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sneumann / mzR

This is the git repository matching the Bioconductor package mzR: parser for netCDF, mzXML, mzData and mzML files (mass spectrometry data)
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New pwiz version 20190301 for testing #191

Open sneumann opened 5 years ago

sneumann commented 5 years ago

Hi, I need help to test https://github.com/sneumann/mzR/commits/feature/updatePwiz20190301 which is an update to the current pwiz codebase.

On Travis my problem is that I can't see the failure:

* checking whether package ‘mzR’ can be installed ... ERROR
Installation failed.
See ‘/home/travis/build/sneumann/mzR/mzR.Rcheck/00install.out’ for details.

In particular, we need to:

Yours, Steffen

lgatto commented 5 years ago

@sneumann - a detailed set of instructions for testing would help to share to load. Do we need new unit tests to make sure we cover the points above?

I tested the latest commit from updatePwiz20190301 successfully on R patched and R devel.

R version 3.5.2 Patched (2019-01-24 r76018)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Manjaro Linux

Matrix products: default
BLAS: /usr/lib/libblas.so.3.8.0
LAPACK: /usr/lib/liblapack.so.3.8.0

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
 [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8    
 [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8   
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] mzR_2.17.2 Rcpp_1.0.0

loaded via a namespace (and not attached):
[1] compiler_3.5.2      ProtGenerics_1.14.0 parallel_3.5.2     
[4] Biobase_2.42.0      codetools_0.2-16    ncdf4_1.16         
[7] BiocGenerics_0.28.0
R Under development (unstable) (2019-02-25 r76160)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Manjaro Linux

Matrix products: default
BLAS: /usr/lib/libblas.so.3.8.0
LAPACK: /usr/lib/liblapack.so.3.8.0

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
 [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8    
 [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8   
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] mzR_2.17.2 Rcpp_1.0.0

loaded via a namespace (and not attached):
[1] compiler_3.6.0      ProtGenerics_1.15.0 parallel_3.6.0     
[4] Biobase_2.43.1      codetools_0.2-16    ncdf4_1.16         
[7] BiocGenerics_0.29.1
sneumann commented 5 years ago

Hi, thanks for chiming in. I found and fixed the XML writing issue, passing check locally here as well. Still a SEGV on https://travis-ci.org/sneumann/mzR/builds/502225782#L1369 which is not related to filterLine which I uncommented for now in de74d0d00660be14dfbc680483a0dc9ffbc9d14d. So testing on windows and mac would help, and I'd need more reproducible (docker ?) cases with SEGV to debug. Yours, Steffen

sneumann commented 5 years ago

Confirmed to R CMD check version 8.0.0-svn354892-1~exp1~20190226195658.47

sneumann commented 5 years ago

We now have (at least one non-timed-out) build on travis: https://travis-ci.org/sneumann/mzR/builds/504564109

jorainer commented 5 years ago

Hm, I got an error with R CMD check and the most recent commit (https://github.com/sneumann/mzR/commit/b8550e10d63720a44a311ef0e562cbfcce7bb0db) on macOS (10.14.4 Beta):

* installing *source* package ‘mzR’ ...
** libs
*** arch - x86_64
rm -f cramp.o ramp_base64.o RcppRamp.o RcppRampModule.o RcppPwiz.o RcppPwizModule.o RcppIdent.o RcppIdentModule.o ./boost/libs/system/src/error_code.o ./boost/libs/regex/src/posix_api.o ./boost/libs/regex/src/fileiter.o ./boost/libs/regex/src/regex_raw_buffer.o ./boost/libs/regex/src/cregex.o ./boost/libs/regex/src/regex_debug.o ./boost/libs/regex/src/instances.o ./boost/libs/regex/src/icu.o ./boost/libs/regex/src/usinstances.o ./boost/libs/regex/src/regex.o ./boost/libs/regex/src/wide_posix_api.o ./boost/libs/regex/src/regex_traits_defaults.o ./boost/libs/regex/src/winstances.o ./boost/libs/regex/src/wc_regex_traits.o ./boost/libs/regex/src/c_regex_traits.o ./boost/libs/regex/src/cpp_regex_traits.o ./boost/libs/regex/src/static_mutex.o ./boost/libs/regex/src/w32_regex_traits.o ./boost/libs/iostreams/src/zlib.o ./boost/libs/iostreams/src/file_descriptor.o ./boost/libs/filesystem/src/operations.o ./boost/libs/filesystem/src/path.o ./boost/libs/filesystem/src/utf8_codecvt_facet.o ./boost/libs/chrono/src/chrono.o ./boost/libs/chrono/src/process_cpu_clocks.o ./boost/libs/chrono/src/thread_clock.o ./pwiz/data/msdata/Version.o ./pwiz/data/identdata/Version.o ./pwiz/data/common/MemoryIndex.o ./pwiz/data/common/CVTranslator.o ./pwiz/data/common/cv.o ./pwiz/data/common/ParamTypes.o ./pwiz/data/common/BinaryIndexStream.o ./pwiz/data/common/diff_std.o ./pwiz/data/common/Unimod.o ./pwiz/data/msdata/mz5/Configuration_mz5.o ./pwiz/data/msdata/mz5/Connection_mz5.o ./pwiz/data/msdata/mz5/Datastructures_mz5.o ./pwiz/data/msdata/mz5/ReferenceRead_mz5.o ./pwiz/data/msdata/mz5/ReferenceWrite_mz5.o ./pwiz/data/msdata/mz5/Translator_mz5.o ./pwiz/data/msdata/SpectrumList_MGF.o ./pwiz/data/msdata/DefaultReaderList.o ./pwiz/data/msdata/ChromatogramList_mzML.o ./pwiz/data/msdata/ChromatogramList_mz5.o ./pwiz/data/msdata/examples.o ./pwiz/data/msdata/Serializer_mzML.o ./pwiz/data/msdata/Serializer_MSn.o ./pwiz/data/msdata/Reader.o ./pwiz/data/msdata/Serializer_mz5.o ./pwiz/data/msdata/Serializer_MGF.o ./pwiz/data/msdata/Serializer_mzXML.o ./pwiz/data/msdata/SpectrumList_mzML.o ./pwiz/data/msdata/SpectrumList_MSn.o ./pwiz/data/msdata/SpectrumList_mz5.o ./pwiz/data/msdata/BinaryDataEncoder.o ./pwiz/data/msdata/Diff.o ./pwiz/data/msdata/MSData.o ./pwiz/data/msdata/References.o ./pwiz/data/msdata/SpectrumList_mzXML.o ./pwiz/data/msdata/IO.o ./pwiz/data/msdata/SpectrumList_BTDX.o ./pwiz/data/msdata/SpectrumInfo.o ./pwiz/data/msdata/RAMPAdapter.o ./pwiz/data/msdata/ramp/ramp.o ./pwiz/data/msdata/LegacyAdapter.o ./pwiz/data/msdata/SpectrumIterator.o ./pwiz/data/msdata/MSDataFile.o ./pwiz/data/msdata/MSNumpress.o ./pwiz/data/msdata/SpectrumListCache.o ./pwiz/data/msdata/Index_mzML.o ./pwiz/data/msdata/SpectrumWorkerThreads.o ./pwiz/data/identdata/IdentDataFile.o ./pwiz/data/identdata/IdentData.o ./pwiz/data/identdata/DefaultReaderList.o ./pwiz/data/identdata/Reader.o ./pwiz/data/identdata/Serializer_protXML.o ./pwiz/data/identdata/Serializer_pepXML.o ./pwiz/data/identdata/Serializer_mzid.o ./pwiz/data/identdata/IO.o ./pwiz/data/identdata/References.o ./pwiz/data/identdata/MascotReader.o ./pwiz/data/proteome/Modification.o ./pwiz/data/proteome/Digestion.o ./pwiz/data/proteome/Peptide.o ./pwiz/data/proteome/AminoAcid.o ./pwiz/utility/minimxml/XMLWriter.o ./pwiz/utility/minimxml/SAXParser.o ./pwiz/utility/chemistry/Chemistry.o ./pwiz/utility/chemistry/ChemistryData.o ./pwiz/utility/chemistry/MZTolerance.o ./pwiz/utility/misc/IntegerSet.o ./pwiz/utility/misc/Base64.o ./pwiz/utility/misc/IterationListener.o ./pwiz/utility/misc/MSIHandler.o ./pwiz/utility/misc/Filesystem.o ./pwiz/utility/misc/TabReader.o ./pwiz/utility/misc/random_access_compressed_ifstream.o ./pwiz/utility/misc/SHA1.o ./pwiz/utility/misc/SHA1Calculator.o ./pwiz/utility/misc/sha1calc.o ./pwiz/utility/misc/BinaryData.o ./random_access_gzFile.o ./RcppExports.o ./boost/libs/thread/src/pthread/once.o ./boost/libs/thread/src/pthread/thread.o rampR.o
find . -name \*~ -exec rm {} \;   ## from cleanup
find . -name \*.o -exec rm {} \;  ## from cleanup
find . -name "#*#" -exec rm {} \; ## from cleanup
/usr/local/opt/llvm/bin/clang++ -std=gnu++11 -I"/Users/jo/R/2019-02/R-3.6-2018-02-04-Bioc3.9-devel/lib/R/include" -I"/Users/jo/R/2019-02/R-3.6-2018-02-04-Bioc3.9-devel/lib/R/include/x86_64" -DNDEBUG -g -I./boost_aux/ -I./boost/ -I./pwiz/ -I./pwiz/data/msdata/ramp/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG    -I"/Users/jo/R/2019-02/R-3.6-2018-02-04-Bioc3.9-devel/lib/R/library/Rcpp/include" -I"/Users/jo/R/2019-02/R-3.6-2018-02-04-Bioc3.9-devel/lib/R/library/zlibbioc/include" -I"/Users/jo/R/2019-02/R-3.6-2018-02-04-Bioc3.9-devel/lib/R/library/Rhdf5lib/include" -I/usr/local/opt/llvm/include -I/usr/local/include  -fPIC  -g -O2  -c cramp.cpp -o cramp.o
In file included from cramp.cpp:49:
./cramp.h:261:17: warning: destination for this 'memmove' call is a pointer to dynamic class 'rampScanInfo'; vtable pointer will be overwritten [-Wdynamic-class-memaccess]
        memmove(this,&rhs,sizeof(rhs));
        ~~~~~~~ ^
./cramp.h:261:17: note: explicitly cast the pointer to silence this warning
        memmove(this,&rhs,sizeof(rhs));
                ^
                (void*)
./cramp.h:315:17: warning: destination for this 'memmove' call is a pointer to dynamic class 'rampRunInfo'; vtable pointer will be overwritten [-Wdynamic-class-memaccess]
        memmove(this,&rhs,sizeof(rhs));
        ~~~~~~~ ^
./cramp.h:315:17: note: explicitly cast the pointer to silence this warning
        memmove(this,&rhs,sizeof(rhs));
                ^
                (void*)
2 warnings generated.
/usr/local/opt/llvm/bin/clang++ -std=gnu++11 -I"/Users/jo/R/2019-02/R-3.6-2018-02-04-Bioc3.9-devel/lib/R/include" -I"/Users/jo/R/2019-02/R-3.6-2018-02-04-Bioc3.9-devel/lib/R/include/x86_64" -DNDEBUG -g -I./boost_aux/ -I./boost/ -I./pwiz/ -I./pwiz/data/msdata/ramp/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG    -I"/Users/jo/R/2019-02/R-3.6-2018-02-04-Bioc3.9-devel/lib/R/library/Rcpp/include" -I"/Users/jo/R/2019-02/R-3.6-2018-02-04-Bioc3.9-devel/lib/R/library/zlibbioc/include" -I"/Users/jo/R/2019-02/R-3.6-2018-02-04-Bioc3.9-devel/lib/R/library/Rhdf5lib/include" -I/usr/local/opt/llvm/include -I/usr/local/include  -fPIC  -g -O2  -c ramp_base64.cpp -o ramp_base64.o
/usr/local/opt/llvm/bin/clang++ -std=gnu++11 -I"/Users/jo/R/2019-02/R-3.6-2018-02-04-Bioc3.9-devel/lib/R/include" -I"/Users/jo/R/2019-02/R-3.6-2018-02-04-Bioc3.9-devel/lib/R/include/x86_64" -DNDEBUG -g -I./boost_aux/ -I./boost/ -I./pwiz/ -I./pwiz/data/msdata/ramp/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG    -I"/Users/jo/R/2019-02/R-3.6-2018-02-04-Bioc3.9-devel/lib/R/library/Rcpp/include" -I"/Users/jo/R/2019-02/R-3.6-2018-02-04-Bioc3.9-devel/lib/R/library/zlibbioc/include" -I"/Users/jo/R/2019-02/R-3.6-2018-02-04-Bioc3.9-devel/lib/R/library/Rhdf5lib/include" -I/usr/local/opt/llvm/include -I/usr/local/include  -fPIC  -g -O2  -c RcppRamp.cpp -o RcppRamp.o
In file included from RcppRamp.cpp:1:
In file included from ./RcppRamp.h:14:
./cramp.h:261:17: warning: destination for this 'memmove' call is a pointer to dynamic class 'rampScanInfo'; vtable pointer will be overwritten [-Wdynamic-class-memaccess]
        memmove(this,&rhs,sizeof(rhs));
        ~~~~~~~ ^
./cramp.h:261:17: note: explicitly cast the pointer to silence this warning
        memmove(this,&rhs,sizeof(rhs));
                ^
                (void*)
./cramp.h:315:17: warning: destination for this 'memmove' call is a pointer to dynamic class 'rampRunInfo'; vtable pointer will be overwritten [-Wdynamic-class-memaccess]
        memmove(this,&rhs,sizeof(rhs));
        ~~~~~~~ ^
./cramp.h:315:17: note: explicitly cast the pointer to silence this warning
        memmove(this,&rhs,sizeof(rhs));
                ^
                (void*)
2 warnings generated.
/usr/local/opt/llvm/bin/clang++ -std=gnu++11 -I"/Users/jo/R/2019-02/R-3.6-2018-02-04-Bioc3.9-devel/lib/R/include" -I"/Users/jo/R/2019-02/R-3.6-2018-02-04-Bioc3.9-devel/lib/R/include/x86_64" -DNDEBUG -g -I./boost_aux/ -I./boost/ -I./pwiz/ -I./pwiz/data/msdata/ramp/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG    -I"/Users/jo/R/2019-02/R-3.6-2018-02-04-Bioc3.9-devel/lib/R/library/Rcpp/include" -I"/Users/jo/R/2019-02/R-3.6-2018-02-04-Bioc3.9-devel/lib/R/library/zlibbioc/include" -I"/Users/jo/R/2019-02/R-3.6-2018-02-04-Bioc3.9-devel/lib/R/library/Rhdf5lib/include" -I/usr/local/opt/llvm/include -I/usr/local/include  -fPIC  -g -O2  -c RcppRampModule.cpp -o RcppRampModule.o
In file included from RcppRampModule.cpp:2:
In file included from ./RcppRamp.h:14:
./cramp.h:261:17: warning: destination for this 'memmove' call is a pointer to dynamic class 'rampScanInfo'; vtable pointer will be overwritten [-Wdynamic-class-memaccess]
        memmove(this,&rhs,sizeof(rhs));
        ~~~~~~~ ^
./cramp.h:261:17: note: explicitly cast the pointer to silence this warning
        memmove(this,&rhs,sizeof(rhs));
                ^
                (void*)
./cramp.h:315:17: warning: destination for this 'memmove' call is a pointer to dynamic class 'rampRunInfo'; vtable pointer will be overwritten [-Wdynamic-class-memaccess]
        memmove(this,&rhs,sizeof(rhs));
        ~~~~~~~ ^
./cramp.h:315:17: note: explicitly cast the pointer to silence this warning
        memmove(this,&rhs,sizeof(rhs));
                ^
                (void*)
2 warnings generated.
/usr/local/opt/llvm/bin/clang++ -std=gnu++11 -I"/Users/jo/R/2019-02/R-3.6-2018-02-04-Bioc3.9-devel/lib/R/include" -I"/Users/jo/R/2019-02/R-3.6-2018-02-04-Bioc3.9-devel/lib/R/include/x86_64" -DNDEBUG -g -I./boost_aux/ -I./boost/ -I./pwiz/ -I./pwiz/data/msdata/ramp/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG    -I"/Users/jo/R/2019-02/R-3.6-2018-02-04-Bioc3.9-devel/lib/R/library/Rcpp/include" -I"/Users/jo/R/2019-02/R-3.6-2018-02-04-Bioc3.9-devel/lib/R/library/zlibbioc/include" -I"/Users/jo/R/2019-02/R-3.6-2018-02-04-Bioc3.9-devel/lib/R/library/Rhdf5lib/include" -I/usr/local/opt/llvm/include -I/usr/local/include  -fPIC  -g -O2  -c RcppPwiz.cpp -o RcppPwiz.o
In file included from RcppPwiz.cpp:1:
In file included from ./RcppPwiz.h:12:
In file included from ./pwiz/data/msdata/MSDataFile.hpp:29:
In file included from ./pwiz/data/msdata/MSData.hpp:30:
In file included from ./pwiz/data/common/ParamTypes.hpp:29:
In file included from ./pwiz/utility/misc/optimized_lexical_cast.hpp:36:
In file included from ./pwiz/utility/misc/Singleton.hpp:26:
In file included from ./boost_aux/boost/utility/singleton.hpp:19:
In file included from ./boost_aux/boost/utility/detail/singleton_manager.hpp:18:
In file included from ./boost/boost/thread/once.hpp:26:
In file included from ./boost/boost/thread/pthread/once_atomic.hpp:20:
In file included from ./boost/boost/atomic.hpp:12:
In file included from ./boost/boost/atomic/atomic.hpp:20:
In file included from ./boost/boost/atomic/fences.hpp:21:
In file included from ./boost/boost/atomic/detail/operations.hpp:17:
In file included from ./boost/boost/atomic/detail/operations_lockfree.hpp:21:
In file included from ./boost/boost/atomic/detail/ops_gcc_atomic.hpp:24:
./boost/boost/atomic/detail/ops_gcc_x86_dcas.hpp:408:16: error: address argument to atomic builtin cannot be const-qualified ('const volatile boost::atomics::detail::gcc_dcas_x86_64::storage_type *' (aka 'const volatile unsigned __int128 *') invalid)
        return __sync_val_compare_and_swap(&storage, value, value);
               ^                           ~~~~~~~~
1 error generated.
make: *** [RcppPwiz.o] Error 1
ERROR: compilation failed for package ‘mzR’
* removing ‘/Users/jo/Projects/git/sneumann/mzR.Rcheck/mzR’

My R version:

R Under development (unstable) (2019-02-03 r76054) -- "Unsuffered Consequences"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin18.5.0/x86_64 (64-bit)

My compiler:

~ ❯❯❯ /usr/local/opt/llvm/bin/clang++ --version
clang version 7.0.1 (tags/RELEASE_701/final)
Target: x86_64-apple-darwin18.5.0
Thread model: posix
InstalledDir: /usr/local/opt/llvm/bin
jorainer commented 5 years ago

Windows also fails with the error message:

In file included from boost/libs/system/src/error_code.cpp:19:0:
./boost/boost/system/detail/error_code.ipp:24:43: fatal error: boost/winapi/error_codes.hpp: No such
 file or directory
 #   include <boost/winapi/error_codes.hpp>

There it might help just adding the missing file.

jorainer commented 5 years ago

Update on macOS: I switched to use LLVM 6 again and with that R CMD check works on mzR without errors but 3 warnings (see full log further below).

The R version:

> sessionInfo()
R Under development (unstable) (2019-03-12 r76227)
Platform: x86_64-apple-darwin18.5.0 (64-bit)
Running under: macOS Mojave 10.14.4

Matrix products: default
BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
LAPACK: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libLAPACK.dylib

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

loaded via a namespace (and not attached):
[1] compiler_3.6.0

And I'm now using clang with version:

~/P/g/sneumann ❯❯❯ /usr/local/opt/llvm@6/bin/clang --version
clang version 6.0.1 (tags/RELEASE_601/final)
Target: x86_64-apple-darwin18.5.0
Thread model: posix
InstalledDir: /usr/local/opt/llvm@6/bin

Full output from R CMD check:

* using log directory ‘/Users/jo/Projects/git/sneumann/mzR.Rcheck’
* using R Under development (unstable) (2019-03-12 r76227)
* using platform: x86_64-apple-darwin18.5.0 (64-bit)
* using session charset: UTF-8
* checking for file ‘mzR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘mzR’ version ‘2.17.1’
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for executable files ... OK
* checking for hidden files and directories ... NOTE
Found the following hidden files and directories:
  .BBSoptions
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* checking for portable file names ... NOTE
Found the following non-portable file paths:
  mzR/src/boost/libs/chrono/stopwatches/include/boost/chrono/stopwatches/collectors/laps_accumulator_set.hpp
  mzR/src/boost/libs/chrono/stopwatches/include/boost/chrono/stopwatches/collectors/laps_sequence_container.hpp
  mzR/src/boost/libs/chrono/stopwatches/include/boost/chrono/stopwatches/formatters/accumulator_set_formatter.hpp
  mzR/src/boost/libs/chrono/stopwatches/include/boost/chrono/stopwatches/formatters/elapsed_formatter.hpp
  mzR/src/boost/libs/chrono/stopwatches/include/boost/chrono/stopwatches/formatters/times_formatter.hpp
  mzR/src/boost/libs/chrono/stopwatches/include/boost/chrono/stopwatches/reporters/clock_default_formatter.hpp
  mzR/src/boost/libs/chrono/stopwatches/include/boost/chrono/stopwatches/reporters/laps_accumulator_set_stopwatch_default_formatter.hpp
  mzR/src/boost/libs/chrono/stopwatches/include/boost/chrono/stopwatches/reporters/laps_stopwatch_default_formatter.hpp
  mzR/src/boost/libs/chrono/stopwatches/include/boost/chrono/stopwatches/reporters/process_default_formatter.hpp
  mzR/src/boost/libs/chrono/stopwatches/include/boost/chrono/stopwatches/reporters/stopwatch_reporter_default_formatter.hpp
  mzR/src/boost/libs/chrono/stopwatches/include/boost/chrono/stopwatches/reporters/stopwatch_reporter.hpp
  mzR/src/boost/libs/chrono/stopwatches/include/boost/chrono/stopwatches/reporters/strict_stopclock.hpp
  mzR/src/boost/libs/chrono/stopwatches/include/boost/chrono/stopwatches/reporters/system_default_formatter.hpp
  mzR/src/boost/libs/chrono/stopwatches/include/boost/chrono/stopwatches/reporters/thread_default_formatter.hpp
  mzR/src/boost/libs/filesystem/example/msvc/directory_symlink_parent_resolution/directory_symlink_parent_resolution.vcxproj

Tarballs are only required to store paths of up to 100 bytes and cannot
store those of more than 256 bytes, with restrictions including to 100
bytes for the final component.
See section ‘Package structure’ in the ‘Writing R Extensions’ manual.
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘mzR’ can be installed ... WARNING
Found the following significant warnings:
  pwiz/utility/misc/TabReader.cpp:44:22: warning: assigning field to itself [-Wself-assign-field]
Found the following additional notes/warnings:
  pwiz/data/identdata/Serializer_pepXML.cpp:1545:5: warning: control may reach end of non-void function [-Wreturn-type]
See ‘/Users/jo/Projects/git/sneumann/mzR.Rcheck/00install.out’ for details.
* checking installed package size ... NOTE
  installed size is 14.0Mb
  sub-directories of 1Mb or more:
    libs  12.6Mb
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Versioned 'LinkingTo' value for ‘Rhdf5lib’ is only usable in R >= 3.0.2
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking line endings in shell scripts ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... WARNING
Non-portable flags in variable 'PKG_CPPFLAGS':
  -g
* checking for GNU extensions in Makefiles ... NOTE
GNU make is a SystemRequirements.
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking include directives in Makefiles ... OK
* checking compiled code ... WARNING
File ‘mzR/libs/mzR.so’:
  Found ‘___stderrp’, possibly from ‘stderr’ (C)
    Object: ‘./pwiz/data/msdata/ramp/ramp.o’
  Found ‘__ZNSt3__14cerrE’, possibly from ‘std::cerr’ (C++)
    Objects: ‘./pwiz/data/common/Unimod.o’,
      ‘./pwiz/data/msdata/SpectrumList_MGF.o’,
      ‘./pwiz/data/msdata/SpectrumList_mzML.o’,
      ‘./pwiz/data/msdata/SpectrumList_MSn.o’,
      ‘./pwiz/data/msdata/SpectrumList_mz5.o’,
      ‘./pwiz/data/msdata/BinaryDataEncoder.o’,
      ‘./pwiz/data/msdata/SpectrumList_mzXML.o’,
      ‘./pwiz/data/msdata/SpectrumList_BTDX.o’,
      ‘./pwiz/data/msdata/SpectrumWorkerThreads.o’,
      ‘./pwiz/utility/misc/sha1calc.o’
  Found ‘__ZNSt3__14coutE’, possibly from ‘std::cout’ (C++)
    Objects: ‘./pwiz/data/msdata/ramp/ramp.o’,
      ‘./pwiz/utility/chemistry/Chemistry.o’,
      ‘./pwiz/utility/misc/sha1calc.o’
  Found ‘_exit’, possibly from ‘exit’ (C)
    Object: ‘./pwiz/data/msdata/ramp/ramp.o’
  Found ‘_printf’, possibly from ‘printf’ (C)
    Object: ‘./pwiz/data/msdata/ramp/ramp.o’
  Found ‘_puts’, possibly from ‘printf’ (C), ‘puts’ (C)
    Object: ‘./pwiz/data/msdata/ramp/ramp.o’

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ...
   ‘mzR.Rmd’ using ‘UTF-8’ ... OK
 NONE
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 3 WARNINGs, 5 NOTEs
See
  ‘/Users/jo/Projects/git/sneumann/mzR.Rcheck/00check.log’
for details.
sneumann commented 5 years ago

I added and pushed missing src/boost/boost/winapi/ now, yet untested on windows. FWIW, I take these from https://github.com/ProteoWizard/pwiz/blob/master/libraries/boost_1_67_0.tar.bz2 Yours, Steffen

jorainer commented 5 years ago

While we fix the above mentioned error on Windows we now get:

./boost/boost/detail/winapi/time.hpp:14:63: fatal error: boost/detail/winapi/detail/deprecated_names
pace.hpp: No such file or directory
 #include <boost/detail/winapi/detail/deprecated_namespace.hpp>
                                                               ^

I'll add this file (from the boost archive you provided above) and continue testsing.

jorainer commented 5 years ago

Adding the file above did only help partially. Now we get (I believe) a more serious error:

In file included from C:/Rtools/mingw_64/x86_64-w64-mingw32/include/c++/bits/stl_algobase.h:71:0,
                 from C:/Rtools/mingw_64/x86_64-w64-mingw32/include/c++/bits/char_traits.h:39,
                 from C:/Rtools/mingw_64/x86_64-w64-mingw32/include/c++/string:40,
                 from pwiz/utility/misc/String.hpp:27,
                 from pwiz/utility/misc/Filesystem.hpp:34,
                 from pwiz/utility/misc/Filesystem.cpp:26:
C:/Rtools/mingw_64/x86_64-w64-mingw32/include/c++/bits/predefined_ops.h: In instantiation of 'bool _
_gnu_cxx::__ops::_Iter_comp_iter<_Compare>::operator()(_Iterator1, _Iterator2) [with _Iterator1 = st
d::_Rb_tree_iterator<std::pair<const int, int> >; _Iterator2 = std::_Rb_tree_iterator<std::pair<cons
t int, int> >; _Compare = {anonymous}::GetFileHandleTypeNumber({anonymous}::SYSTEM_HANDLE_INFORMATIO
N*)::<lambda(const auto:1&, const auto:2&)>]':
C:/Rtools/mingw_64/x86_64-w64-mingw32/include/c++/bits/stl_algo.h:5474:30:   required from '_Forward
Iterator std::__max_element(_ForwardIterator, _ForwardIterator, _Compare) [with _ForwardIterator = s
td::_Rb_tree_iterator<std::pair<const int, int> >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<{ano
nymous}::GetFileHandleTypeNumber({anonymous}::SYSTEM_HANDLE_INFORMATION*)::<lambda(const auto:1&, co
nst auto:2&)> >]'
C:/Rtools/mingw_64/x86_64-w64-mingw32/include/c++/bits/stl_algo.h:5522:47:   required from '_FIter s
td::max_element(_FIter, _FIter, _Compare) [with _FIter = std::_Rb_tree_iterator<std::pair<const int,
 int> >; _Compare = {anonymous}::GetFileHandleTypeNumber({anonymous}::SYSTEM_HANDLE_INFORMATION*)::<
lambda(const auto:1&, const auto:2&)>]'
pwiz/utility/misc/Filesystem.cpp:199:152:   required from here
C:/Rtools/mingw_64/x86_64-w64-mingw32/include/c++/bits/predefined_ops.h:121:46: error: invalid use o
f 'auto'
         { return bool(_M_comp(*__it1, *__it2)); }
                                              ^

I am not sure how to fix that...

sneumann commented 5 years ago

Hi, I can confirm the failure with mingw-gcc 4.9.3. It occurs with -std=c++0x and -std=gnu++11. It does not occur with -std=gnu++14 or the default if you leave out -std=... altogether.

Afterwards it gets further, but then hitting ProteoWizard/pwiz/issues/372

sneumann commented 5 years ago

Maybe @David-J-R is a capable C++ hacker here ... Yours, Steffen

chambm commented 3 years ago

@sneumann Did you know pwiz makes subset source tarballs available as artifacts? They are made in several flavors: with and without the libraries (e.g. the subset of boost that pwiz uses, eigen, zlib), with and without test sources and data, and with and without vendor support. That seems like an easier way to go than the checkoutpwiz script. It's unfortunate that R is locked in with POSIX so it can't compile with Visual C++ and make use of the vendor support.

sneumann commented 3 years ago

Awesome! Can you link to the recommended artefact? Yours Steffen

I blame Android for the brevity and typos

chambm commented 3 years ago

This one has libraries but not tests or vendor support: https://teamcity.labkey.org/guestAuth/repository/download/bt81/1144174:id/pwiz-src-without-tv-3_0_20290_13f6ea4.tar.bz2 If you wanted to use one in a build, I could pin it in TeamCity so it doesn't get automatically deleted, or you can mirror it in this repo (either in tar form or extracted, although it's 43mb which pushes the limits of a single file in GitHub). If the size is a problem I can look at squeezing out some unnecessary stuff; I haven't tried to optimize it in a long time.

chambm commented 3 years ago

Note I edit my comment to fix the URL for guest access (so you might won't see it if you're reading it in email).