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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_1.14.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/ptairMS.Rcheck’
* using R version 4.4.3 (2025-02-28)
* using platform: aarch64-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 Ventura 13.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘ptairMS/DESCRIPTION’ ... OK
* this is package ‘ptairMS’ version ‘1.14.0’
* 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 15.0.0 (clang-1500.0.40.1)’
* 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           97.494  5.905 106.628
writeEset            18.985  1.134  20.191
imputeMat            17.985  1.333  19.363
alignSamples         16.417  1.571  18.107
getPeakList          15.098  1.128  16.336
impute               14.566  1.303  15.930
annotation           14.409  1.254  15.706
convert_to_mzML      13.519  0.541  14.116
plot                 12.370  0.715  13.220
rmPeakList           11.459  0.695  12.217
resetSampleMetadata  11.107  0.758  11.942
plotFeatures         11.141  0.717  11.886
plotRaw              11.025  0.816  11.906
setSampleMetadata    11.032  0.591  11.650
defineKnots          11.002  0.583  11.599
importSampleMetadata 10.905  0.635  11.559
exportSampleMetada   10.546  0.633  12.219
updatePtrSet         10.210  0.787  11.062
getDirectory         10.262  0.544  11.835
getFileNames          9.918  0.766  10.735
plotCalib             9.725  0.770  10.508
createPtrSet          9.688  0.694  10.458
plotTIC               9.580  0.554  10.275
changeTimeLimits      8.976  0.808   9.821
getSampleMetadata     8.983  0.714   9.755
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 ERROR
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
   1. └─ptairMS (local) test_alignSamples()
   2.   └─testthat::expect_equal(nrow(Biobase::exprs(eset)), 1) at test-alignment.R:40:3
  ── Failure ('test-annotation.R:32:1'): annotateVOC function and findIsotope ────
  Biobase::fData(bacteria.eset)[1, "isotope"] not equal to row.names(Biobase::fData(bacteria.eset))[2].
  1/1 mismatches
  x[1]: "60.0514"
  y[1]: "59.0608"
  Backtrace:
      ▆
   1. └─ptairMS (local) test_annotateVOC_and_isotope()
   2.   └─testthat::expect_equal(...) at test-annotation.R:28:3
  
  [ FAIL 3 | WARN 0 | SKIP 0 | PASS 56 ]
  Error: Test failures
  Execution halted
* 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: 1 ERROR, 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-arm64/Resources/library’
* installing *source* package ‘ptairMS’ ...
** using staged installation
** libs
using C++ compiler: ‘Apple clang version 15.0.0 (clang-1500.0.40.1)’
using SDK: ‘MacOSX11.3.sdk’
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c RcppExports.cpp -o RcppExports.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c align.cpp -o align.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c findEqualGreaterM.cpp -o findEqualGreaterM.o
clang++ -arch arm64 -std=gnu++17 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/arm64/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-arm64/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 4.4.3 (2025-02-28) -- "Trophy Case"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: aarch64-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 3 | WARN 0 | SKIP 0 | PASS 56 ]

══ Failed tests ════════════════════════════════════════════════════════════════
── Failure ('test-alignment.R:59:1'): alignSamples() works correctly. ──────────
nrow(Biobase::exprs(eset)) not equal to 2.
1/1 mismatches
[1] 3 - 2 == 1
Backtrace:
    ▆
 1. └─ptairMS (local) test_alignSamples()
 2.   └─testthat::expect_equal(nrow(Biobase::exprs(eset)), 2) at test-alignment.R:34:3
── Failure ('test-alignment.R:59:1'): alignSamples() works correctly. ──────────
nrow(Biobase::exprs(eset)) not equal to 1.
1/1 mismatches
[1] 2 - 1 == 1
Backtrace:
    ▆
 1. └─ptairMS (local) test_alignSamples()
 2.   └─testthat::expect_equal(nrow(Biobase::exprs(eset)), 1) at test-alignment.R:40:3
── Failure ('test-annotation.R:32:1'): annotateVOC function and findIsotope ────
Biobase::fData(bacteria.eset)[1, "isotope"] not equal to row.names(Biobase::fData(bacteria.eset))[2].
1/1 mismatches
x[1]: "60.0514"
y[1]: "59.0608"
Backtrace:
    ▆
 1. └─ptairMS (local) test_annotateVOC_and_isotope()
 2.   └─testthat::expect_equal(...) at test-annotation.R:28:3

[ FAIL 3 | WARN 0 | SKIP 0 | PASS 56 ]
Error: Test failures
Execution halted