search

sneumann / mzR

This is the git repository matching the Bioconductor package mzR: parser for netCDF, mzXML, mzData and mzML files (mass spectrometry data)
40 stars 26 forks source link

Warning on all platforms #236

Open lgatto opened 3 years ago

lgatto commented 3 years ago

We have a set of warnings on all platforms in both release and devel:

* checking whether package ‘mzR’ can be installed ... WARNING
Found the following significant warnings:
  cramp.h:261:38: warning: ‘void* memmove(void*, const void*, size_t)’ writing to an object of type ‘class rampScanInfo’ with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess]
  cramp.h:315:38: warning: ‘void* memmove(void*, const void*, size_t)’ writing to an object of type ‘class rampRunInfo’ with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess]
  cramp.h:149:10: warning: ‘cRamp::m_declaredScansOnly’ will be initialized after [-Wreorder]
  cramp.h:148:18: warning:   ‘rampRunInfo* cRamp::m_runInfo’ [-Wreorder]
  cramp.cpp:72:1: warning:   when initialized here [-Wreorder]
  /usr/include/x86_64-linux-gnu/bits/string_fortified.h:106:34: warning: ‘char* __builtin_strncpy(char*, const char*, long unsigned int)’ specified bound 256 equals destination size [-Wstringop-truncation]
  ./boost/boost/get_pointer.hpp:27:40: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
  ./boost/boost/iostreams/chain.hpp:256:14: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
  RcppPwiz.cpp:745:29: warning: suggest parentheses around comparison in operand of ‘|’ [-Wparentheses]
  boost/libs/filesystem/src/operations.cpp:1991:18: warning: ‘int readdir_r(DIR*, dirent*, dirent**)’ is deprecated [-Wdeprecated-declarations]
  boost/libs/filesystem/src/operations.cpp:1991:47: warning: ‘int readdir_r(DIR*, dirent*, dirent**)’ is deprecated [-Wdeprecated-declarations]
  ./boost/boost/thread/detail/thread_group.hpp:78:18: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
  pwiz/data/msdata/SpectrumList_mzXML.cpp:84:30: warning: catching polymorphic type ‘struct pwiz::msdata::SpectrumList_mzXML::index_not_found’ by value [-Wcatch-value=]
  /usr/include/x86_64-linux-gnu/bits/string_fortified.h:106:34: warning: ‘char* __builtin_strncpy(char*, const char*, long unsigned int)’ specified bound 2000 equals destination size [-Wstringop-truncation]
  pwiz/data/identdata/Serializer_protXML.cpp:478:10: warning: ‘pwiz::identdata::{anonymous}::Handler_protXML::strict’ will be initialized after [-Wreorder]
  pwiz/data/identdata/Serializer_protXML.cpp:85:9: warning:   ‘int pwiz::identdata::{anonymous}::Handler_protXML::nPeptides’ [-Wreorder]
  pwiz/data/identdata/Serializer_protXML.cpp:91:5: warning:   when initialized here [-Wreorder]
  pwiz/data/proteome/Modification.cpp:89:5: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]

@sneumann - any idea how to address these?

lgatto commented 3 years ago

Relevant also with regard to this question. I have now bumped release and devel to trigger a rebuild, but I'm not sure the new binaries will become available due because of these warnings.

sneumann commented 3 years ago

Hi, I recently started https://github.com/sneumann/mzR/tree/feature/updatePwiz_3_0_20290 which does already INSTALL on Ubuntu 20.04, but catches a SEGV when doing something. I would prefer such warnings as shown above to be fixed in the new branch, in case we manage to fix it first. Some C++ wizard will be needed :-( Yours, Steffen P.S.: I don't think WARNINGs stop the new binaries from being released in BioC devel.

sneumann commented 3 years ago

I'll try to have a look together with @hechth. Yours, Steffen