< std::ostream > out_ ;
++ std::unique_ptr< std::ostream > out_ ;
+
+ void print_msg( const google::protobuf::Message& ) ;
+
+@@ -69,7 +69,7 @@ class SamWriter : public Stream
+ enum bad_stuff { goodness = 0, no_hit, multiple_hits, no_seqid, no_seq, bad_cigar, bad_stuff_max } ;
+ static const char *descr[] ;
+
+- std::auto_ptr< std::ostream > out_ ;
++ std::unique_ptr< std::ostream > out_ ;
+ string nm_ ;
+ int discarded[bad_stuff_max] ;
+
+@@ -120,7 +120,7 @@ class SamWriter : public Stream
+ class FastaAlnWriter : public Stream
+ {
+ private:
+- std::auto_ptr< std::ostream > out_ ;
++ std::unique_ptr< std::ostream > out_ ;
+
+ public:
+ FastaAlnWriter( const pair< ostream*, string > &p ) : out_( p.first ) {}
+@@ -135,7 +135,7 @@ class FastaAlnWriter : public Stream
+ class FastqWriter : public Stream
+ {
+ private:
+- std::auto_ptr< std::ostream > out_ ;
++ std::unique_ptr< std::ostream > out_ ;
+ bool with_qual_ ;
+
+ public:
+@@ -146,7 +146,7 @@ class FastqWriter : public Stream
+ class TableWriter : public Stream
+ {
+ private:
+- std::auto_ptr< std::ostream > out_ ;
++ std::unique_ptr< std::ostream > out_ ;
+
+ public:
+ TableWriter( const pair< ostream*, string > &p ) : out_( p.first ) {}
+@@ -173,7 +173,7 @@ class GenTextAlignment : public Filter
+ class WigCoverageWriter : public Stream
+ {
+ private:
+- std::auto_ptr< std::ostream > out_ ;
++ std::unique_ptr< std::ostream > out_ ;
+
+ public:
+ WigCoverageWriter( const pair< ostream*, string > &p ) : out_( p.first ) {}
+--- a/src/stream.cc
++++ b/src/stream.cc
+@@ -78,7 +78,7 @@ int transfer( Stream& in, Stream& out )
+
+ int anfo_reader__num_files_ = 0 ;
+
+-AnfoReader::AnfoReader( std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, const std::string& name ) : is_( is ), name_( name )
++AnfoReader::AnfoReader( std::unique_ptr< google::protobuf::io::ZeroCopyInputStream > is, const std::string& name ) : is_( is ), name_( name )
+ {
+ std::string magic ;
+ CodedInputStream cis( is_.get() ) ;
+@@ -418,7 +418,7 @@ bool ChunkedReader::get_next_chunk()
+ return true ;
+ }
+
+-ChunkedReader::ChunkedReader( std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, const std::string& name ) : is_( is ), name_( name )
++ChunkedReader::ChunkedReader( std::unique_ptr< google::protobuf::io::ZeroCopyInputStream > is, const std::string& name ) : is_( is ), name_( name )
+ {
+ {
+ std::string magic ;
+@@ -1090,7 +1090,7 @@ namespace {
+ class StreamWithProgress : public google::protobuf::io::ZeroCopyInputStream
+ {
+ private:
+- std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ;
++ std::unique_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ;
+ std::string name_ ;
+ int64_t total_, read_ ;
+ Chan out_ ;
+@@ -1111,7 +1111,7 @@ namespace {
+ }
+
+ public:
+- StreamWithProgress( std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, const string& name, int64_t total )
++ StreamWithProgress( std::unique_ptr< google::protobuf::io::ZeroCopyInputStream > is, const string& name, int64_t total )
+ : is_( is ), name_( basename( name ) ), total_( total ), read_( 0 ) {}
+
+ virtual bool Next( const void **data, int *size ) { return check( is_->Next( data, size ) ) ; }
+@@ -1146,7 +1146,7 @@ namespace {
+ return true ;
+ }
+
+- StreamHolder make_input_stream_( std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, const string& name, bool solexa_scores, char origin, const string& genome )
++ StreamHolder make_input_stream_( std::unique_ptr< google::protobuf::io::ZeroCopyInputStream > is, const string& name, bool solexa_scores, char origin, const string& genome )
+ {
+ // peek into stream, but put it back. then check magic numbers and
+ // create the right stream
+@@ -1176,7 +1176,7 @@ namespace {
+ {
+ #if HAVE_LIBBZ2 && HAVE_BZLIB_H
+ console.output( Console::debug, name + ": BZip compressed" ) ;
+- std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > bs( new BunzipStream( is ) ) ;
++ std::unique_ptr< google::protobuf::io::ZeroCopyInputStream > bs( new BunzipStream( is ) ) ;
+ return make_input_stream_( bs, name, solexa_scores, origin, genome ) ;
+ #else
+ throw "found BZip'ed file, but have no libbz2 support" ;
+@@ -1186,7 +1186,7 @@ namespace {
+ {
+ #if HAVE_LIBZ && HAVE_ZLIB_H
+ console.output( Console::debug, name + ": GZip compressed" ) ;
+- std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > zs( new InflateStream( is ) ) ;
++ std::unique_ptr< google::protobuf::io::ZeroCopyInputStream > zs( new InflateStream( is ) ) ;
+ return make_input_stream_( zs, name, solexa_scores, origin, genome ) ;
+ #else
+ throw "found GZip'ed file, but have no zlib support" ;
+@@ -1230,12 +1230,12 @@ Header UniversalReader::fetch_header()
+ if( !str_ ) {
+ if( !is_.get() ) {
+ int fd = throw_errno_if_minus1( open( name_.c_str(), O_RDONLY ), "opening (UniversalReader) ", name_.c_str() ) ;
+- std::auto_ptr< google::protobuf::io::FileInputStream > s( new google::protobuf::io::FileInputStream( fd ) ) ;
++ std::unique_ptr< google::protobuf::io::FileInputStream > s( new google::protobuf::io::FileInputStream( fd ) ) ;
+ s->SetCloseOnDelete( true ) ;
+ struct stat st ;
+ if( fstat( fd, &st ) ) is_ = s ;
+ else is_.reset( new StreamWithProgress(
+- std::auto_ptr<google::protobuf::io::ZeroCopyInputStream>(s), name_, st.st_size ) ) ;
++ std::unique_ptr<google::protobuf::io::ZeroCopyInputStream>(s), name_, st.st_size ) ) ;
+ }
+ str_ = make_input_stream_( is_, name_, solexa_scores_, origin_, genome_ ) ;
+ }
+@@ -1375,7 +1375,7 @@ void BamReader::read_string( unsigned l,
+ }
+ }
+
+-BamReader::BamReader( auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, const string& name, const string& genome ) :
++BamReader::BamReader( std::unique_ptr< google::protobuf::io::ZeroCopyInputStream > is, const string& name, const string& genome ) :
+ is_( is ), name_( name ), genome_( genome ), buf_(0), buf_size_(0)
+ {
+ if( read_uint32() != 0x014d4142 ) throw "missing BAM magic number" ;
+--- a/src/stream.h
++++ b/src/stream.h
+@@ -316,11 +316,11 @@ struct ParseError : public Exception {
+ class AnfoReader : public Stream
+ {
+ private:
+- std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ;
++ std::unique_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ;
+ std::string name_ ;
+
+ public:
+- AnfoReader( std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, const std::string& name ) ;
++ AnfoReader( std::unique_ptr< google::protobuf::io::ZeroCopyInputStream > is, const std::string& name ) ;
+ virtual Result fetch_result() ;
+
+ //! \internal
+@@ -342,7 +342,7 @@ class AnfoReader : public Stream
+ class UniversalReader : public Stream
+ {
+ private:
+- std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ;
++ std::unique_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ;
+ std::string name_ ;
+ StreamHolder str_ ;
+
+@@ -382,9 +382,9 @@ class ChunkedWriter : public Stream
+ enum method { none, fastlz, gzip, bzip } ;
+
+ private:
+- std::auto_ptr< google::protobuf::io::ZeroCopyOutputStream > zos_ ; // final output
++ std::unique_ptr< google::protobuf::io::ZeroCopyOutputStream > zos_ ; // final output
+ std::vector< char > buf_ ; // in-memory buffer
+- std::auto_ptr< google::protobuf::io::ArrayOutputStream > aos_ ; // output to buffer
++ std::unique_ptr< google::protobuf::io::ArrayOutputStream > aos_ ; // output to buffer
+ Chan chan_ ;
+ std::string name_ ;
+ int64_t wrote_ ;
+@@ -411,15 +411,15 @@ class ChunkedWriter : public Stream
+ class ChunkedReader : public Stream
+ {
+ private:
+- std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ;
++ std::unique_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ;
+ std::vector< char > buf_ ; // in-memory buffer
+- std::auto_ptr< google::protobuf::io::ArrayInputStream > ais_ ; // output to buffer
++ std::unique_ptr< google::protobuf::io::ArrayInputStream > ais_ ; // output to buffer
+ std::string name_ ;
+
+ bool get_next_chunk() ;
+
+ public:
+- ChunkedReader( std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, const std::string& name ) ;
++ ChunkedReader( std::unique_ptr< google::protobuf::io::ZeroCopyInputStream > is, const std::string& name ) ;
+ virtual Result fetch_result() ;
+
+ //! \internal
+@@ -744,7 +744,7 @@ class ConcatStream : public StreamBundle
+ class FastqReader : public Stream
+ {
+ private:
+- std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ;
++ std::unique_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ;
+ bool sol_scores_ ;
+ char origin_ ;
+
+@@ -759,7 +759,7 @@ class FastqReader : public Stream
+ }
+
+ public:
+- FastqReader( std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, bool solexa_scores, char origin ) :
++ FastqReader( std::unique_ptr< google::protobuf::io::ZeroCopyInputStream > is, bool solexa_scores, char origin ) :
+ is_( is ), sol_scores_(solexa_scores), origin_(origin) { read_next_message() ; }
+
+ virtual Result fetch_result() { Result r ; std::swap( r, res_ ) ; read_next_message() ; return r ; }
+@@ -769,7 +769,7 @@ class FastqReader : public Stream
+ class SamReader : public Stream
+ {
+ private:
+- std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ;
++ std::unique_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ;
+ string name_, genome_ ;
+ Chan progress_ ;
+ int nmsg_ ;
+@@ -792,7 +792,7 @@ class SamReader : public Stream
+ }
+
+ public:
+- SamReader( std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, const string& n, const string& g ) :
++ SamReader( std::unique_ptr< google::protobuf::io::ZeroCopyInputStream > is, const string& n, const string& g ) :
+ is_( is ), name_( n ), genome_( g ), nmsg_(0) { read_next_message() ; }
+
+ virtual Header fetch_header() { hdr_.add_is_sorted_by_coordinate( "" ) ; return Stream::fetch_header() ; }
+@@ -803,7 +803,7 @@ class SamReader : public Stream
+ class SffReader : public Stream
+ {
+ private:
+- std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ;
++ std::unique_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ;
+ string name_ ;
+ unsigned remaining_ ;
+ unsigned number_of_flows_ ;
+@@ -818,7 +818,7 @@ class SffReader : public Stream
+ void skip( int ) ;
+
+ public:
+- SffReader( auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, const string& name ) :
++ SffReader( std::unique_ptr< google::protobuf::io::ZeroCopyInputStream > is, const string& name ) :
+ is_( is ), name_( name ), buf_(0), buf_size_(0) {}
+
+ virtual Header fetch_header() ;
+@@ -829,7 +829,7 @@ class SffReader : public Stream
+ class BamReader : public Stream
+ {
+ private:
+- std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ;
++ std::unique_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ;
+ string name_ ;
+ string genome_ ;
+ vector< string > refseqs_ ;
+@@ -843,7 +843,7 @@ class BamReader : public Stream
+ void read_string( unsigned, string* ) ;
+
+ public:
+- BamReader( auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, const string& name, const string& genome ) ;
++ BamReader( std::unique_ptr< google::protobuf::io::ZeroCopyInputStream > is, const string& name, const string& genome ) ;
+ virtual Result fetch_result() ;
+ virtual string type_name() const { return "BamReader(" + name_ + ")" ; }
+ } ;
+@@ -877,7 +877,7 @@ std::pair< PipeOutputStream*, std::strin
+ //! \brief adapts a ZeroCopyOutputStream into a streambuf
+ class zero_copy_output_buf : public std::streambuf {
+ private:
+- std::auto_ptr< google::protobuf::io::ZeroCopyOutputStream > os_ ;
++ std::unique_ptr< google::protobuf::io::ZeroCopyOutputStream > os_ ;
+
+ public:
+ zero_copy_output_buf( google::protobuf::io::ZeroCopyOutputStream* os ) : os_(os) {}
+--- a/src/concurrent_stream.cc
++++ b/src/concurrent_stream.cc
+@@ -175,7 +175,7 @@ Result ConcurrentStream::fetch_result()
+ {
+ mutex_lock( mutex_ ) ;
+ assert( !outgoing_empty() ) ;
+- auto_ptr< Result > r( outgoing_[ next_out_++ ] ) ;
++ std::unique_ptr< Result > r( outgoing_[ next_out_++ ] ) ;
+ next_out_ %= size_ ;
+ cond_signal( room_for_output_ ) ;
+ mutex_unlock( mutex_ ) ;
+@@ -209,7 +209,7 @@ void ConcurrentStream::dequeue( Stream *
+ mutex_lock( mutex_ ) ;
+ while( incoming_empty() ) cond_wait( input_available_, mutex_ ) ;
+
+- auto_ptr< Result > r( incoming_[ next_in_ ] ) ;
++ std::unique_ptr< Result > r( incoming_[ next_in_ ] ) ;
+ if( r.get() ) {
+ ++next_in_ ;
+ next_in_ %= size_ ;
+--- a/src/misc_streams.cc
++++ b/src/misc_streams.cc
+@@ -486,7 +486,7 @@ RegionFilter::Regions3 RegionFilter::all
+
+ RegionFilter::RegionFilter( const pair< istream*, string >& p )
+ {
+- auto_ptr< istream > deffile( p.first ) ;
++ std::unique_ptr< istream > deffile( p.first ) ;
+ const string &fn = p.second ;
+
+ Regions3::iterator i = all_regions.find( fn ) ;
=====================================
debian/patches/series
=====================================
@@ -3,3 +3,4 @@
03-include-unistd-forF_OK.patch
04-reorder-template-for-new-scope-rules.patch
05-autoreconf.patch
+06-gcc12.patch
=====================================
debian/upstream/metadata
=====================================
@@ -1,3 +1,6 @@
+Bug-Database: https://github.com/mpieva/anfo/issues
+Bug-Submit: https://github.com/mpieva/anfo/issues/new
+Repository: https://github.com/udo-stenzel/anfo.git
Repository-Browse: https://github.com/udo-stenzel/anfo
Registry:
- Name: OMICtools
View it on GitLab: https://salsa.debian.org/med-team/anfo/-/compare/5a189e1cc0eaaaa7cac96395ce8d48daad8925c8...24384abbcc03a54c793bd34e241617e809078223
--
View it on GitLab: https://salsa.debian.org/med-team/anfo/-/compare/5a189e1cc0eaaaa7cac96395ce8d48daad8925c8...24384abbcc03a54c793bd34e241617e809078223
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