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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:mzR.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings mzR_2.26.1.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.13-bioc/meat/mzR.Rcheck’
* using R version 4.1.1 (2021-08-10)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘mzR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘mzR’ version ‘2.26.1’
* 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 hidden files and directories ... NOTE
Found the following hidden files and directories:
  .BBSoptions
  .git_fetch_output.txt
  .git_merge_output.txt
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘mzR’ can be installed ... WARNING
Found the following significant warnings:
  cramp.cpp:73:27: warning: field 'm_declaredScansOnly' will be initialized after field 'm_runInfo' [-Wreorder]
  pwiz/data/identdata/Serializer_protXML.cpp:97:9: warning: field 'strict' will be initialized after field 'nPeptides' [-Wreorder]
  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/biocbuild/bbs-3.13-bioc/meat/mzR.Rcheck/00install.out’ for details.
* checking installed package size ... NOTE
  installed size is 12.5Mb
  sub-directories of 1Mb or more:
    libs  11.9Mb
* 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 ... OK
* checking for GNU extensions in Makefiles ... NOTE
GNU make is a SystemRequirements.
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking use of PKG_*FLAGS in Makefiles ... OK
* checking include directives in Makefiles ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
File ‘/Library/Frameworks/R.framework/Versions/4.1/Resources/library/mzR/libs/mzR.so’:
  Found ‘__ZNSt3__14cerrE’, possibly from ‘std::cerr’ (C++)
  Found ‘___stderrp’, possibly from ‘stderr’ (C)
  Found ‘___stdoutp’, possibly from ‘stdout’ (C)
  Found ‘_abort’, possibly from ‘abort’ (C)
  Found ‘_exit’, possibly from ‘exit’ (C)
  Found ‘_rand_r’, possibly from ‘rand_r’ (C)

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. The detected symbols are linked into the code but
might come from libraries and not actually be called.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.R’
 ERROR
Running the tests in ‘tests/runTests.R’ failed.
Last 13 lines of output:
   
  1 Test Suite : 
  mzR RUnit Tests - 40 test functions, 1 error, 0 failures
  ERROR in test_copyWriteMSData: Error in object@backend$getPeakList(scans) : 
    dims [product 72184] do not match the length of object [36092]
  
  Test files with failing tests
  
     test_write.R 
       test_copyWriteMSData 
  
  
  Error in BiocGenerics:::testPackage("mzR") : 
    unit tests failed for package mzR
  Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 1 ERROR, 1 WARNING, 5 NOTEs
See
  ‘/Users/biocbuild/bbs-3.13-bioc/meat/mzR.Rcheck/00check.log’
for details.