[Debichem-devel] Bug#1105536: libmstoolkit: FTBFS with make --shuffle=reverse: ar: mzp.MSNumpress.o: No such file or directory
Lucas Nussbaum
lucas at debian.org
Tue May 13 20:03:40 BST 2025
Source: libmstoolkit
Version: 82-7.2
Severity: minor
Tags: trixie sid ftbfs
User: lucas at debian.org
Usertags: ftbfs-shuffle
Hi,
GNU Make now has a --shuffle option that simulates non-deterministic ordering
of target prerequisites. See
https://trofi.github.io/posts/238-new-make-shuffle-mode.html and also previous
work in Debian by Santiago Vila:
https://people.debian.org/~sanvila/make-shuffle/
This package fails to build with make --shuffle=reverse.
This is likely to be caused by a missing dependency in
debian/rules or an upstream Makefile.
More information about this mass bug filing is available at
https://wiki.debian.org/qa.debian.org/FTBFS/Shuffle
Relevant part (hopefully):
> make[3]: Entering directory '/build/reproducible-path/libmstoolkit-82'
> Makefile:88: update target 'MSReaderLite.o' due to: target does not exist
> g++ -O3 -static -g -I. -I./include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DGCC -DHAVE_EXPAT_CONFIG_H -D_NOSQLITE ./src/MSToolkit/MSReader.cpp -c -o MSReaderLite.o
> Makefile:85: update target 'MSReader.o' due to: target does not exist
> g++ -O3 -static -g -I. -I./include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DGCC -DHAVE_EXPAT_CONFIG_H ./src/MSToolkit/MSReader.cpp -c
> Makefile:97: update target 'pepXMLWriter.o' due to: target does not exist
> g++ -O3 -static -g -I. -I./include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DGCC -DHAVE_EXPAT_CONFIG_H ./src/MSToolkit/pepXMLWriter.cpp -c
> Makefile:94: update target 'mzMLWriter.o' due to: target does not exist
> g++ -O3 -static -g -I. -I./include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DGCC -DHAVE_EXPAT_CONFIG_H ./src/MSToolkit/mzMLWriter.cpp -c
> ./src/MSToolkit/mzMLWriter.cpp: In member function ‘bool MSToolkit::MzMLWriter::writeSpectra(MSToolkit::MSObject&)’:
> ./src/MSToolkit/mzMLWriter.cpp:260:1: warning: no return statement in function returning non-void [-Wreturn-type]
> 260 | }
> | ^
> Makefile:91: update target 'MSObject.o' due to: target does not exist
> g++ -O3 -static -g -I. -I./include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DGCC -DHAVE_EXPAT_CONFIG_H ./src/MSToolkit/MSObject.cpp -c
> Makefile:82: update target 'Spectrum.o' due to: target does not exist
> g++ -O3 -static -g -I. -I./include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DGCC -DHAVE_EXPAT_CONFIG_H ./src/MSToolkit/Spectrum.cpp -c
> Makefile:76: update target 'mzp.PWIZface_lite.o' due to: target does not exist
> g++ -O3 -static -g -I. -I./include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DGCC -DHAVE_EXPAT_CONFIG_H src/mzParser/PWIZface.cpp -c -o mzp.PWIZface_lite.o
> Makefile:76: update target 'mzp.BasicChromatogram_lite.o' due to: target does not exist
> g++ -O3 -static -g -I. -I./include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DGCC -DHAVE_EXPAT_CONFIG_H src/mzParser/BasicChromatogram.cpp -c -o mzp.BasicChromatogram_lite.o
> Makefile:76: update target 'mzp.mzpMz5Structs_lite.o' due to: target does not exist
> g++ -O3 -static -g -I. -I./include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DGCC -DHAVE_EXPAT_CONFIG_H src/mzParser/mzpMz5Structs.cpp -c -o mzp.mzpMz5Structs_lite.o
> Makefile:76: update target 'mzp.mzpMz5Config_lite.o' due to: target does not exist
> g++ -O3 -static -g -I. -I./include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DGCC -DHAVE_EXPAT_CONFIG_H src/mzParser/mzpMz5Config.cpp -c -o mzp.mzpMz5Config_lite.o
> Makefile:76: update target 'mzp.mz5handler_lite.o' due to: target does not exist
> g++ -O3 -static -g -I. -I./include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DGCC -DHAVE_EXPAT_CONFIG_H src/mzParser/mz5handler.cpp -c -o mzp.mz5handler_lite.o
> Makefile:76: update target 'mzp.Czran_lite.o' due to: target does not exist
> g++ -O3 -static -g -I. -I./include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DGCC -DHAVE_EXPAT_CONFIG_H src/mzParser/Czran.cpp -c -o mzp.Czran_lite.o
> Makefile:76: update target 'mzp.saxmzxmlhandler_lite.o' due to: target does not exist
> g++ -O3 -static -g -I. -I./include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DGCC -DHAVE_EXPAT_CONFIG_H src/mzParser/saxmzxmlhandler.cpp -c -o mzp.saxmzxmlhandler_lite.o
> Makefile:76: update target 'mzp.saxmzmlhandler_lite.o' due to: target does not exist
> g++ -O3 -static -g -I. -I./include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DGCC -DHAVE_EXPAT_CONFIG_H src/mzParser/saxmzmlhandler.cpp -c -o mzp.saxmzmlhandler_lite.o
> Makefile:76: update target 'mzp.saxhandler_lite.o' due to: target does not exist
> g++ -O3 -static -g -I. -I./include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DGCC -DHAVE_EXPAT_CONFIG_H src/mzParser/saxhandler.cpp -c -o mzp.saxhandler_lite.o
> Makefile:76: update target 'mzp.RAMPface_lite.o' due to: target does not exist
> g++ -O3 -static -g -I. -I./include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DGCC -DHAVE_EXPAT_CONFIG_H src/mzParser/RAMPface.cpp -c -o mzp.RAMPface_lite.o
> Makefile:76: update target 'mzp.mzParser_lite.o' due to: target does not exist
> g++ -O3 -static -g -I. -I./include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DGCC -DHAVE_EXPAT_CONFIG_H src/mzParser/mzParser.cpp -c -o mzp.mzParser_lite.o
> Makefile:76: update target 'mzp.BasicSpectrum_lite.o' due to: target does not exist
> g++ -O3 -static -g -I. -I./include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DGCC -DHAVE_EXPAT_CONFIG_H src/mzParser/BasicSpectrum.cpp -c -o mzp.BasicSpectrum_lite.o
> Makefile:76: update target 'mzp.mzp_base64_lite.o' due to: target does not exist
> g++ -O3 -static -g -I. -I./include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DGCC -DHAVE_EXPAT_CONFIG_H src/mzParser/mzp_base64.cpp -c -o mzp.mzp_base64_lite.o
> src/mzParser/mzp_base64.cpp: In function ‘int b64_decode_mio(char*, char*, size_t)’:
> src/mzParser/mzp_base64.cpp:125:30: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister]
> 125 | int register a;
> | ^
> src/mzParser/mzp_base64.cpp:126:30: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister]
> 126 | int register b;
> | ^
> Makefile:72: update target 'mzp.MSNumpress.o' due to: target does not exist
> g++ -O3 -static -g -I. -I./include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DGCC -DHAVE_EXPAT_CONFIG_H src/mzParser/MSNumpress.cpp -c -o mzp.MSNumpress.o
> Makefile:72: update target 'mzp.PWIZface.o' due to: target does not exist
> g++ -O3 -static -g -I. -I./include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DGCC -DHAVE_EXPAT_CONFIG_H src/mzParser/PWIZface.cpp -c -o mzp.PWIZface.o
> Makefile:72: update target 'mzp.BasicChromatogram.o' due to: target does not exist
> g++ -O3 -static -g -I. -I./include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DGCC -DHAVE_EXPAT_CONFIG_H src/mzParser/BasicChromatogram.cpp -c -o mzp.BasicChromatogram.o
> Makefile:72: update target 'mzp.mzpMz5Structs.o' due to: target does not exist
> g++ -O3 -static -g -I. -I./include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DGCC -DHAVE_EXPAT_CONFIG_H src/mzParser/mzpMz5Structs.cpp -c -o mzp.mzpMz5Structs.o
> Makefile:72: update target 'mzp.mzpMz5Config.o' due to: target does not exist
> g++ -O3 -static -g -I. -I./include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DGCC -DHAVE_EXPAT_CONFIG_H src/mzParser/mzpMz5Config.cpp -c -o mzp.mzpMz5Config.o
> Makefile:72: update target 'mzp.mz5handler.o' due to: target does not exist
> g++ -O3 -static -g -I. -I./include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DGCC -DHAVE_EXPAT_CONFIG_H src/mzParser/mz5handler.cpp -c -o mzp.mz5handler.o
> Makefile:72: update target 'mzp.Czran.o' due to: target does not exist
> g++ -O3 -static -g -I. -I./include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DGCC -DHAVE_EXPAT_CONFIG_H src/mzParser/Czran.cpp -c -o mzp.Czran.o
> Makefile:72: update target 'mzp.saxmzxmlhandler.o' due to: target does not exist
> g++ -O3 -static -g -I. -I./include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DGCC -DHAVE_EXPAT_CONFIG_H src/mzParser/saxmzxmlhandler.cpp -c -o mzp.saxmzxmlhandler.o
> Makefile:72: update target 'mzp.saxmzmlhandler.o' due to: target does not exist
> g++ -O3 -static -g -I. -I./include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DGCC -DHAVE_EXPAT_CONFIG_H src/mzParser/saxmzmlhandler.cpp -c -o mzp.saxmzmlhandler.o
> Makefile:72: update target 'mzp.saxhandler.o' due to: target does not exist
> g++ -O3 -static -g -I. -I./include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DGCC -DHAVE_EXPAT_CONFIG_H src/mzParser/saxhandler.cpp -c -o mzp.saxhandler.o
> Makefile:72: update target 'mzp.RAMPface.o' due to: target does not exist
> g++ -O3 -static -g -I. -I./include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DGCC -DHAVE_EXPAT_CONFIG_H src/mzParser/RAMPface.cpp -c -o mzp.RAMPface.o
> Makefile:72: update target 'mzp.mzParser.o' due to: target does not exist
> g++ -O3 -static -g -I. -I./include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DGCC -DHAVE_EXPAT_CONFIG_H src/mzParser/mzParser.cpp -c -o mzp.mzParser.o
> Makefile:72: update target 'mzp.BasicSpectrum.o' due to: target does not exist
> g++ -O3 -static -g -I. -I./include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DGCC -DHAVE_EXPAT_CONFIG_H src/mzParser/BasicSpectrum.cpp -c -o mzp.BasicSpectrum.o
> Makefile:72: update target 'mzp.mzp_base64.o' due to: target does not exist
> g++ -O3 -static -g -I. -I./include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DGCC -DHAVE_EXPAT_CONFIG_H src/mzParser/mzp_base64.cpp -c -o mzp.mzp_base64.o
> src/mzParser/mzp_base64.cpp: In function ‘int b64_decode_mio(char*, char*, size_t)’:
> src/mzParser/mzp_base64.cpp:125:30: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister]
> 125 | int register a;
> | ^
> src/mzParser/mzp_base64.cpp:126:30: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister]
> 126 | int register b;
> | ^
> Makefile:62: update target 'clean_objects' due to: target does not exist
> rm -f *.o msSingleScan.*
> Makefile:38: update target 'arlib' due to: target does not exist
> ar rcs libmstoolkitlite.a mzp.MSNumpress.o mzp.mzp_base64_lite.o mzp.BasicSpectrum_lite.o mzp.mzParser_lite.o mzp.RAMPface_lite.o mzp.saxhandler_lite.o mzp.saxmzmlhandler_lite.o mzp.saxmzxmlhandler_lite.o mzp.Czran_lite.o mzp.mz5handler_lite.o mzp.mzpMz5Config_lite.o mzp.mzpMz5Structs_lite.o mzp.BasicChromatogram_lite.o mzp.PWIZface_lite.o Spectrum.o MSObject.o mzMLWriter.o pepXMLWriter.o MSReaderLite.o
> ar: mzp.MSNumpress.o: No such file or directory
> make[3]: *** [Makefile:39: arlib] Error 1 shuffle=reverse
The full build log is available from:
http://qa-logs.debian.net/2025/05/05/shuffle/reverse/libmstoolkit_82-7.2_unstable_reverse.log
If you reassign this bug to another package, please mark it as 'affects'-ing
this package. See https://www.debian.org/Bugs/server-control#affects
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