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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:metabCombiner.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings metabCombiner_1.6.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.15-bioc/meat/metabCombiner.Rcheck’
* using R version 4.2.1 (2022-06-23)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘metabCombiner/DESCRIPTION’ ... OK
* this is package ‘metabCombiner’ version ‘1.6.0’
* 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 for sufficient/correct file permissions ... 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 ... WARNING
Codoc mismatches from documentation object 'labelRowsParam':
labelRowsParam
  Code: function(useID = FALSE, maxRankX = 3, maxRankY = 3, minScore =
                 0.5, delta = 0.1, method = "score", maxRTerr = 10,
                 resolveConflicts = FALSE, rtOrder = TRUE, remove =
                 FALSE, balanced = TRUE, brackets_ignore = c("(", "[",
                 "{"))
  Docs: function(maxRankX = 3, maxRankY = 3, minScore = 0.5, delta =
                 0.1, method = "score", maxRTerr = 10, resolveConflicts
                 = FALSE, rtOrder = TRUE, remove = FALSE, balanced =
                 TRUE, useID = FALSE, brackets_ignore = c("(", "[",
                 "{"))
  Mismatches in argument names (first 3):
    Position: 1 Code: useID Docs: maxRankX
    Position: 2 Code: maxRankX Docs: maxRankY
    Position: 3 Code: maxRankY Docs: minScore
reduceTableParam
  Code: function(useID = FALSE, maxRankX = 2, maxRankY = 2, minScore =
                 0.5, maxRTerr = 10, delta = 0.1, rtOrder = TRUE,
                 brackets_ignore = c("(", "[", "{"))
  Docs: function(maxRankX = 2, maxRankY = 2, minScore = 0.5, maxRTerr =
                 10, delta = 0.1, rtOrder = TRUE, useID = FALSE,
                 brackets_ignore = c("(", "[", "{"))
  Mismatches in argument names (first 3):
    Position: 1 Code: useID Docs: maxRankX
    Position: 2 Code: maxRankX Docs: maxRankY
    Position: 3 Code: maxRankY Docs: minScore

* 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 is not available
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                user system elapsed
evaluateParams 9.472  0.099   9.588
updateTables   5.319  0.034   5.358
labelRows      5.285  0.051   5.348
calcScores     5.097  0.072   5.269
write2file     5.139  0.029   5.173
* 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 WARNING, 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.15-bioc/meat/metabCombiner.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL metabCombiner
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.2/Resources/library’
* installing *source* package ‘metabCombiner’ ...
** using staged installation
** libs
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c binByMZ.c -o binByMZ.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c findDuplicates.c -o findDuplicates.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c labelRows.c -o labelRows.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c metabCombiner_init.c -o metabCombiner_init.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c resolveRows.c -o resolveRows.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c selectAnchors.c -o selectAnchors.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c write2file.c -o write2file.o
clang -mmacosx-version-min=10.13 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o metabCombiner.so binByMZ.o findDuplicates.o labelRows.o metabCombiner_init.o resolveRows.o selectAnchors.o write2file.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Library/Frameworks/R.framework/Versions/4.2/Resources/library/00LOCK-metabCombiner/00new/metabCombiner/libs
** R
** data
** demo
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (metabCombiner)

R version 4.2.1 (2022-06-23) -- "Funny-Looking Kid"
Copyright (C) 2022 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin17.0 (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 8 | SKIP 0 | PASS 33 ]

[ FAIL 0 | WARN 8 | SKIP 0 | PASS 33 ]
> 
> proc.time()
   user  system elapsed 
 29.938   0.723  30.684