##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:DIAlignR.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings DIAlignR_2.15.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/DIAlignR.Rcheck’
* using R Under development (unstable) (2025-01-22 r87618)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 14.2.0
* running under: macOS Monterey 12.7.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘DIAlignR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘DIAlignR’ version ‘2.15.1’
* 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 ‘DIAlignR’ can be installed ... OK
* used C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
* used SDK: ‘MacOSX11.3.sdk’
* checking C++ specification ... NOTE
  Specified C++14: please drop specification unless essential
* checking installed package size ... INFO
  installed size is 11.5Mb
  sub-directories of 1Mb or more:
    extdata   4.0Mb
    metabo    4.1Mb
    ptms      1.5Mb
* checking package 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 whether startup messages can be suppressed ... 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 ... NOTE
alignTargetedRuns: no visible binding for global variable ‘peptide_id’
alignTargetedRuns : <anonymous>: no visible global function definition
  for ‘.’
alignTargetedRuns: no visible binding for global variable ‘intensity’
alignToRoot4: no visible binding for global variable ‘trees’
alignToRoot4: no visible binding for global variable ‘precursors’
alignToRoot4: no visible binding for global variable ‘intensity’
childXICs: possible error in cummax(v = cummax(ifelse(is.na(x), -Inf,
  x))): unused argument (v = cummax(ifelse(is.na(x), -Inf, x)))
distMat.rSqrd : <anonymous> : <anonymous>: no visible binding for
  global variable ‘RT.ref’
distMat.rSqrd : <anonymous> : <anonymous>: no visible binding for
  global variable ‘RT.eXp’
fetchPrecursorsInfo: no visible binding for global variable
  ‘transition_id’
fetchPrecursorsInfo: no visible global function definition for ‘.’
fetchPrecursorsInfo: no visible binding for global variable
  ‘transition_group_id’
fetchTransitionsFromRun: no visible binding for global variable
  ‘intensity’
fetchTransitionsFromRun: no visible global function definition for ‘.’
fetchTransitionsFromRun: no visible binding for global variable
  ‘transition_group_id’
fetchTransitionsFromRun: no visible binding for global variable
  ‘peak_group_rank’
fetchTransitionsFromRun: no visible global function definition for
  ‘head’
getNativeIDs: no visible binding for global variable ‘peptide_id’
getPeptideScores: no visible binding for global variable ‘col2’
getPeptideScores: no visible binding for global variable ‘run’
getQuery: no visible binding for global variable
  ‘identifying.transitionPEPfilter’
getRTdf: no visible binding for global variable ‘peak_group_rank’
getRTdf: no visible binding for global variable ‘m_score’
getRTdf: no visible global function definition for ‘.’
getRTdf: no visible binding for global variable ‘transition_group_id’
getRTdf: no visible binding for global variable ‘RT’
getRefRun : <anonymous>: no visible binding for global variable
  ‘pvalue’
ipfReassignFDR: no visible binding for global variable ‘ref_run’
ipfReassignFDR: no visible binding for global variable ‘run’
ipfReassignFDR: no visible global function definition for ‘.’
ipfReassignFDR: no visible binding for global variable ‘i.to’
ipfReassignFDR: no visible binding for global variable ‘m_score_new’
ipfReassignFDR: no visible binding for global variable ‘ms2_m_score’
ipfReassignFDR: no visible binding for global variable ‘m_score’
mstAlignRuns: no visible binding for global variable ‘ropenms’
mstAlignRuns: no visible binding for global variable ‘peptide_id’
mstAlignRuns : <anonymous>: no visible global function definition for
  ‘.’
mstAlignRuns: no visible binding for global variable ‘intensity’
mstScript1: no visible binding for global variable ‘ropenms’
mstScript2: no visible binding for global variable ‘fileInfo’
mstScript2: no visible binding for global variable ‘peptide_id’
mstScript2: no visible binding for global variable ‘features’
mstScript2 : <anonymous>: no visible global function definition for ‘.’
mstScript2 : <anonymous>: no visible binding for global variable
  ‘features’
mstScript2: no visible binding for global variable ‘intensity’
populateReferenceExperimentFeatureAlignmentMap: no visible binding for
  global variable ‘run’
populateReferenceExperimentFeatureAlignmentMap: no visible binding for
  global variable ‘transition_group_id’
populateReferenceExperimentFeatureAlignmentMap: no visible binding for
  global variable ‘feature_id’
progAlignRuns: no visible binding for global variable ‘peptide_id’
progAlignRuns : <anonymous>: no visible global function definition for
  ‘.’
progAlignRuns: no visible binding for global variable ‘intensity’
progComb3: no visible binding for global variable ‘precursors’
progComb3: no visible binding for global variable ‘ropenms’
progSplit2: no visible binding for global variable ‘trees’
progSplit2: no visible binding for global variable ‘scoreFile’
progSplit2: no visible binding for global variable ‘precursors’
progSplit2 : <anonymous>: no visible global function definition for ‘.’
progSplit2: no visible binding for global variable ‘ropenms’
progSplit4: no visible binding for global variable ‘precursors’
progSplit4 : <anonymous>: no visible global function definition for ‘.’
progSplit4: no visible binding for global variable ‘intensity’
progTree1: no visible binding for global variable ‘ropenms’
progTree1: no visible binding for global variable ‘peptide_id’
reIntensity: no visible binding for global variable ‘run’
reIntensity: no visible binding for global variable ‘alignment_rank’
recalculateIntensity: no visible binding for global variable
  ‘peptide_id’
recalculateIntensity: no visible binding for global variable
  ‘chromatogramIndex’
script2: no visible binding for global variable ‘fileInfo’
script2: no visible binding for global variable ‘peptide_id’
script2 : <anonymous>: no visible global function definition for ‘.’
script2: no visible binding for global variable ‘features’
script2: no visible binding for global variable ‘globalFits’
script2: no visible binding for global variable ‘RSE’
script2: no visible binding for global variable ‘intensity’
setRootRank : <anonymous>: no visible global function definition for
  ‘.’
writeOutFeatureAlignmentMap: no visible binding for global variable
  ‘reference_feature_id’
writeOutFeatureAlignmentMap: no visible binding for global variable
  ‘experiment_feature_id’
writeOutFeatureAlignmentMap: no visible binding for global variable
  ‘ALIGNMENT_GROUP_ID’
writeOutFeatureAlignmentMap: no visible binding for global variable
  ‘REFERENCE’
writeOutFeatureAlignmentMap: no visible global function definition for
  ‘.’
writeOutFeatureAlignmentMap: no visible binding for global variable
  ‘i.to’
writeTables: no visible binding for global variable ‘peptide_id’
writeTables: no visible binding for global variable ‘run’
writeTables: no visible binding for global variable ‘precursor’
Undefined global functions or variables:
  . ALIGNMENT_GROUP_ID REFERENCE RSE RT RT.eXp RT.ref alignment_rank
  chromatogramIndex col2 experiment_feature_id feature_id features
  fileInfo globalFits head i.to identifying.transitionPEPfilter
  intensity m_score m_score_new ms2_m_score peak_group_rank peptide_id
  precursor precursors pvalue ref_run reference_feature_id ropenms run
  scoreFile transition_group_id transition_id trees
Consider adding
  importFrom("datasets", "trees")
  importFrom("utils", "head")
to your NAMESPACE file.
* 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 ... NOTE
Documented arguments not in \usage in Rd file 'alignToRef.Rd':
  ‘feature_alignment_mapping’

Documented arguments not in \usage in Rd file 'blobXICs.Rd':
  ‘nativeId’

Documented arguments not in \usage in Rd file 'extractXIC_group2.Rd':
  ‘mz’

Documented arguments not in \usage in Rd file 'getOswAnalytes.Rd':
  ‘dataPath’ ‘filenames’

Documented arguments not in \usage in Rd file 'getOswFiles.Rd':
  ‘dataPath’ ‘filenames’

Documented arguments not in \usage in Rd file 'perBatch.Rd':
  ‘rownum’

Documented arguments not in \usage in Rd file 'readSqMassHeader.Rd':
  ‘mzmlName’

Documented arguments not in \usage in Rd file 'setAlignmentRank.Rd':
  ‘XICs.eXp’

Documented arguments not in \usage in Rd file 'traverseDown.Rd':
  ‘analytes’

Documented arguments not in \usage in Rd file 'writeTables.Rd':
  ‘filename’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* 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
File ‘/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/DIAlignR/libs/DIAlignR.so’:
  Found ‘__ZNSt3__14coutE’, possibly from ‘std::cout’ (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 nor [v]sprintf. 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
Examples with CPU (user + system) or elapsed time > 5s
                    user system elapsed
alignTargetedRuns 11.104 12.104   7.963
* 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:
  Backtrace:
      ▆
   1. └─testthat::expect_equal(outData[[1]], expData, tolerance = 1e-04) at test_utils.R:76:13
   2.   ├─testthat::compare(act$val, exp$val, ..., tolerance = tolerance)
   3.   └─testthat:::compare.default(act$val, exp$val, ..., tolerance = tolerance)
   4.     ├─base::all.equal(x, y, ...)
   5.     └─data.table:::all.equal.data.table(x, y, ...)
   6.       ├─base::all.equal(x, y, tolerance = tolerance, ..., check.attributes = check.attributes)
   7.       └─bit64::all.equal.integer64(...)
   8.         ├─base::is.na(current)
   9.         └─bit64::is.na.integer64(current)
  
  [ FAIL 1 | WARN 0 | SKIP 8 | PASS 631 ]
  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, 4 NOTEs
See
  ‘/Users/biocbuild/bbs-3.21-bioc/meat/DIAlignR.Rcheck/00check.log’
for details.

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL DIAlignR
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library’
* installing *source* package ‘DIAlignR’ ...
** this is package ‘DIAlignR’ version ‘2.15.1’
** using staged installation
** libs
using C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
using C++14
using SDK: ‘MacOSX11.3.sdk’
clang++ -arch x86_64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/RcppEigen/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -DR_NO_REMAP -c ChromatogramPeak.cpp -o ChromatogramPeak.o
clang++ -arch x86_64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/RcppEigen/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -DR_NO_REMAP -c DPosition.cpp -o DPosition.o
clang++ -arch x86_64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/RcppEigen/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -DR_NO_REMAP -c MSChromatogram.cpp -o MSChromatogram.o
clang++ -arch x86_64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/RcppEigen/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -DR_NO_REMAP -c PeakIntegrator.cpp -o PeakIntegrator.o
clang++ -arch x86_64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/RcppEigen/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -DR_NO_REMAP -c RcppExports.cpp -o RcppExports.o
clang++ -arch x86_64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/RcppEigen/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -DR_NO_REMAP -c Rmain.cpp -o Rmain.o
In file included from Rmain.cpp:19:
./miscell.h:14:19: warning: unused function 'detect_end_na' [-Wunused-function]
static bool const detect_end_na(double a, double b);
                  ^
./miscell.h:16:19: warning: unused function 'detect_start_na' [-Wunused-function]
static bool const detect_start_na(double a, double b);
                  ^
./miscell.h:18:19: warning: unused function 'lessZero' [-Wunused-function]
static bool const lessZero(double a);
                  ^
3 warnings generated.
clang++ -arch x86_64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/RcppEigen/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -DR_NO_REMAP -c SavitzkyGolayFilter.cpp -o SavitzkyGolayFilter.o
clang++ -arch x86_64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/RcppEigen/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -DR_NO_REMAP -c affinealignment.cpp -o affinealignment.o
clang++ -arch x86_64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/RcppEigen/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -DR_NO_REMAP -c affinealignobj.cpp -o affinealignobj.o
clang++ -arch x86_64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/RcppEigen/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -DR_NO_REMAP -c alignment.cpp -o alignment.o
clang++ -arch x86_64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/RcppEigen/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -DR_NO_REMAP -c chromSimMatrix.cpp -o chromSimMatrix.o
clang++ -arch x86_64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/RcppEigen/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -DR_NO_REMAP -c constrainMat.cpp -o constrainMat.o
constrainMat.cpp:78:10: warning: unused variable 'mapped' [-Wunused-variable]
  double mapped = 0.0;
         ^
1 warning generated.
clang++ -arch x86_64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/RcppEigen/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -DR_NO_REMAP -c gapPenalty.cpp -o gapPenalty.o
clang++ -arch x86_64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/RcppEigen/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -DR_NO_REMAP -c integrateArea.cpp -o integrateArea.o
clang++ -arch x86_64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/RcppEigen/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -DR_NO_REMAP -c interface.cpp -o interface.o
clang++ -arch x86_64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/RcppEigen/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -DR_NO_REMAP -c miscell.cpp -o miscell.o
miscell.cpp:53:19: warning: unused function 'lessZero' [-Wunused-function]
static bool const lessZero(double a){
                  ^
1 warning generated.
clang++ -arch x86_64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/RcppEigen/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -DR_NO_REMAP -c run_alignment.cpp -o run_alignment.o
clang++ -arch x86_64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/RcppEigen/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -DR_NO_REMAP -c simpleFcn.cpp -o simpleFcn.o
clang++ -arch x86_64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/RcppEigen/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -DR_NO_REMAP -c spline.cpp -o spline.o
clang++ -arch x86_64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/RcppEigen/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -DR_NO_REMAP -c utils.cpp -o utils.o
utils.cpp:48:9: warning: unused variable 'idx' [-Wunused-variable]
    int idx = n*(1-p);
        ^
1 warning generated.
clang++ -arch x86_64 -std=gnu++14 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/x86_64/lib -o DIAlignR.so ChromatogramPeak.o DPosition.o MSChromatogram.o PeakIntegrator.o RcppExports.o Rmain.o SavitzkyGolayFilter.o affinealignment.o affinealignobj.o alignment.o chromSimMatrix.o constrainMat.o gapPenalty.o integrateArea.o interface.o miscell.o run_alignment.o simpleFcn.o spline.o utils.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/00LOCK-DIAlignR/00new/DIAlignR/libs
** R
** data
** 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
Warning in fun(libname, pkgname) :
  Package 'DIAlignR' is deprecated and will be removed from Bioconductor
  version 3.22
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
Warning in fun(libname, pkgname) :
  Package 'DIAlignR' is deprecated and will be removed from Bioconductor
  version 3.22
** testing if installed package keeps a record of temporary installation path
* DONE (DIAlignR)

R Under development (unstable) (2025-01-22 r87618) -- "Unsuffered Consequences"
Copyright (C) 2025 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.

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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(DIAlignR)
Warning message:
In fun(libname, pkgname) :
  Package 'DIAlignR' is deprecated and will be removed from Bioconductor
  version 3.22
> 
> test_check("DIAlignR")
[1] "hroest_K120808_Strep10%PlasmaBiolRepl1_R03_SW_filt"
[2] "hroest_K120809_Strep0%PlasmaBiolRepl2_R04_SW_filt" 
[3] "hroest_K120809_Strep10%PlasmaBiolRepl2_R04_SW_filt"
Time difference of 0.04707193 secs
Time difference of 0.208879 secs
Time difference of 0.1824851 secs
Time difference of 0.02486897 secs
Time difference of 0.009777069 secs
Time difference of 0.09713888 secs
Time difference of 1.263538 secs
Time difference of 0.02280092 secs
Time difference of 0.3539228 secs
[1] "hroest_K120808_Strep10%PlasmaBiolRepl1_R03_SW_filt"
[2] "hroest_K120809_Strep0%PlasmaBiolRepl2_R04_SW_filt" 
Time difference of 0.01693797 secs
Time difference of 0.1674359 secs
Time difference of 0.116529 secs
Time difference of 0.01726007 secs
Time difference of 0.00812912 secs
Time difference of 0.056638 secs
Time difference of 0.7148879 secs
Time difference of 0.02291489 secs
Time difference of 0.7835219 secs
[1] "hroest_K120808_Strep10%PlasmaBiolRepl1_R03_SW_filt"
[2] "hroest_K120809_Strep0%PlasmaBiolRepl2_R04_SW_filt" 
[3] "hroest_K120809_Strep10%PlasmaBiolRepl2_R04_SW_filt"
Time difference of 0.01663995 secs
Time difference of 0.1933808 secs
Time difference of 0.1216481 secs
Time difference of 0.09676695 secs
Time difference of 0.009456158 secs
Time difference of 0.06787896 secs
Time difference of 1.000192 secs
Time difference of 0.02172089 secs
Time difference of 0.275198 secs
[1] "hroest_K120808_Strep10%PlasmaBiolRepl1_R03_SW_filt"
[2] "hroest_K120809_Strep0%PlasmaBiolRepl2_R04_SW_filt" 
[3] "hroest_K120809_Strep10%PlasmaBiolRepl2_R04_SW_filt"
Time difference of 0.02028298 secs
Time difference of 0.01410985 secs
Time difference of 0.0002958775 secs
Time difference of 0.0936451 secs
Time difference of 0.009297848 secs
Time difference of 0.04050493 secs
Time difference of 0.01606703 secs
Time difference of 0.006863832 secs
Time difference of 0.07316303 secs
[1] "hroest_K120809_Strep0%PlasmaBiolRepl2_R04_SW_filt" 
[2] "hroest_K120809_Strep10%PlasmaBiolRepl2_R04_SW_filt"
[1] "PestMix1_8Step1Plasma1SWATH20-50" "PestMix1_8Step8Plasma1SWATH20-50"
Time difference of 0.007975101 secs
Time difference of 0.02452111 secs
Time difference of 0.008620977 secs
Time difference of 0.01247597 secs
Time difference of 0.005944014 secs
Time difference of 0.04088402 secs
Time difference of 0.065166 secs
Time difference of 0.00673604 secs
Time difference of 0.1819041 secs
[1] "chludwig_K150309_004b_SW_1_16" "chludwig_K150309_008_SW_1_4"  
[3] "chludwig_K150309_013_SW_0"    
Time difference of 0.01038504 secs
Time difference of 0.01270413 secs
Time difference of 0.0009260178 secs
Time difference of 0.01893997 secs
Time difference of 0.011832 secs
Time difference of 0.057199 secs
Time difference of 0.006462097 secs
Time difference of 0.02070713 secs
Time difference of 0.1980641 secs
<simpleWarning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric,     drop.square = drop.square, normalize = normalize, statistics = control$statistics,     surface = control$surface, cell = control$cell, iterations = iterations,     iterTrace = control$iterTrace, trace.hat = control$trace.hat): span too small.   fewer data values than degrees of freedom.>
<simpleWarning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric,     drop.square = drop.square, normalize = normalize, statistics = control$statistics,     surface = control$surface, cell = control$cell, iterations = iterations,     iterTrace = control$iterTrace, trace.hat = control$trace.hat): span too small.   fewer data values than degrees of freedom.>
<simpleWarning in sqrt(sum.squares/one.delta): NaNs produced>
<simpleError in simpleLoess(y, x, w, span, degree = degree, parametric = parametric,     drop.square = drop.square, normalize = normalize, statistics = control$statistics,     surface = control$surface, cell = control$cell, iterations = iterations,     iterTrace = control$iterTrace, trace.hat = control$trace.hat): span is too small>
                                                runName
run0 hroest_K120808_Strep10%PlasmaBiolRepl1_R03_SW_filt
run1  hroest_K120809_Strep0%PlasmaBiolRepl2_R04_SW_filt
run2 hroest_K120809_Strep10%PlasmaBiolRepl2_R04_SW_filt
Time difference of 0.1038792 secs
Time difference of 0.01494598 secs
Time difference of 0.002393007 secs
Time difference of 0.009866953 secs
Time difference of 0.04753518 secs
Time difference of 0.01326489 secs
Time difference of 0.01319408 secs
Time difference of 0.1000261 secs
                                                runName
run0 hroest_K120808_Strep10%PlasmaBiolRepl1_R03_SW_filt
run1  hroest_K120809_Strep0%PlasmaBiolRepl2_R04_SW_filt
run2 hroest_K120809_Strep10%PlasmaBiolRepl2_R04_SW_filt
Time difference of 0.02992606 secs
[1] "run0 run1\nrun2 run2"
Time difference of 0.5304508 secs
Time difference of 0.1042321 secs
Time difference of 0.008720875 secs
Time difference of 0.06363511 secs
Time difference of 0.989907 secs
Time difference of 0.01262999 secs
Time difference of 0.301537 secs
                                                runName
run0 hroest_K120808_Strep10%PlasmaBiolRepl1_R03_SW_filt
run1  hroest_K120809_Strep0%PlasmaBiolRepl2_R04_SW_filt
run2 hroest_K120809_Strep10%PlasmaBiolRepl2_R04_SW_filt
Time difference of 0.1608801 secs
Time difference of 0.749294 secs
Time difference of 5.835643 secs
Time difference of 0.4707031 secs
                                                runName
run0 hroest_K120808_Strep10%PlasmaBiolRepl1_R03_SW_filt
run1  hroest_K120809_Strep0%PlasmaBiolRepl2_R04_SW_filt
run2 hroest_K120809_Strep10%PlasmaBiolRepl2_R04_SW_filt
Time difference of 0.1084402 secs
[1] "Written /Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/DIAlignR/extdata/temp_prog1.RData"
[1] "Written /Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/DIAlignR/extdata/temp_0_2.rds"
[1] "progTree1 is done."
Time difference of 1.323683 secs
Time difference of 0.2659938 secs
[1] "Written /Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/DIAlignR/extdata/temp_1_2.rds"
Time difference of 0.4222178 secs
[1] "Written /Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/DIAlignR/extdata/temp_2_2.rds"
Time difference of 0.2881801 secs
Time difference of 0.1472831 secs
[1] "Written /Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/DIAlignR/extdata/temp_all_2.rds"
Time difference of 0.210701 secs
                                                runName
run0 hroest_K120808_Strep10%PlasmaBiolRepl1_R03_SW_filt
run1  hroest_K120809_Strep0%PlasmaBiolRepl2_R04_SW_filt
run2 hroest_K120809_Strep10%PlasmaBiolRepl2_R04_SW_filt
Time difference of 0.09609699 secs
[1] "Written /Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/DIAlignR/extdata/temp_prog1.RData"
[1] "Written /Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/DIAlignR/extdata/temp_0_2.rds"
[1] "progTree1 is done."
Time difference of 0.9082642 secs
Time difference of 0.6337099 secs
[1] "Written /Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/DIAlignR/extdata/temp_1_2.rds"
Time difference of 0.3895791 secs
[1] "Written /Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/DIAlignR/extdata/temp_2_2.rds"
Time difference of 0.2639191 secs
Time difference of 0.00991106 secs
[1] "Written /Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/DIAlignR/extdata/temp_all_2.rds"
Error in reticulate::use_condaenv(condaEnv, required = TRUE) : 
  Unable to locate conda environment 'TricEnvr'.
Error in reticulate::use_condaenv(condaEnv, required = TRUE) : 
  Unable to locate conda environment 'TricEnvr'.
Error in reticulate::use_condaenv(condaEnv, required = TRUE) : 
  Unable to locate conda environment 'TricEnvr'.
[ FAIL 1 | WARN 0 | SKIP 8 | PASS 631 ]

══ Skipped tests (8) ═══════════════════════════════════════════════════════════
• empty test (5): 'test_get_filenames.R:77:1', 'test_get_filenames.R:82:1',
  'test_utils.R:200:1', 'test_utils.R:203:1', 'test_utils.R:206:1'
• ropenms not available for testing. A conda environment with name TricEnvr is
  MUST for testing. (3): 'test_pyopenms.R:4:3', 'test_pyopenms.R:8:3',
  'test_pyopenms.R:27:3'

══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test_utils.R:76:13'): test_getRefExpFeatureMap ──────────────────────
Error in `is.na.integer64(current)`: REAL() can only be applied to a 'numeric', not a 'integer'
Backtrace:
    ▆
 1. └─testthat::expect_equal(outData[[1]], expData, tolerance = 1e-04) at test_utils.R:76:13
 2.   ├─testthat::compare(act$val, exp$val, ..., tolerance = tolerance)
 3.   └─testthat:::compare.default(act$val, exp$val, ..., tolerance = tolerance)
 4.     ├─base::all.equal(x, y, ...)
 5.     └─data.table:::all.equal.data.table(x, y, ...)
 6.       ├─base::all.equal(x, y, tolerance = tolerance, ..., check.attributes = check.attributes)
 7.       └─bit64::all.equal.integer64(...)
 8.         ├─base::is.na(current)
 9.         └─bit64::is.na.integer64(current)

[ FAIL 1 | WARN 0 | SKIP 8 | PASS 631 ]
Error: Test failures
Execution halted