']. Expected a two-element tuple or list.)

Debian Bug Tracking System Tue, 17 Dec 2024 09:09:28 -0800

Your message dated Tue, 17 Dec 2024 17:04:15 +0000
with message-id <e1tnazx-0064pc...@fasolo.debian.org>
and subject line Bug#1090091: fixed in bedops 2.4.41+dfsg-3
has caused the Debian Bug report #1090091,
regarding bedops: FTBFS: ERROR: Invalid value `None` in 
intersphinx_mapping['http://docs.python.org/']. Expected a two-element tuple or 
list.
to be marked as done.


This means that you claim that the problem has been dealt with.
If this is not the case it is now your responsibility to reopen the
Bug report if necessary, and/or fix the problem forthwith.

(NB: If you are a system administrator and have no idea what this
message is talking about, this may indicate a serious mail system
misconfiguration somewhere. Please contact ow...@bugs.debian.org
immediately.)


-- 
1090091: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1090091
Debian Bug Tracking System
Contact ow...@bugs.debian.org with problems

--- Begin Message ---

Package: src:bedops
Version: 2.4.41+dfsg-2
Severity: serious
Tags: ftbfs

Dear maintainer:

During a rebuild of all packages in unstable, your package failed to build:

--------------------------------------------------------------------------------
[...]
 debian/rules binary
dh binary
   dh_update_autotools_config
   dh_autoreconf
   dh_auto_configure
   dh_auto_build
        make -j2 "INSTALL=install --strip-program=true"
make[1]: Entering directory '/<<PKGBUILDDIR>>'
make  -f system.mk/Makefile.linux
make[2]: Entering directory '/<<PKGBUILDDIR>>'
#bzcat  | tar -x -C third-party
#cd third-party/jansson-2.6 && ./configure 
--prefix=/<<PKGBUILDDIR>>/third-party/jansson-2.6 && make && make install && cd 
/<<PKGBUILDDIR>> && rm -f jansson && ln -sf jansson-2.6 third-party/jansson
#bzcat  | tar -x -C third-party
#cd third-party/bzip2-1.0.6 && make libbz2.a && cd /<<PKGBUILDDIR>> && rm -f 
bzip2 && ln -sf bzip2-1.0.6 third-party/bzip2

[... snipped ...]

../../../../interfaces/general-headers/data/starch/starchApi.hpp: In member 
function âint starch::Starch::zReadLine()â:
../../../../interfaces/general-headers/data/starch/starchApi.hpp:1913:24: 
warning: âchar* strncpy(char*, const char*, size_t)â specified bound 
depends on the length of the source argument [-Wstringop-truncation]
 1913 |                 strncpy(reinterpret_cast<char *>( zLineBuf ), 
reinterpret_cast<const char *>( zRemainderBuf ), strlen(reinterpret_cast<const 
char *>( zRemainderBuf )) + 1);
      |                 
~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/general-headers/data/starch/starchApi.hpp:1913:118: 
note: length computed here
 1913 |                 strncpy(reinterpret_cast<char *>( zLineBuf ), 
reinterpret_cast<const char *>( zRemainderBuf ), strlen(reinterpret_cast<const 
char *>( zRemainderBuf )) + 1);
      |                                                                         
                                       
~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In static member function âstatic bool 
starch::Starch::hasStarchRevision1LegacyHeader(FILE*)â,
    inlined from âstatic bool 
starch::Starch::hasStarchRevision1LegacyHeader(std::string&)â at 
../../../../interfaces/general-headers/data/starch/starchApi.hpp:634:52,
    inlined from âstatic bool starch::Starch::isStarch(std::string&)â at 
../../../../interfaces/general-headers/data/starch/starchApi.hpp:698:56,
    inlined from âBed::bed_check_iterator<BedType*, 
Sz>::bed_check_iterator(std::istream&, const std::string&, 
Ext::PooledMemory<BedType, SZ>&, const std::string&, bool) [with BedType = 
Bed::BasicCoords<true, true>; long unsigned int SZ = 16]â at 
../../../../interfaces/general-headers/data/bed/BedCheckIterator.hpp:92:90:
../../../../interfaces/general-headers/data/starch/starchApi.hpp:541:49: 
warning: âchar* strncpy(char*, const char*, size_t)â specified bound 
depends on the length of the source argument [-Wstringop-truncation]
  541 |                                     std::strncpy(_recTokBuf, _token, 
strlen(_token) + 1);
      |                                     
~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/general-headers/data/starch/starchApi.hpp:541:76: note: 
length computed here
  541 |                                     std::strncpy(_recTokBuf, _token, 
strlen(_token) + 1);
      |                                                                      
~~~~~~^~~~~~~~
In member function âvoid starch::Starch::setCurrentChromosome(char*)â,
    inlined from âconst char* starch::Starch::getCurrentChromosome()â at 
../../../../interfaces/general-headers/data/starch/starchApi.hpp:718:130,
    inlined from âbool starch::Starch::isEOF()â at 
../../../../interfaces/general-headers/data/starch/starchApi.hpp:729:80,
    inlined from âBed::bed_check_iterator<BedType*, 
Sz>::bed_check_iterator(std::istream&, const std::string&, 
Ext::PooledMemory<BedType, SZ>&, const std::string&, bool) [with BedType = 
Bed::BasicCoords<true, true>; long unsigned int SZ = 16]â at 
../../../../interfaces/general-headers/data/bed/BedCheckIterator.hpp:136:36:
../../../../interfaces/general-headers/data/starch/starchApi.hpp:887:24: 
warning: âchar* strncpy(char*, const char*, size_t)â specified bound 
depends on the length of the source argument [-Wstringop-truncation]
  887 |                 strncpy(currentChromosome, _cC, strlen(_cC) + 1);
      |                 ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/general-headers/data/starch/starchApi.hpp:887:55: note: 
length computed here
  887 |                 strncpy(currentChromosome, _cC, strlen(_cC) + 1);
      |                                                 ~~~~~~^~~~~
In member function âvoid starch::Starch::setCurrentChromosome(char*)â,
    inlined from âconst char* starch::Starch::getCurrentChromosome()â at 
../../../../interfaces/general-headers/data/starch/starchApi.hpp:718:130,
    inlined from âbool starch::Starch::isEOF()â at 
../../../../interfaces/general-headers/data/starch/starchApi.hpp:729:80,
    inlined from âBed::bed_check_iterator<BedType*, Sz> 
Bed::bed_check_iterator<BedType*, Sz>::operator++(int) [with BedType = 
Bed::BasicCoords<true, true>; long unsigned int SZ = 16]â at 
../../../../interfaces/general-headers/data/bed/BedCheckIterator.hpp:292:36,
    inlined from âBed::bed_check_iterator<BedType*, Sz> 
Bed::bed_check_iterator<BedType*, Sz>::operator++(int) [with BedType = 
Bed::BasicCoords<true, true>; long unsigned int SZ = 16]â at 
../../../../interfaces/general-headers/data/bed/BedCheckIterator.hpp:267:24,
    inlined from âint checkSort(const char**, unsigned int)â at 
CheckSort.cpp:51:28:
../../../../interfaces/general-headers/data/starch/starchApi.hpp:887:24: 
warning: âchar* strncpy(char*, const char*, size_t)â specified bound 
depends on the length of the source argument [-Wstringop-truncation]
  887 |                 strncpy(currentChromosome, _cC, strlen(_cC) + 1);
      |                 ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/general-headers/data/starch/starchApi.hpp:887:55: note: 
length computed here
  887 |                 strncpy(currentChromosome, _cC, strlen(_cC) + 1);
      |                                                 ~~~~~~^~~~~
mkdir -p ../bin && cp update-sort-bed-slurm.py 
../bin/update-sort-bed-slurm-typical
mkdir -p ../bin && cp update-sort-bed-starch-slurm.py 
../bin/update-sort-bed-starch-slurm-typical
mkdir -p ../bin && cp update-sort-bed-migrate-candidates.py 
../bin/update-sort-bed-migrate-candidates-typical
mkdir -p ../bin && g++ -o ../bin/sort-bed-typical -g -O2 
-ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong 
-fstack-clash-protection -Wformat -Werror=format-security -fcf-protection   -s 
-Wall -Wextra -pedantic -ansi -O3 -std=c++11   
-iquote../../../../interfaces/general-headers objects-typical/starchConstants.o 
objects-typical/starchFileHelpers.o objects-typical/starchHelpers.o 
objects-typical/starchMetadataHelpers.o objects-typical/unstarchHelpers.o 
objects-typical/starchSha1Digest.o objects-typical/starchBase64Coding.o 
objects-typical/SortDetails.o objects-typical/Sort.o 
objects-typical/CheckSort.o -ljansson -lz -lbz2
rm -rf objects-typical
make[4]: Leaving directory '/<<PKGBUILDDIR>>/applications/bed/sort-bed/src'
make -C applications/bed/starch/src -f Makefile build
make[4]: Entering directory '/<<PKGBUILDDIR>>/applications/bed/starch/src'
mkdir -p objects
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong 
-fstack-clash-protection -Wformat -Werror=format-security -fcf-protection 
-D__STDC_CONSTANT_MACROS -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE=1 
-DUSE_ZLIB -DUSE_BZLIB -O2 -Wformat -Wall -Wextra -Wswitch-enum -std=c++11  -s  
-c ../../../../interfaces/src/data/starch/starchConstants.c -o 
objects/starchConstants.o -iquote../../../../interfaces/general-headers 
-iquote../../../..
mkdir -p objects
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong 
-fstack-clash-protection -Wformat -Werror=format-security -fcf-protection 
-D__STDC_CONSTANT_MACROS -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE=1 
-DUSE_ZLIB -DUSE_BZLIB -O2 -Wformat -Wall -Wextra -Wswitch-enum -std=c++11  -s  
-c ../../../../interfaces/src/data/starch/unstarchHelpers.c -o 
objects/unstarchHelpers.o -iquote../../../../interfaces/general-headers 
-iquote../../../..
../../../../interfaces/src/data/starch/unstarchHelpers.c: In function âvoid 
starch::UNSTARCH_printMetadataSignature(const unsigned char*)â:
../../../../interfaces/src/data/starch/unstarchHelpers.c:2276:13: warning: type 
qualifiers ignored on cast result type [-Wignored-qualifiers]
 2276 |             static_cast<const size_t>( 
STARCH2_MD_FOOTER_BASE64_ENCODED_SHA1_LENGTH ),
      |             
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/src/data/starch/unstarchHelpers.c:2278:13: warning: type 
qualifiers ignored on cast result type [-Wignored-qualifiers]
 2278 |             static_cast<const size_t>( mdSha1BufferLength ));
      |             ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/src/data/starch/unstarchHelpers.c: In function âchar* 
starch::UNSTARCH_observedSignatureForChromosome(FILE**, const Metadata*, 
uint64_t, const char*, CompressionType)â:
../../../../interfaces/src/data/starch/unstarchHelpers.c:2640:33: warning: type 
qualifiers ignored on cast result type [-Wignored-qualifiers]
 2640 |                                 static_cast<const size_t>( 
STARCH2_MD_FOOTER_BASE64_ENCODED_SHA1_LENGTH ),
      |                                 
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/src/data/starch/unstarchHelpers.c:2642:33: warning: type 
qualifiers ignored on cast result type [-Wignored-qualifiers]
 2642 |                                 static_cast<const size_t>( 
STARCH2_MD_FOOTER_SHA1_LENGTH ));
      |                                 
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/src/data/starch/unstarchHelpers.c: In function âint 
starch::UNSTARCH_createInverseTransformTokens(const unsigned char*, char, 
char*, char*)â:
../../../../interfaces/src/data/starch/unstarchHelpers.c:1651:24: warning: 
âchar* strncpy(char*, const char*, size_t)â specified bound depends on the 
length of the source argument [-Wstringop-truncation]
 1651 |                 strncpy(elemTok1, reinterpret_cast<const char *>( 
buffer ), strlen(reinterpret_cast<const char *>( buffer )) + 1);
      |                 
~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/src/data/starch/unstarchHelpers.c:1651:83: note: length 
computed here
 1651 |                 strncpy(elemTok1, reinterpret_cast<const char *>( 
buffer ), strlen(reinterpret_cast<const char *>( buffer )) + 1);
      |                                                                         
    ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/src/data/starch/unstarchHelpers.c:1678:16: warning: 
âchar* strncpy(char*, const char*, size_t)â specified bound depends on the 
length of the source argument [-Wstringop-truncation]
 1678 |         strncpy(elemTok2, reinterpret_cast<const char *>( buffer ), 
strlen(reinterpret_cast<const char *>( buffer )) + 1);
      |         
~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/src/data/starch/unstarchHelpers.c:1678:75: note: length 
computed here
 1678 |         strncpy(elemTok2, reinterpret_cast<const char *>( buffer ), 
strlen(reinterpret_cast<const char *>( buffer )) + 1);
      |                                                                     
~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/src/data/starch/unstarchHelpers.c:1667:16: warning: 
âchar* strncpy(char*, const char*, size_t)â specified bound depends on the 
length of the source argument [-Wstringop-truncation]
 1667 |         strncpy(elemTok1, reinterpret_cast<const char *>( buffer ), 
strlen(reinterpret_cast<const char *>( buffer )) + 1);
      |         
~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/src/data/starch/unstarchHelpers.c:1667:75: note: length 
computed here
 1667 |         strncpy(elemTok1, reinterpret_cast<const char *>( buffer ), 
strlen(reinterpret_cast<const char *>( buffer )) + 1);
      |                                                                     
~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/src/data/starch/unstarchHelpers.c: In function âint 
starch::UNSTARCH_extractDataWithGzip(FILE**, FILE*, const char*, const 
Metadata*, uint64_t, Boolean)â:
../../../../interfaces/src/data/starch/unstarchHelpers.c:200:32: warning: 
âchar* strncpy(char*, const char*, size_t)â output truncated before 
terminating nul copying as many bytes from a string as its length 
[-Wstringop-truncation]
  200 |                         strncpy(reinterpret_cast<char *>( zLineBuf ), 
reinterpret_cast<const char *>( zRemainderBuf ), strlen(reinterpret_cast<const 
char *>( zRemainderBuf )));
      |                         
~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/src/data/starch/unstarchHelpers.c:200:32: note: length 
computed here
  200 |                         strncpy(reinterpret_cast<char *>( zLineBuf ), 
reinterpret_cast<const char *>( zRemainderBuf ), strlen(reinterpret_cast<const 
char *>( zRemainderBuf )));
      |                         
~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/src/data/starch/unstarchHelpers.c: In function âchar* 
starch::UNSTARCH_observedSignatureForChromosome(FILE**, const Metadata*, 
uint64_t, const char*, CompressionType)â:
../../../../interfaces/src/data/starch/unstarchHelpers.c:2559:40: warning: 
âchar* strncpy(char*, const char*, size_t)â output truncated before 
terminating nul copying as many bytes from a string as its length 
[-Wstringop-truncation]
 2559 |                                 strncpy(reinterpret_cast<char *>( 
zLineBuf ), reinterpret_cast<const char *>( zRemainderBuf ), 
strlen(reinterpret_cast<const char *>( zRemainderBuf )));
      |                                 
~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/src/data/starch/unstarchHelpers.c:2559:40: note: length 
computed here
 2559 |                                 strncpy(reinterpret_cast<char *>( 
zLineBuf ), reinterpret_cast<const char *>( zRemainderBuf ), 
strlen(reinterpret_cast<const char *>( zRemainderBuf )));
      |                                 
~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
mkdir -p objects
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong 
-fstack-clash-protection -Wformat -Werror=format-security -fcf-protection 
-D__STDC_CONSTANT_MACROS -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE=1 
-DUSE_ZLIB -DUSE_BZLIB -O2 -Wformat -Wall -Wextra -Wswitch-enum -std=c++11  -s  
-c ../../../../interfaces/src/data/starch/starchHelpers.c -o 
objects/starchHelpers.o -iquote../../../../interfaces/general-headers 
-iquote../../../..
../../../../interfaces/src/data/starch/starchHelpers.c: In function âint 
starch::STARCH_createTransformTokensForHeaderlessInput(const char*, char, 
char**, int64_t*, int64_t*, char**)â:
../../../../interfaces/src/data/starch/starchHelpers.c:560:28: warning: 
âchar* strncpy(char*, const char*, size_t)â specified bound depends on the 
length of the source argument [-Wstringop-truncation]
  560 |                     strncpy(*chr, reinterpret_cast<const char *>( 
buffer ), strlen(buffer) + 1);
      |                     
~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/src/data/starch/starchHelpers.c:560:83: note: length 
computed here
  560 |                     strncpy(*chr, reinterpret_cast<const char *>( 
buffer ), strlen(buffer) + 1);
      |                                                                         
    ~~~~~~^~~~~~~~
../../../../interfaces/src/data/starch/starchHelpers.c: In function âint 
starch::STARCH_transformInput(Metadata**, const FILE*, CompressionType, const 
char*, const char*)â:
../../../../interfaces/src/data/starch/starchHelpers.c:964:28: warning: 
âchar* strncat(char*, const char*, size_t)â specified bound depends on the 
length of the source argument [-Wstringop-overflow=]
  964 |                     strncat(nonCoordLineBuf, reinterpret_cast<const 
char *>( chromosome ), strlen(chromosome) + 1);
      |                     
~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/src/data/starch/starchHelpers.c:964:98: note: length 
computed here
  964 |                     strncat(nonCoordLineBuf, reinterpret_cast<const 
char *>( chromosome ), strlen(chromosome) + 1);
      |                                                                         
                   ~~~~~~^~~~~~~~~~~~
../../../../interfaces/src/data/starch/starchHelpers.c: In function âint 
starch::STARCH2_transformHeaderedBEDInput(const FILE*, Metadata**, 
CompressionType, const char*, const char*, Boolean, Boolean, 
Bed::LineCountType)â:
../../../../interfaces/src/data/starch/starchHelpers.c:2464:28: warning: 
âchar* strncat(char*, const char*, size_t)â specified bound depends on the 
length of the source argument [-Wstringop-overflow=]
 2464 |                     strncat(nonCoordLineBuf, reinterpret_cast<const 
char *>( chromosome ), strlen(chromosome) + 1);
      |                     
~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/src/data/starch/starchHelpers.c:2464:98: note: length 
computed here
 2464 |                     strncat(nonCoordLineBuf, reinterpret_cast<const 
char *>( chromosome ), strlen(chromosome) + 1);
      |                                                                         
                   ~~~~~~^~~~~~~~~~~~
mkdir -p objects
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong 
-fstack-clash-protection -Wformat -Werror=format-security -fcf-protection 
-D__STDC_CONSTANT_MACROS -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE=1 
-DUSE_ZLIB -DUSE_BZLIB -O2 -Wformat -Wall -Wextra -Wswitch-enum -std=c++11  -s  
-c ../../../../interfaces/src/data/starch/starchMetadataHelpers.c -o 
objects/starchMetadataHelpers.o -iquote../../../../interfaces/general-headers 
-iquote../../../..
../../../../interfaces/src/data/starch/starchMetadataHelpers.c: In function 
âint starch::STARCH_updateMetadataForChromosome(Metadata**, char*, char*, 
uint64_t, Bed::LineCountType, Bed::BaseCountType, Bed::BaseCountType, Boolean, 
Boolean, char*, Bed::LineLengthType)â:
../../../../interfaces/src/data/starch/starchMetadataHelpers.c:311:20: warning: 
âchar* strncpy(char*, const char*, size_t)â specified bound depends on the 
length of the source argument [-Wstringop-truncation]
  311 |             strncpy(iter->filename, fn, strlen(fn) + 1);
      |             ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/src/data/starch/starchMetadataHelpers.c:311:47: note: 
length computed here
  311 |             strncpy(iter->filename, fn, strlen(fn) + 1);
      |                                         ~~~~~~^~~~
../../../../interfaces/src/data/starch/starchMetadataHelpers.c:330:24: warning: 
âchar* strncpy(char*, const char*, size_t)â specified bound depends on the 
length of the source argument [-Wstringop-truncation]
  330 |                 strncpy(iter->signature, signature, strlen(signature) + 
1);
      |                 
~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/src/data/starch/starchMetadataHelpers.c:330:59: note: 
length computed here
  330 |                 strncpy(iter->signature, signature, strlen(signature) + 
1);
      |                                                     ~~~~~~^~~~~~~~~~~
../../../../interfaces/src/data/starch/starchMetadataHelpers.c: In function 
âint starch::STARCH_readLegacyMetadata(const char*, Metadata**, 
CompressionType*, ArchiveVersion**, uint64_t*, Boolean*, Boolean)â:
../../../../interfaces/src/data/starch/starchMetadataHelpers.c:2221:32: 
warning: âchar* strncpy(char*, const char*, size_t)â specified bound 
depends on the length of the source argument [-Wstringop-truncation]
 2221 |                         strncpy(recTokBuf, token, strlen(token) + 1);
      |                         ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/src/data/starch/starchMetadataHelpers.c:2221:57: note: 
length computed here
 2221 |                         strncpy(recTokBuf, token, strlen(token) + 1);
      |                                                   ~~~~~~^~~~~~~
mkdir -p objects
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong 
-fstack-clash-protection -Wformat -Werror=format-security -fcf-protection 
-D__STDC_CONSTANT_MACROS -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE=1 
-DUSE_ZLIB -DUSE_BZLIB -O2 -Wformat -Wall -Wextra -Wswitch-enum -std=c++11  -s  
-c ../../../../interfaces/src/data/starch/starchFileHelpers.c -o 
objects/starchFileHelpers.o -iquote../../../../interfaces/general-headers 
-iquote../../../..
mkdir -p objects
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong 
-fstack-clash-protection -Wformat -Werror=format-security -fcf-protection 
-D__STDC_CONSTANT_MACROS -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE=1 
-DUSE_ZLIB -DUSE_BZLIB -O2 -Wformat -Wall -Wextra -Wswitch-enum -std=c++11  -s  
-c ../../../../interfaces/src/data/starch/starchSha1Digest.c -o 
objects/starchSha1Digest.o -iquote../../../../interfaces/general-headers 
-iquote../../../..
mkdir -p objects
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong 
-fstack-clash-protection -Wformat -Werror=format-security -fcf-protection 
-D__STDC_CONSTANT_MACROS -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE=1 
-DUSE_ZLIB -DUSE_BZLIB -O2 -Wformat -Wall -Wextra -Wswitch-enum -std=c++11  -s  
-c ../../../../interfaces/src/data/starch/starchBase64Coding.c -o 
objects/starchBase64Coding.o -iquote../../../../interfaces/general-headers 
-iquote../../../..
mkdir -p ../bin
cp starchcluster_gnuParallel.tcsh ../bin/starchcluster_gnuParallel-typical
mkdir -p ../bin
cp starchcluster_sge.tcsh ../bin/starchcluster_sge-typical
mkdir -p ../bin
cp starchcluster_slurm.tcsh ../bin/starchcluster_slurm-typical
mkdir -p ../bin
cp starch-diff.py ../bin/starch-diff-typical
mkdir -p ../lib
ar rcs ../lib/libstarch.a objects/starchConstants.o objects/unstarchHelpers.o 
objects/starchHelpers.o objects/starchMetadataHelpers.o 
objects/starchFileHelpers.o objects/starchSha1Digest.o 
objects/starchBase64Coding.o
mkdir -p ../bin
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong 
-fstack-clash-protection -Wformat -Werror=format-security -fcf-protection 
-D__STDC_CONSTANT_MACROS -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE=1 
-DUSE_ZLIB -DUSE_BZLIB -O2 -Wformat -Wall -Wextra -Wswitch-enum -std=c++11  -s  
-c starch.c -o objects/starch.o -iquote../../../../interfaces/general-headers 
-iquote../../../..
starch.c: In function âint main(int, char**)â:
starch.c:106:40: warning: type qualifiers ignored on cast result type 
[-Wignored-qualifiers]
  106 |                                        static_cast<const 
CompressionType>( type ),
      |                                        
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
starch.c:121:50: warning: type qualifiers ignored on cast result type 
[-Wignored-qualifiers]
  121 |                                                  static_cast<const 
CompressionType>( type ),
      |                                                  
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
starch.c:123:50: warning: type qualifiers ignored on cast result type 
[-Wignored-qualifiers]
  123 |                                                  static_cast<const 
Boolean>( kStarchFinalizeTransformTrue ),
      |                                                  
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
starch.c:146:40: warning: type qualifiers ignored on cast result type 
[-Wignored-qualifiers]
  146 |                                        static_cast<const 
CompressionType>( type ),
      |                                        
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
starch.c:161:50: warning: type qualifiers ignored on cast result type 
[-Wignored-qualifiers]
  161 |                                                  static_cast<const 
CompressionType>( type ),
      |                                                  
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
starch.c:163:50: warning: type qualifiers ignored on cast result type 
[-Wignored-qualifiers]
  163 |                                                  static_cast<const 
Boolean>( kStarchFinalizeTransformTrue ),
      |                                                  
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
starch.c:191:36: warning: type qualifiers ignored on cast result type 
[-Wignored-qualifiers]
  191 |                                    static_cast<const CompressionType>( 
type ),
      |                                    
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
starch.c:194:36: warning: type qualifiers ignored on cast result type 
[-Wignored-qualifiers]
  194 |                                    static_cast<const Boolean>( 
bedGeneratePerChrSignatureFlag ),
      |                                    
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
starch.c:195:36: warning: type qualifiers ignored on cast result type 
[-Wignored-qualifiers]
  195 |                                    static_cast<const Boolean>( 
bedHeaderFlag ),
      |                                    
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
starch.c:196:36: warning: type qualifiers ignored on cast result type 
[-Wignored-qualifiers]
  196 |                                    static_cast<const Boolean>( 
bedReportProgressFlag ),
      |                                    
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
starch.c:197:36: warning: type qualifiers ignored on cast result type 
[-Wignored-qualifiers]
  197 |                                    static_cast<const LineCountType>( 
bedReportProgressN )) != STARCH_EXIT_SUCCESS)
      |                                    
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong 
-fstack-clash-protection -Wformat -Werror=format-security -fcf-protection 
-D__STDC_CONSTANT_MACROS -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE=1 
-DUSE_ZLIB -DUSE_BZLIB -O2 -Wformat -Wall -Wextra -Wswitch-enum -std=c++11  -s  
objects/starch.o -o ../bin/starch-typical ../lib/libstarch.a -ljansson -lz -lbz2
mkdir -p ../bin
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong 
-fstack-clash-protection -Wformat -Werror=format-security -fcf-protection 
-D__STDC_CONSTANT_MACROS -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE=1 
-DUSE_ZLIB -DUSE_BZLIB -O2 -Wformat -Wall -Wextra -Wswitch-enum -std=c++11  -s  
-c unstarch.c -o objects/unstarch.o 
-iquote../../../../interfaces/general-headers -iquote../../../..
unstarch.c: In function âint main(int, char**)â:
unstarch.c:401:59: warning: type qualifiers ignored on cast result type 
[-Wignored-qualifiers]
  401 |                                                           
static_cast<const unsigned long long>( metadataOffset ),
      |                                                           
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
unstarch.c:402:59: warning: type qualifiers ignored on cast result type 
[-Wignored-qualifiers]
  402 |                                                           
static_cast<const Boolean>( headerFlag )) != 0) {
      |                                                           
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
unstarch.c:422:58: warning: type qualifiers ignored on cast result type 
[-Wignored-qualifiers]
  422 |                                                          
static_cast<const unsigned long long>( metadataOffset ),
      |                                                          
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
unstarch.c:423:58: warning: type qualifiers ignored on cast result type 
[-Wignored-qualifiers]
  423 |                                                          
static_cast<const Boolean>( headerFlag )) != 0) {
      |                                                          
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
unstarch.c:452:59: warning: type qualifiers ignored on cast result type 
[-Wignored-qualifiers]
  452 |                                                           
static_cast<const unsigned long long>( sizeof(starchRevision2HeaderBytes) ),
      |                                                           
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
unstarch.c:453:59: warning: type qualifiers ignored on cast result type 
[-Wignored-qualifiers]
  453 |                                                           
static_cast<const Boolean>( headerFlag )) != 0) {
      |                                                           
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
unstarch.c:473:58: warning: type qualifiers ignored on cast result type 
[-Wignored-qualifiers]
  473 |                                                          
static_cast<const unsigned long long>( sizeof(starchRevision2HeaderBytes) ),
      |                                                          
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
unstarch.c:474:58: warning: type qualifiers ignored on cast result type 
[-Wignored-qualifiers]
  474 |                                                          
static_cast<const Boolean>( headerFlag )) != 0) {
      |                                                          
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
unstarch.c:567:39: warning: type qualifiers ignored on cast result type 
[-Wignored-qualifiers]
  567 |         UNSTARCH_printCompressionType(static_cast<const 
CompressionType>( type ));
      |                                       
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
unstarch.c:798:78: warning: type qualifiers ignored on cast result type 
[-Wignored-qualifiers]
  798 |                                                                         
     static_cast<const unsigned long long>( sizeof(starchRevision2HeaderBytes) 
),
      |                                                                         
     ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
unstarch.c:809:82: warning: type qualifiers ignored on cast result type 
[-Wignored-qualifiers]
  809 |                                                                         
         static_cast<const unsigned long long>( 
sizeof(starchRevision2HeaderBytes) ),
      |                                                                         
         
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
unstarch.c: In function âvoid 
starch::UNSTARCH_printMetadataSha1Signature(unsigned char*)â:
unstarch.c:1334:13: warning: type qualifiers ignored on cast result type 
[-Wignored-qualifiers]
 1334 |             static_cast<const size_t>( 
STARCH2_MD_FOOTER_BASE64_ENCODED_SHA1_LENGTH ),
      |             
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
unstarch.c:1336:13: warning: type qualifiers ignored on cast result type 
[-Wignored-qualifiers]
 1336 |             static_cast<const size_t>( sha1BufferLength ));
      |             ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong 
-fstack-clash-protection -Wformat -Werror=format-security -fcf-protection 
-D__STDC_CONSTANT_MACROS -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE=1 
-DUSE_ZLIB -DUSE_BZLIB -O2 -Wformat -Wall -Wextra -Wswitch-enum -std=c++11  -s  
objects/unstarch.o -o ../bin/unstarch-typical ../lib/libstarch.a -ljansson -lz 
-lbz2
mkdir -p ../bin
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong 
-fstack-clash-protection -Wformat -Werror=format-security -fcf-protection 
-D__STDC_CONSTANT_MACROS -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE=1 
-DUSE_ZLIB -DUSE_BZLIB -O2 -Wformat -Wall -Wextra -Wswitch-enum -std=c++11  -s  
-c starchcat.c -o objects/starchcat.o 
-iquote../../../../interfaces/general-headers -iquote../../../..
In file included from /usr/include/c++/14/cassert:44,
                 from starchcat.c:33:
starchcat.c: In function âint main(int, char**)â:
starchcat.c:136:71: warning: type qualifiers ignored on cast result type 
[-Wignored-qualifiers]
  136 |             assert( STARCHCAT_allocMetadataRecords      ( &mdRecords, 
static_cast<const unsigned int>( numRecords ) ) );
      |                                                                       
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
starchcat.c:137:75: warning: type qualifiers ignored on cast result type 
[-Wignored-qualifiers]
  137 |             assert( STARCHCAT_allocMetadataJSONObjects  ( 
&metadataJSONs, static_cast<const unsigned int>( numRecords ) ) );
      |                                                                         
  ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
starchcat.c:138:87: warning: type qualifiers ignored on cast result type 
[-Wignored-qualifiers]
  138 |             assert( STARCHCAT_buildMetadataRecords      ( 
&metadataJSONs, &mdRecords, static_cast<const unsigned int>( firstArgc ), 
static_cast<const int>( argc ), const_cast<const char **>( argv ) ) );
      |                                                                         
              ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
starchcat.c:138:133: warning: type qualifiers ignored on cast result type 
[-Wignored-qualifiers]
  138 |             assert( STARCHCAT_buildMetadataRecords      ( 
&metadataJSONs, &mdRecords, static_cast<const unsigned int>( firstArgc ), 
static_cast<const int>( argc ), const_cast<const char **>( argv ) ) );
      |                                                                         
                                                            
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
starchcat.c:139:75: warning: type qualifiers ignored on cast result type 
[-Wignored-qualifiers]
  139 |             assert( STARCHCAT_checkMetadataJSONVersions ( 
&metadataJSONs, static_cast<const unsigned int>( numRecords ) ) );
      |                                                                         
  ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
starchcat.c:140:145: warning: type qualifiers ignored on cast result type 
[-Wignored-qualifiers]
  140 |             assert( STARCHCAT_buildUniqueChromosomeList ( &chromosomes, 
&numChromosomes, reinterpret_cast<const MetadataRecord *>( mdRecords ), 
static_cast<const unsigned int>( numRecords ) ) );
      |                                                                         
                                                                        
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
starchcat.c:141:69: warning: type qualifiers ignored on cast result type 
[-Wignored-qualifiers]
  141 |             assert( STARCHCAT_allocChromosomeSummary    ( &summary, 
static_cast<const unsigned int>( numChromosomes ) ) );
      |                                                                     
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
starchcat.c:142:124: warning: type qualifiers ignored on cast result type 
[-Wignored-qualifiers]
  142 |             assert( STARCHCAT_buildChromosomeSummary    ( &summary, 
reinterpret_cast<const MetadataRecord *>( mdRecords ), static_cast<const 
unsigned int>( numRecords ), const_cast<const char **>( chromosomes ), 
static_cast<const unsigned int>( numChromosomes ) ) );
      |                                                                         
                                                   
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
starchcat.c:142:213: warning: type qualifiers ignored on cast result type 
[-Wignored-qualifiers]
  142 |             assert( STARCHCAT_buildChromosomeSummary    ( &summary, 
reinterpret_cast<const MetadataRecord *>( mdRecords ), static_cast<const 
unsigned int>( numRecords ), const_cast<const char **>( chromosomes ), 
static_cast<const unsigned int>( numChromosomes ) ) );
      |                                                                         
                                                                                
                                                            
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
starchcat.c:143:71: warning: type qualifiers ignored on cast result type 
[-Wignored-qualifiers]
  143 |             assert( STARCHCAT_allocChromosomeSummaries  ( &summaries, 
static_cast<const unsigned int>( numChromosomes ) ) );
      |                                                                       
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
starchcat.c:144:127: warning: type qualifiers ignored on cast result type 
[-Wignored-qualifiers]
  144 |             assert( STARCHCAT_buildChromosomeSummaries  ( &summaries, 
reinterpret_cast<const ChromosomeSummary *>( summary ), static_cast<const 
unsigned int>( numChromosomes ) ) );
      |                                                                         
                                                      
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
starchcat.c:164:61: warning: type qualifiers ignored on cast result type 
[-Wignored-qualifiers]
  164 |                                                             
static_cast<const CompressionType>( outputType ),
      |                                                             
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
starchcat.c:178:61: warning: type qualifiers ignored on cast result type 
[-Wignored-qualifiers]
  178 |                                                             
static_cast<const CompressionType>( outputType ),
      |                                                             
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
starchcat.c:223:60: warning: type qualifiers ignored on cast result type 
[-Wignored-qualifiers]
  223 |         assert( STARCHCAT_freeMetadataRecords( &mdRecords, 
static_cast<const unsigned int>( numRecords ) ) );
      |                                                            
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
starchcat.c:233:68: warning: type qualifiers ignored on cast result type 
[-Wignored-qualifiers]
  233 |         assert (STARCHCAT_freeMetadataJSONObjects( &metadataJSONs, 
static_cast<const unsigned int>( numRecords ) ) );
      |                                                                    
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
starchcat.c: In function âint 
starch::STARCHCAT2_rewriteInputRecordToOutput(Metadata**, const char*, 
CompressionType, const char*, const MetadataRecord*, size_t*, Boolean, Boolean, 
Bed::LineCountType)â:
starchcat.c:1338:71: warning: type qualifiers ignored on cast result type 
[-Wignored-qualifiers]
 1338 |                                 UNSTARCH_reverseTransformCoordinates( 
static_cast<const LineCountType>( t_lineIdx ),
      |                                                                       
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
starchcat.c:1806:71: warning: type qualifiers ignored on cast result type 
[-Wignored-qualifiers]
 1806 |                                 UNSTARCH_reverseTransformCoordinates( 
static_cast<const LineCountType>( t_lineIdx ),
      |                                                                       
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
starchcat.c: In function âint 
starch::STARCHCAT_rewriteInputRecordToOutput(Metadata**, const char*, 
CompressionType, const char*, const MetadataRecord*)â:
starchcat.c:2450:25: warning: type qualifiers ignored on cast result type 
[-Wignored-qualifiers]
 2450 |                         static_cast<const uint64_t>( inRec->mdOffset ),
      |                         ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
starchcat.c:2451:25: warning: type qualifiers ignored on cast result type 
[-Wignored-qualifiers]
 2451 |                         static_cast<const Boolean>( inRec->hFlag )) != 
0 ) {
      |                         ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
starchcat.c:2471:28: warning: type qualifiers ignored on cast result type 
[-Wignored-qualifiers]
 2471 |                            static_cast<const uint64_t>( inRec->mdOffset 
),
      |                            
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
starchcat.c:2472:28: warning: type qualifiers ignored on cast result type 
[-Wignored-qualifiers]
 2472 |                            static_cast<const Boolean>( inRec->hFlag )) 
!= 0 ) {
      |                            ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
starchcat.c:2509:23: warning: type qualifiers ignored on cast result type 
[-Wignored-qualifiers]
 2509 |                       static_cast<const CompressionType>( outType ),
      |                       ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
starchcat.c:2511:23: warning: type qualifiers ignored on cast result type 
[-Wignored-qualifiers]
 2511 |                       static_cast<const Boolean>( 
kStarchFinalizeTransformFalse ),
      |                       
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
starchcat.c: In function âint 
starch::STARCHCAT2_mergeInputRecordsToOutput(const char*, Metadata**, const 
char*, CompressionType, const ChromosomeSummary*, size_t*)â:
starchcat.c:3152:54: warning: type qualifiers ignored on cast result type 
[-Wignored-qualifiers]
 3152 |                 if (STARCHCAT2_setupBzip2InputStream(static_cast<const 
size_t>( inRecIdx ),
      |                                                      
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
starchcat.c:3316:69: warning: type qualifiers ignored on cast result type 
[-Wignored-qualifiers]
 3316 |                                                                     
static_cast<const size_t>( summary->numRecords ),
      |                                                                     
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
starchcat.c:3455:77: warning: type qualifiers ignored on cast result type 
[-Wignored-qualifiers]
 3455 |                                                                         
    static_cast<const Boolean>( flushZStreamFlag ),
      |                                                                         
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
starchcat.c: In function âint 
starch::STARCHCAT_mergeInputRecordsToOutput(Metadata**, const char*, 
CompressionType, const ChromosomeSummary*)â:
starchcat.c:4265:43: warning: type qualifiers ignored on cast result type 
[-Wignored-qualifiers]
 4265 |                                           static_cast<const 
CompressionType>( outType ),
      |                                           
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
starchcat.c:4267:43: warning: type qualifiers ignored on cast result type 
[-Wignored-qualifiers]
 4267 |                                           static_cast<const Boolean>( 
kStarchFinalizeTransformFalse ),
      |                                           
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
starchcat.c: In function âint starch::STARCHCAT_mergeChromosomeStreams(const 
ChromosomeSummaries*, CompressionType, const char*)â:
starchcat.c:4402:60: warning: type qualifiers ignored on cast result type 
[-Wignored-qualifiers]
 4402 |                                                            
static_cast<const CompressionType>( outputType ),
      |                                                            
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
starchcat.c:4420:63: warning: type qualifiers ignored on cast result type 
[-Wignored-qualifiers]
 4420 |                                                               
static_cast<const CompressionType>( outputType ),
      |                                                               
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
starchcat.c:4447:57: warning: type qualifiers ignored on cast result type 
[-Wignored-qualifiers]
 4447 |                                                         
static_cast<const CompressionType>( outputType ),
      |                                                         
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
starchcat.c:4479:39: warning: type qualifiers ignored on cast result type 
[-Wignored-qualifiers]
 4479 |                                       static_cast<const Boolean>( hFlag 
),
      |                                       
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
starchcat.c: In function âint 
starch::STARCHCAT_freeChromosomeSummaries(ChromosomeSummaries**)â:
starchcat.c:4541:62: warning: type qualifiers ignored on cast result type 
[-Wignored-qualifiers]
 4541 |     STARCHCAT_freeChromosomeSummary( &((*chrSums)->summary), 
static_cast<const unsigned int>( (*chrSums)->numChromosomes ));
      |                                                              
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
starchcat.c: In function âint starch::STARCHCAT2_mergeChromosomeStreams(const 
ChromosomeSummaries*, CompressionType, const char*, size_t*, Boolean, Boolean, 
Bed::LineCountType)â:
starchcat.c:5902:61: warning: type qualifiers ignored on cast result type 
[-Wignored-qualifiers]
 5902 |                                                             
static_cast<const CompressionType>( outputType ),
      |                                                             
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
starchcat.c:5929:64: warning: type qualifiers ignored on cast result type 
[-Wignored-qualifiers]
 5929 |                                                                
static_cast<const CompressionType>( outputType ),
      |                                                                
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
starchcat.c:5952:64: warning: type qualifiers ignored on cast result type 
[-Wignored-qualifiers]
 5952 |                                                                
static_cast<const CompressionType>( outputType ),
      |                                                                
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
starchcat.c:5990:59: warning: type qualifiers ignored on cast result type 
[-Wignored-qualifiers]
 5990 |                                                           
static_cast<const CompressionType>( outputType ),
      |                                                           
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
starchcat.c:6025:38: warning: type qualifiers ignored on cast result type 
[-Wignored-qualifiers]
 6025 |                                      static_cast<const Boolean>( hFlag 
),
      |                                      ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
starchcat.c:6053:13: warning: type qualifiers ignored on cast result type 
[-Wignored-qualifiers]
 6053 |             static_cast<const size_t>( 
STARCH2_MD_FOOTER_BASE64_ENCODED_SHA1_LENGTH ),
      |             
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
starchcat.c:6055:13: warning: type qualifiers ignored on cast result type 
[-Wignored-qualifiers]
 6055 |             static_cast<const size_t>( STARCH2_MD_FOOTER_SHA1_LENGTH ));
      |             ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
starchcat.c: In function âint 
starch::STARCHCAT2_fillExtractionBufferFromBzip2Stream(Boolean*, char*, char*, 
size_t*, BZFILE**, size_t*, char*, size_t*, TransformState*)â:
starchcat.c:6719:55: warning: type qualifiers ignored on cast result type 
[-Wignored-qualifiers]
 6719 |                 UNSTARCH_reverseTransformCoordinates( static_cast<const 
LineCountType>( *t_lineIdxPtr ),
      |                                                       
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
starchcat.c: In function âint 
starch::STARCHCAT2_fillExtractionBufferFromGzipStream(Boolean*, FILE**, char*, 
char*, size_t*, z_stream*, size_t*, char**, size_t*, TransformState*)â:
starchcat.c:7060:59: warning: type qualifiers ignored on cast result type 
[-Wignored-qualifiers]
 7060 |                     UNSTARCH_reverseTransformCoordinates( 
static_cast<const LineCountType>( *t_lineIdxPtr ),
      |                                                           
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
starchcat.c: In function âint 
starch::STARCHCAT2_transformCompressionBuffer(const char*, char*, 
TransformState*)â:
starchcat.c:7428:25: warning: the address of 
âstarch::transformState::r_chromosomeâ will never be NULL [-Waddress]
 7428 |     if ((!retransState->r_chromosome) || 
(strlen(retransState->r_chromosome) == 0))
      |           ~~~~~~~~~~~~~~^~~~~~~~~~~~
In file included from starchcat.c:50:
starchcat.h:107:30: note: âstarch::transformState::r_chromosomeâ declared 
here
  107 |     char                     r_chromosome[TOKEN_CHR_MAX_LENGTH];
      |                              ^~~~~~~~~~~~
starchcat.c: In function âint 
starch::STARCHCAT2_mergeInputRecordsToOutput(const char*, Metadata**, const 
char*, CompressionType, const ChromosomeSummary*, size_t*)â:
starchcat.c:3123:16: warning: âchar* strncpy(char*, const char*, size_t)â 
specified bound depends on the length of the source argument 
[-Wstringop-truncation]
 3123 |         strncpy(transformStates[inRecIdx]->t_currentChromosome, inChr, 
strlen(inChr) + 1);
      |         
~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
starchcat.c:3123:78: note: length computed here
 3123 |         strncpy(transformStates[inRecIdx]->t_currentChromosome, inChr, 
strlen(inChr) + 1);
      |                                                                        
~~~~~~^~~~~~~
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong 
-fstack-clash-protection -Wformat -Werror=format-security -fcf-protection 
-D__STDC_CONSTANT_MACROS -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE=1 
-DUSE_ZLIB -DUSE_BZLIB -O2 -Wformat -Wall -Wextra -Wswitch-enum -std=c++11  -s  
objects/starchcat.o -o ../bin/starchcat-typical ../lib/libstarch.a -ljansson 
-lz -lbz2
mkdir -p ../bin
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong 
-fstack-clash-protection -Wformat -Werror=format-security -fcf-protection 
-D__STDC_CONSTANT_MACROS -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE=1 
-DUSE_ZLIB -DUSE_BZLIB -O2 -Wformat -Wall -Wextra -Wswitch-enum -std=c++11  -s  
-c starchstrip.c -o objects/starchstrip.o 
-iquote../../../../interfaces/general-headers -iquote../../../..
starchstrip.c: In function âvoid 
starch::STARCHSTRIP_write_updated_metadata(FILE*)â:
starchstrip.c:124:13: warning: type qualifiers ignored on cast result type 
[-Wignored-qualifiers]
  124 |             static_cast<const size_t>( 
STARCH2_MD_FOOTER_BASE64_ENCODED_SHA1_LENGTH ),
      |             
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
starchstrip.c:126:13: warning: type qualifiers ignored on cast result type 
[-Wignored-qualifiers]
  126 |             static_cast<const size_t>( STARCH2_MD_FOOTER_SHA1_LENGTH ));
      |             ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong 
-fstack-clash-protection -Wformat -Werror=format-security -fcf-protection 
-D__STDC_CONSTANT_MACROS -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE=1 
-DUSE_ZLIB -DUSE_BZLIB -O2 -Wformat -Wall -Wextra -Wswitch-enum -std=c++11  -s  
objects/starchstrip.o -o ../bin/starchstrip-typical ../lib/libstarch.a 
-ljansson -lz -lbz2
rm -rf objects
make[4]: Leaving directory '/<<PKGBUILDDIR>>/applications/bed/starch/src'
In file included from 
../../../../interfaces/general-headers/data/bed/AllocateIterator_BED_starch_minmem.hpp:39:
../../../../interfaces/general-headers/data/starch/starchApi.hpp: In static 
member function âstatic bool 
starch::Starch::hasStarchRevision1LegacyHeader(FILE*)â:
../../../../interfaces/general-headers/data/starch/starchApi.hpp:541:49: 
warning: âchar* strncpy(char*, const char*, size_t)â specified bound 
depends on the length of the source argument [-Wstringop-truncation]
  541 |                                     std::strncpy(_recTokBuf, _token, 
strlen(_token) + 1);
      |                                     
~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/general-headers/data/starch/starchApi.hpp:541:76: note: 
length computed here
  541 |                                     std::strncpy(_recTokBuf, _token, 
strlen(_token) + 1);
      |                                                                      
~~~~~~^~~~~~~~
../../../../interfaces/general-headers/data/starch/starchApi.hpp: In member 
function âint starch::Starch::zReadLine()â:
../../../../interfaces/general-headers/data/starch/starchApi.hpp:1913:24: 
warning: âchar* strncpy(char*, const char*, size_t)â specified bound 
depends on the length of the source argument [-Wstringop-truncation]
 1913 |                 strncpy(reinterpret_cast<char *>( zLineBuf ), 
reinterpret_cast<const char *>( zRemainderBuf ), strlen(reinterpret_cast<const 
char *>( zRemainderBuf )) + 1);
      |                 
~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/general-headers/data/starch/starchApi.hpp:1913:118: 
note: length computed here
 1913 |                 strncpy(reinterpret_cast<char *>( zLineBuf ), 
reinterpret_cast<const char *>( zRemainderBuf ), strlen(reinterpret_cast<const 
char *>( zRemainderBuf )) + 1);
      |                                                                         
                                       
~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
rm -rf objects_typical
make[4]: Leaving directory '/<<PKGBUILDDIR>>/applications/bed/bedmap/src'
make[3]: Leaving directory '/<<PKGBUILDDIR>>'
make[2]: Leaving directory '/<<PKGBUILDDIR>>'
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
   dh_auto_test
   create-stamp debian/debhelper-build-stamp
   dh_prep
   dh_auto_install
        make -j2 install DESTDIR=/<<BUILDDIR>>/bedops-2.4.41\+dfsg/debian/tmp 
AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true"
make[1]: Entering directory '/<<PKGBUILDDIR>>'
mkdir -p bin
cp applications/bed/conversion/src/wrappers/bam2bed 
applications/bed/conversion/src/wrappers/bam2bed_gnuParallel 
applications/bed/conversion/src/wrappers/bam2bed_sge 
applications/bed/conversion/src/wrappers/bam2bed_slurm 
applications/bed/conversion/src/wrappers/bam2starch 
applications/bed/conversion/src/wrappers/bam2starch_gnuParallel 
applications/bed/conversion/src/wrappers/bam2starch_sge 
applications/bed/conversion/src/wrappers/bam2starch_slurm 
applications/bed/conversion/src/wrappers/gff2bed 
applications/bed/conversion/src/wrappers/gff2starch 
applications/bed/conversion/src/wrappers/gtf2bed 
applications/bed/conversion/src/wrappers/gtf2starch 
applications/bed/conversion/src/wrappers/gvf2bed 
applications/bed/conversion/src/wrappers/gvf2starch 
applications/bed/conversion/src/wrappers/psl2bed 
applications/bed/conversion/src/wrappers/psl2starch 
applications/bed/conversion/src/wrappers/rmsk2bed 
applications/bed/conversion/src/wrappers/rmsk2starch 
applications/bed/conversion/src/wrappers
 /sam2bed applications/bed/conversion/src/wrappers/sam2starch 
applications/bed/conversion/src/wrappers/vcf2bed 
applications/bed/conversion/src/wrappers/vcf2starch 
applications/bed/conversion/src/wrappers/wig2bed 
applications/bed/conversion/src/wrappers/wig2starch bin
cp applications/bed/starch/bin/starchcluster_sge-typical bin/starchcluster_sge
cp applications/bed/starch/bin/starchcluster_gnuParallel-typical 
bin/starchcluster_gnuParallel
cp applications/bed/starch/bin/starchcluster_slurm-typical 
bin/starchcluster_slurm
cp applications/bed/starch/bin/starch-diff-typical bin/starch-diff
cp applications/bed/sort-bed/bin/sort-bed-typical bin/sort-bed
cp applications/bed/sort-bed/bin/update-sort-bed-slurm-typical 
bin/update-sort-bed-slurm
cp applications/bed/sort-bed/bin/update-sort-bed-starch-slurm-typical 
bin/update-sort-bed-starch-slurm
cp applications/bed/sort-bed/bin/update-sort-bed-migrate-candidates-typical 
bin/update-sort-bed-migrate-candidates
cp applications/bed/bedops/bin/bedops-typical bin/bedops
cp applications/bed/closestfeats/bin/closest-features-typical 
bin/closest-features
cp applications/bed/bedmap/bin/bedmap-typical bin/bedmap
cp applications/bed/bedextract/bin/bedextract-typical bin/bedextract
cp applications/bed/starch/bin/starch-typical bin/starch
cp applications/bed/starch/bin/unstarch-typical bin/unstarch
cp applications/bed/starch/bin/starchcat-typical bin/starchcat
cp applications/bed/starch/bin/starchstrip-typical bin/starchstrip
cp applications/bed/conversion/bin/convert2bed-typical bin/convert2bed
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
   debian/rules override_dh_install-arch
make[1]: Entering directory '/<<PKGBUILDDIR>>'
dh_install -a
mv bin/starch bin/bedops-starch
mkdir -p debian/bedops/usr/bin/
cp bin/* debian/bedops/usr/bin/
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
   dh_install -Nbedops
   debian/rules override_dh_installdocs-indep
make[1]: Entering directory '/<<PKGBUILDDIR>>'
cd docs && make html
make[2]: Entering directory '/<<PKGBUILDDIR>>/docs'
sphinx-build -b html -d _build/doctrees   . _build/html
Running Sphinx v8.1.3
loading translations [en]... done
making output directory... done
Converting `source_suffix = '.rst'` to `source_suffix = {'.rst': 
'restructuredtext'}`.
ERROR: Invalid value `None` in intersphinx_mapping['http://docs.python.org/']. 
Expected a two-element tuple or list.

Configuration error:
Invalid `intersphinx_mapping` configuration (1 error).
make[2]: *** [Makefile:53: html] Error 2
make[2]: Leaving directory '/<<PKGBUILDDIR>>/docs'
make[1]: *** [debian/rules:35: override_dh_installdocs-indep] Error 2
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
make: *** [debian/rules:25: binary] Error 2
dpkg-buildpackage: error: debian/rules binary subprocess returned exit status 2
--------------------------------------------------------------------------------

The above is just how the build ends and not necessarily the most relevant part.
If required, the full build log is available here:

https://people.debian.org/~sanvila/build-logs/202412/

About the archive rebuild: The build was made on virtual machines from AWS,
using sbuild and a reduced chroot with only build-essential packages.

If you could not reproduce the bug please contact me privately, as I
am willing to provide ssh access to a virtual machine where the bug is
fully reproducible.

If this is really a bug in one of the build-depends, please use
reassign and affects, so that this is still visible in the BTS web
page for this package.

Thanks.

--- End Message ---

--- Begin Message ---

Source: bedops
Source-Version: 2.4.41+dfsg-3
Done: Michael R. Crusoe <cru...@debian.org>

We believe that the bug you reported is fixed in the latest version of
bedops, which is due to be installed in the Debian FTP archive.

A summary of the changes between this version and the previous one is
attached.

Thank you for reporting the bug, which will now be closed.  If you
have further comments please address them to 1090...@bugs.debian.org,
and the maintainer will reopen the bug report if appropriate.

Debian distribution maintenance software
pp.
Michael R. Crusoe <cru...@debian.org> (supplier of updated bedops package)

(This message was generated automatically at their request; if you
believe that there is a problem with it please contact the archive
administrators by mailing ftpmas...@ftp-master.debian.org)


-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA512

Format: 1.8
Date: Tue, 17 Dec 2024 17:40:45 +0100
Source: bedops
Architecture: source
Version: 2.4.41+dfsg-3
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team 
<debian-med-packag...@lists.alioth.debian.org>
Changed-By: Michael R. Crusoe <cru...@debian.org>
Closes: 1090091
Changes:
 bedops (2.4.41+dfsg-3) unstable; urgency=medium
 .
   * Team upload.
   * Docs: added patch removing the use of intersphinx, it is unneeded
     and had the wrong layout. Closes: #1090091
   * d/control: need tcsh for the man pages
   * Standards-Version: 4.7.0 (routine-update)
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bedops_2.4.41+dfsg-3.debian.tar.xz
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bedops_2.4.41+dfsg-3_source.buildinfo
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 66b20be95d9d5e06d41a433f514f3aad8ada3f4ddbaf6e53472c7a24411f3064 10900 
bedops_2.4.41+dfsg-3.debian.tar.xz
 9518b12fcff3ccfa5dfd72f9598d476bf0e001a465515d2c1223271fd565679a 7603 
bedops_2.4.41+dfsg-3_source.buildinfo
Files:
 c0afacc40508cf933d7f2e8ea9a7e9cb 2227 science optional bedops_2.4.41+dfsg-3.dsc
 3ca9861afade636440c41b7a824de9a8 10900 science optional 
bedops_2.4.41+dfsg-3.debian.tar.xz
 4d53646fea532b05e981dfaee8c64a68 7603 science optional 
bedops_2.4.41+dfsg-3_source.buildinfo
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--- End Message ---

Bug#1090091: marked as done (bedops: FTBFS: ERROR: Invalid value `None` in intersphinx_mapping['http://docs.python.org/']. Expected a two-element tuple or list.)

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