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.
