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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:ptairMS.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings ptairMS_1.13.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/ptairMS.Rcheck’
* using R version 4.4.1 (2024-06-14)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘ptairMS/DESCRIPTION’ ... OK
* this is package ‘ptairMS’ version ‘1.13.0’
* 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 ‘ptairMS’ can be installed ... WARNING
Found the following significant warnings:
  Warning: replacing previous import ‘Biobase::cache’ by ‘bit64::cache’ when loading ‘ptairMS’
See ‘/Users/biocbuild/bbs-3.20-bioc/meat/ptairMS.Rcheck/00install.out’ for details.
* used C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
* used SDK: ‘MacOSX11.3.sdk’
* 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 code 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 ... WARNING
'::' or ':::' imports not declared from:
  ‘htmlwidgets’ ‘plyr’
There are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
  ‘getCalibrationInfo’ ‘getPeakList’ ‘getPeaksInfo’ ‘getTimeInfo’
  ‘processFileTemporalNominalMass’ ‘tofToMz’
* 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 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
detectPeak           95.182  2.854  98.848
writeEset            17.303  0.602  18.030
imputeMat            17.031  0.668  17.818
alignSamples         16.278  0.797  17.189
getPeakList          15.285  0.566  15.970
annotation           15.012  0.524  15.631
impute               14.813  0.619  15.517
convert_to_mzML      12.906  0.590  13.564
plotFeatures         12.406  0.427  12.904
plot                 11.573  0.387  12.029
updatePtrSet         11.569  0.368  12.009
plotTIC              11.525  0.395  11.991
plotRaw              10.748  0.482  11.295
plotCalib            10.806  0.397  11.280
resetSampleMetadata  10.589  0.340  11.001
setSampleMetadata    10.507  0.360  10.956
rmPeakList           10.480  0.349  10.883
defineKnots          10.425  0.388  10.883
getSampleMetadata    10.071  0.375  10.523
getDirectory          9.944  0.364  10.382
createPtrSet          9.794  0.437  10.307
exportSampleMetada    9.645  0.355  10.055
changeTimeLimits      9.405  0.324   9.800
importSampleMetadata  8.961  0.359   9.386
getFileNames          8.490  0.341   8.924
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 2 WARNINGs, 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.20-bioc/meat/ptairMS.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL ptairMS
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library’
* installing *source* package ‘ptairMS’ ...
** using staged installation
** libs
using C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
using SDK: ‘MacOSX11.3.sdk’
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c RcppExports.cpp -o RcppExports.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c align.cpp -o align.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c findEqualGreaterM.cpp -o findEqualGreaterM.o
clang++ -arch x86_64 -std=gnu++17 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/x86_64/lib -o ptairMS.so RcppExports.o align.o findEqualGreaterM.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/00LOCK-ptairMS/00new/ptairMS/libs
** R
** inst
** byte-compile and prepare package for lazy loading
Warning: replacing previous import ‘Biobase::cache’ by ‘bit64::cache’ when loading ‘ptairMS’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
Warning: replacing previous import ‘Biobase::cache’ by ‘bit64::cache’ when loading ‘ptairMS’
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
Warning: replacing previous import ‘Biobase::cache’ by ‘bit64::cache’ when loading ‘ptairMS’
** testing if installed package keeps a record of temporary installation path
* DONE (ptairMS)

R version 4.4.1 (2024-06-14) -- "Race for Your Life"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20

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(ptairMS)
Warning message:
replacing previous import 'Biobase::cache' by 'bit64::cache' when loading 'ptairMS' 
> 
> test_check("ptairMS")
Control1.h5 : 3 peaks detected 
Control2.h5 : 4 peaks detected 
Specie-a1.h5 : 2 peaks detected 
Specie-a2.h5 : 3 peaks detected 
specie-b1.h5 : 4 peaks detected 
specie-b2.h5 : 3 peaks detected 
Control1.h5 : 2 peaks detected 
Control2.h5 : 2 peaks detected 
Specie-a1.h5 : 3 peaks detected 
Specie-a2.h5 : 3 peaks detected 
specie-b1.h5 : 2 peaks detected 
specie-b2.h5 : 3 peaks detected 
Control1.h5 : 4 peaks detected 
Control2.h5 : 6 peaks detected 
Specie-a1.h5 : 3 peaks detected 
Specie-a2.h5 : 4 peaks detected 
specie-b1.h5 : 5 peaks detected 
specie-b2.h5 : 4 peaks detected 
Control1.h5 : 3 peaks detected 
Control2.h5 : 2 peaks detected 
Specie-a1.h5 : 3 peaks detected 
Specie-a2.h5 : 3 peaks detected 
specie-b1.h5 : 4 peaks detected 
specie-b2.h5 : 4 peaks detected 
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 59 ]
> 
> proc.time()
   user  system elapsed 
 86.682   3.888  91.521