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###
### Running command:
###
###   D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:metabCombiner.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings metabCombiner_1.5.0.tar.gz
###
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##############################################################################


* using log directory 'D:/biocbuild/bbs-3.15-bioc/meat/metabCombiner.Rcheck'
* using R Under development (unstable) (2021-11-21 r81221)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'metabCombiner/DESCRIPTION' ... OK
* this is package 'metabCombiner' version '1.5.0'
* package encoding: UTF-8
* 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 ... OK
* checking for portable file names ... OK
* checking whether package 'metabCombiner' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... OK
* 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 contents of 'data' directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking compiled code ... NOTE
Note: information on .o files for x64 is not available
File 'D:/biocbuild/bbs-3.15-bioc/R/library/metabCombiner/libs/x64/metabCombiner.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)

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 'testthat.R'
 OK
* 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 NOTE
See
  'D:/biocbuild/bbs-3.15-bioc/meat/metabCombiner.Rcheck/00check.log'
for details.

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###
### Running command:
###
###   D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL metabCombiner
###
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* installing to library 'D:/biocbuild/bbs-3.15-bioc/R/library'
* installing *source* package 'metabCombiner' ...
** using staged installation
** libs
"C:/rtools40/mingw64/bin/"gcc  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c binByMZ.c -o binByMZ.o
"C:/rtools40/mingw64/bin/"gcc  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c findDuplicates.c -o findDuplicates.o
"C:/rtools40/mingw64/bin/"gcc  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c labelRows.c -o labelRows.o
"C:/rtools40/mingw64/bin/"gcc  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c metabCombiner_init.c -o metabCombiner_init.o
"C:/rtools40/mingw64/bin/"gcc  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c resolveRows.c -o resolveRows.o
resolveRows.c: In function 'resolveRows':
resolveRows.c:250:6: warning: variable 'sgnum' set but not used [-Wunused-but-set-variable]
  int sgnum = 0;
      ^~~~~
resolveRows.c:249:14: warning: unused variable 'filename' [-Wunused-variable]
  const char *filename = "output.txt";
              ^~~~~~~~
"C:/rtools40/mingw64/bin/"gcc  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c selectAnchors.c -o selectAnchors.o
"C:/rtools40/mingw64/bin/"gcc  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c write2file.c -o write2file.o
C:/rtools40/mingw64/bin/gcc -shared -s -static-libgcc -o metabCombiner.dll tmp.def binByMZ.o findDuplicates.o labelRows.o metabCombiner_init.o resolveRows.o selectAnchors.o write2file.o -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LD:/biocbuild/bbs-3.15-bioc/R/bin/x64 -lR
installing to D:/biocbuild/bbs-3.15-bioc/R/library/00LOCK-metabCombiner/00new/metabCombiner/libs/x64
** R
** data
** demo
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'metabCombiner'
    finding HTML links ... done
    Qdata                                   html  
    adductdata                              html  
    adjustData                              html  
    batchCombine                            html  
    calcScores                              html  
    calcScoresParam                         html  
    combinedTable                           html  
    combinerCheck                           html  
    crossValFit                             html  
    datasets                                html  
    detectFields                            html  
    evaluateParams                          html  
    featdata                                html  
    filterAnchors                           html  
    filterRT                                html  
    findDuplicates                          html  
    fit_gam                                 html  
    fit_loess                               html  
    fitgamParam                             html  
    fitloessParam                           html  
    getAnchors                              html  
    getCoefficients                         html  
    getData                                 html  
    getExtra                                html  
    getModel                                html  
    getSamples                              html  
    getStats                                html  
    iddata                                  html  
    identityAnchorSelection                 html  
    isCombinedTable                         html  
    isMetabCombiner                         html  
    isMetabData                             html  
    iterativeAnchorSelection                html  
    labelRows                               html  
    labelRowsParam                          html  
    metabBatches                            html  
    metabCombine                            html  
    metabCombiner-class                     html  
    metabCombiner                           html  
    metabData-class                         html  
    metabData                               html  
    mzGroup                                 html  
    mzdata                                  html  
    nonmatched                              html  
    objective                               html  
    plasma20                                html  
    plasma30                                html  
    plot_fit                                html  
    rtdata                                  html  
    scorePairs                              html  
    selectAnchors                           html  
    selectAnchorsParam                      html  
    write2file                              html  
    x                                       html  
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (metabCombiner)
Making 'packages.html' ...Warning in packageDescription(i, lib.loc = lib, fields = "Title", encoding = "UTF-8") :
  DESCRIPTION file of package 'cTRAP' is missing or broken
 done

R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(testthat)
> library(metabCombiner)
Loading required package: dplyr

Attaching package: 'dplyr'

The following object is masked from 'package:testthat':

    matches

The following objects are masked from 'package:stats':

    filter, lag

The following objects are masked from 'package:base':

    intersect, setdiff, setequal, union

> 
> test_check("metabCombiner")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 33 ]
> 
> proc.time()
   user  system elapsed 
  12.79    0.67   13.45