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###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD check --install=check:DIAlignR.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings DIAlignR_2.13.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/DIAlignR.Rcheck’
* using R version 4.4.1 (2024-06-14)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
    gcc (GCC) 12.2.1 20220819 (openEuler 12.2.1-14)
    GNU Fortran (GCC) 10.3.1
* running under: openEuler 22.03 (LTS-SP1)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘DIAlignR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘DIAlignR’ version ‘2.13.0’
* 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 ‘DIAlignR’ can be installed ... OK
* used C++ compiler: ‘g++ (GCC) 10.3.1’
* checking C++ specification ... NOTE
  Specified C++14: please drop specification unless essential
* checking installed package size ... NOTE
  installed size is 30.2Mb
  sub-directories of 1Mb or more:
    extdata   4.0Mb
    libs     19.3Mb
    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 loading without being on the library search path ... 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 ‘/home/biocbuild/R/R-4.4.1/site-library/DIAlignR/libs/DIAlignR.so’:
  Found ‘_ZSt4cout’, 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 10.178 10.041   6.666
* 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:
  ══ 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 ════════════════════════════════════════════════════════════════
  ── Failure ('test_utils.R:276:3'): test_ipfReassignFDR ─────────────────────────
  `finalTbl` not equal to `expData`.
  Column 'RT': 'is.NA' value mismatch: 2 in current 0 in target
  
  [ 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, 5 NOTEs
See
  ‘/home/biocbuild/bbs-3.20-bioc/meat/DIAlignR.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD INSTALL DIAlignR
###
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* installing to library ‘/home/biocbuild/R/R-4.4.1/site-library’
* installing *source* package ‘DIAlignR’ ...
** using staged installation
** libs
using C++ compiler: ‘g++ (GCC) 10.3.1’
using C++14
g++ -std=gnu++14 -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.4.1/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.4.1/site-library/RcppEigen/include' -I/usr/local/include    -fPIC  -g -O2  -Wall  -c ChromatogramPeak.cpp -o ChromatogramPeak.o
g++ -std=gnu++14 -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.4.1/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.4.1/site-library/RcppEigen/include' -I/usr/local/include    -fPIC  -g -O2  -Wall  -c DPosition.cpp -o DPosition.o
g++ -std=gnu++14 -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.4.1/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.4.1/site-library/RcppEigen/include' -I/usr/local/include    -fPIC  -g -O2  -Wall  -c MSChromatogram.cpp -o MSChromatogram.o
g++ -std=gnu++14 -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.4.1/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.4.1/site-library/RcppEigen/include' -I/usr/local/include    -fPIC  -g -O2  -Wall  -c PeakIntegrator.cpp -o PeakIntegrator.o
g++ -std=gnu++14 -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.4.1/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.4.1/site-library/RcppEigen/include' -I/usr/local/include    -fPIC  -g -O2  -Wall  -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++14 -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.4.1/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.4.1/site-library/RcppEigen/include' -I/usr/local/include    -fPIC  -g -O2  -Wall  -c Rmain.cpp -o Rmain.o
Rmain.cpp: In function ‘Rcpp::NumericVector areaIntegrator(Rcpp::List, Rcpp::List, double, double, std::string, std::string, bool, bool, int, int)’:
Rmain.cpp:273:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::vector<double> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  273 |     for(int i = 0; i<vov2.size(); i++) sgolay.smoothChroms(vov2[i]);
      |                    ~^~~~~~~~~~~~
Rmain.cpp: In function ‘Rcpp::NumericMatrix sgolayCpp(Rcpp::NumericMatrix, int, int)’:
Rmain.cpp:305:19: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  305 |   for(int i = 0; i<d.size(); i++){
      |                  ~^~~~~~~~~
Rmain.cpp: In function ‘Rcpp::NumericMatrix getAlignedTimesCpp(Rcpp::List, Rcpp::List, int, int, std::string, double, std::string, std::string, const std::vector<double>&, double, double, double, bool, double, double, int, bool, double)’:
Rmain.cpp:368:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::vector<double> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  368 |     for(int i = 0; i<intensity1.size(); i++){
      |                    ~^~~~~~~~~~~~~~~~~~
Rmain.cpp: In function ‘Rcpp::List getChildXICpp(Rcpp::List, Rcpp::List, int, int, std::string, double, std::string, std::string, const std::vector<double>&, double, double, double, bool, double, double, int, bool, double, double, std::string, std::string, bool)’:
Rmain.cpp:771:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::vector<double> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  771 |     for(int i = 0; i<intensity1.size(); i++){
      |                    ~^~~~~~~~~~~~~~~~~~
Rmain.cpp:818:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  818 |   for(int i = 0; i < keep.size(); i++){
      |                  ~~^~~~~~~~~~~~~
Rmain.cpp:824:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::vector<double> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  824 |   for(int j = 0; j <intensity1NN.size(); j++){
      |                  ~~^~~~~~~~~~~~~~~~~~~~
Rmain.cpp:827:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  827 |     for(int i = 0; i < keep.size(); i++){
      |                    ~~^~~~~~~~~~~~~
Rmain.cpp:837:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  837 |   for(int i = 0; i < keep.size(); i++) alignedChildTime[keep[i]] = t1NN[i];
      |                  ~~^~~~~~~~~~~~~
Rmain.cpp:862:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::vector<double> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  862 |   for (int i = 0; i < intensity1NN.size(); i++){
      |                   ~~^~~~~~~~~~~~~~~~~~~~~
Rmain.cpp:873:28: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  873 |     for(int i =0, j = 0; i < alignedChildTime.size(); i++){
      |                          ~~^~~~~~~~~~~~~~~~~~~~~~~~~
Rmain.cpp: In function ‘Rcpp::List otherChildXICpp(Rcpp::List, Rcpp::List, int, int, Rcpp::NumericMatrix, std::vector<double>, double, std::string)’:
Rmain.cpp:944:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::vector<double> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  944 |     for(int i = 0; i<intensity1.size(); i++){
      |                    ~^~~~~~~~~~~~~~~~~~
Rmain.cpp:972:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::vector<double> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  972 |   for(int j = 0; j <intensity1NN.size(); j++){
      |                  ~~^~~~~~~~~~~~~~~~~~~~
Rmain.cpp:975:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  975 |     for(int i = 0; i < keep.size(); i++){
      |                    ~~^~~~~~~~~~~~~
Rmain.cpp:1008:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::vector<double> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
 1008 |   for (int i = 0; i < intensity1NN.size(); i++){
      |                   ~~^~~~~~~~~~~~~~~~~~~~~
In file included from Rmain.cpp:19:
miscell.h: At global scope:
miscell.h:14:19: warning: ‘const bool DIAlign::detect_end_na(double, double)’ declared ‘static’ but never defined [-Wunused-function]
   14 | static bool const detect_end_na(double a, double b);
      |                   ^~~~~~~~~~~~~
miscell.h:16:19: warning: ‘const bool DIAlign::detect_start_na(double, double)’ declared ‘static’ but never defined [-Wunused-function]
   16 | static bool const detect_start_na(double a, double b);
      |                   ^~~~~~~~~~~~~~~
miscell.h:18:19: warning: ‘const bool DIAlign::lessZero(double)’ declared ‘static’ but never defined [-Wunused-function]
   18 | static bool const lessZero(double a);
      |                   ^~~~~~~~
In file included from miscell.h:9,
                 from Rmain.cpp:19:
spline.h:390:10: warning: ‘double DIAlign::{anonymous}::tk::spline::deriv(int, double) const’ defined but not used [-Wunused-function]
  390 |   double spline::deriv(int order, double x) const
      |          ^~~~~~
spline.h:364:10: warning: ‘double DIAlign::{anonymous}::tk::spline::operator()(double) const’ defined but not used [-Wunused-function]
  364 |   double spline::operator() (double x) const
      |          ^~~~~~
spline.h:273:8: warning: ‘void DIAlign::{anonymous}::tk::spline::set_points(const std::vector<double>&, const std::vector<double>&, bool)’ defined but not used [-Wunused-function]
  273 |   void spline::set_points(const std::vector<double>& x,
      |        ^~~~~~
spline.h:261:8: warning: ‘void DIAlign::{anonymous}::tk::spline::set_boundary(DIAlign::{anonymous}::tk::spline::bd_type, double, DIAlign::{anonymous}::tk::spline::bd_type, double, bool)’ defined but not used [-Wunused-function]
  261 |   void spline::set_boundary(spline::bd_type left, double left_value,
      |        ^~~~~~
g++ -std=gnu++14 -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.4.1/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.4.1/site-library/RcppEigen/include' -I/usr/local/include    -fPIC  -g -O2  -Wall  -c SavitzkyGolayFilter.cpp -o SavitzkyGolayFilter.o
g++ -std=gnu++14 -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.4.1/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.4.1/site-library/RcppEigen/include' -I/usr/local/include    -fPIC  -g -O2  -Wall  -c affinealignment.cpp -o affinealignment.o
affinealignment.cpp: In function ‘double DIAlign::AffineAlignment::getOlapAffineAlignStartIndices(double*, double*, double*, int, int, int&, int&, DIAlign::Traceback::tbJump&)’:
affinealignment.cpp:485:16: warning: ‘MaxColIndex’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  485 |   OlapStartCol = MaxColIndex;
      |   ~~~~~~~~~~~~~^~~~~~~~~~~~~
affinealignment.cpp:484:16: warning: ‘MaxRowIndex’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  484 |   OlapStartRow = MaxRowIndex;
      |   ~~~~~~~~~~~~~^~~~~~~~~~~~~
g++ -std=gnu++14 -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.4.1/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.4.1/site-library/RcppEigen/include' -I/usr/local/include    -fPIC  -g -O2  -Wall  -c affinealignobj.cpp -o affinealignobj.o
g++ -std=gnu++14 -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.4.1/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.4.1/site-library/RcppEigen/include' -I/usr/local/include    -fPIC  -g -O2  -Wall  -c alignment.cpp -o alignment.o
g++ -std=gnu++14 -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.4.1/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.4.1/site-library/RcppEigen/include' -I/usr/local/include    -fPIC  -g -O2  -Wall  -c chromSimMatrix.cpp -o chromSimMatrix.o
chromSimMatrix.cpp: In function ‘std::vector<double> DIAlign::SimilarityMatrix::perSampleEucLenVecOfVec(const std::vector<std::vector<double> >&)’:
chromSimMatrix.cpp:32:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
   32 |   for (int i = 0; i < mag.size(); i++){
      |                   ~~^~~~~~~~~~~~
chromSimMatrix.cpp: In function ‘std::vector<double> DIAlign::SimilarityMatrix::perSampleSqrSumVecOfVec(const std::vector<std::vector<double> >&)’:
chromSimMatrix.cpp:45:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
   45 |   for (int i = 0; i < mag.size(); i++){
      |                   ~~^~~~~~~~~~~~
chromSimMatrix.cpp: In function ‘std::vector<double> DIAlign::SimilarityMatrix::perSampleMeanVecOfVec(const std::vector<std::vector<double> >&)’:
chromSimMatrix.cpp:57:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
   57 |   for (int i = 0; i < mean.size(); i++){
      |                   ~~^~~~~~~~~~~~~
chromSimMatrix.cpp: In function ‘std::vector<double> DIAlign::SimilarityMatrix::perSampleSumVecOfVec(const std::vector<std::vector<double> >&)’:
chromSimMatrix.cpp:70:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
   70 |   for (int i = 0; i < sum.size(); i++){
      |                   ~~^~~~~~~~~~~~
chromSimMatrix.cpp: In function ‘DIAlign::SimMatrix DIAlign::SimilarityMatrix::getSimilarityMatrix(const std::vector<std::vector<double> >&, const std::vector<std::vector<double> >&, std::string, std::string, double, double, int)’:
chromSimMatrix.cpp:414:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  414 |     for(int i = 0; i < MASK.size(); i++){
      |                    ~~^~~~~~~~~~~~~
g++ -std=gnu++14 -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.4.1/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.4.1/site-library/RcppEigen/include' -I/usr/local/include    -fPIC  -g -O2  -Wall  -c constrainMat.cpp -o constrainMat.o
constrainMat.cpp: In function ‘void DIAlign::ConstrainMatrix::calcNoBeefMask2(DIAlign::SimMatrix&, std::vector<double>, std::vector<double>, std::vector<double>, int, bool)’:
constrainMat.cpp:78:10: warning: unused variable ‘mapped’ [-Wunused-variable]
   78 |   double mapped = 0.0;
      |          ^~~~~~
g++ -std=gnu++14 -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.4.1/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.4.1/site-library/RcppEigen/include' -I/usr/local/include    -fPIC  -g -O2  -Wall  -c gapPenalty.cpp -o gapPenalty.o
gapPenalty.cpp: In function ‘double DIAlign::getGapPenalty(const DIAlign::SimMatrix&, double, std::string)’:
gapPenalty.cpp:26:35: warning: ‘gapPenalty’ may be used uninitialized in this function [-Wmaybe-uninitialized]
   26 |   return std::max(0.01, gapPenalty); // gapPenalty must be positive.
      |                                   ^
g++ -std=gnu++14 -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.4.1/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.4.1/site-library/RcppEigen/include' -I/usr/local/include    -fPIC  -g -O2  -Wall  -c integrateArea.cpp -o integrateArea.o
g++ -std=gnu++14 -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.4.1/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.4.1/site-library/RcppEigen/include' -I/usr/local/include    -fPIC  -g -O2  -Wall  -c interface.cpp -o interface.o
g++ -std=gnu++14 -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.4.1/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.4.1/site-library/RcppEigen/include' -I/usr/local/include    -fPIC  -g -O2  -Wall  -c miscell.cpp -o miscell.o
miscell.cpp: In function ‘void DIAlign::xicIntersect(std::vector<std::vector<double> >&, std::vector<std::vector<double> >&)’:
miscell.cpp:10:30: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare]
   10 |   for (unsigned int i = 0; i < len; i++){
      |                            ~~^~~~~
miscell.cpp:15:29: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare]
   15 |   for(unsigned int i = 0; i < len; i++){
      |                           ~~^~~~~
miscell.cpp:26:30: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare]
   26 |   for (unsigned int i = 0; i < len; i++){
      |                            ~~^~~~~
miscell.cpp:39:30: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare]
   39 |   for (unsigned int i = 0; i < len; i++) len2[i] = intensity[i].size();
      |                            ~~^~~~~
miscell.cpp: In function ‘std::vector<std::vector<double> > DIAlign::imputeChromatogram(const std::vector<std::vector<double> >&, const std::vector<double>&, const std::vector<int>&)’:
miscell.cpp:125:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  125 |   for(int i =0; i< middle.size(); i++){
      |                 ~^~~~~~~~~~~~~~~
miscell.cpp:131:19: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::vector<double> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  131 |   for(int i =0; i < (Anew.size()-1); i++){
      |                 ~~^~~~~~~~~~~~~~~~~
miscell.cpp:139:19: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  139 |     for(int j=0; j<result.size(); j++){
      |                  ~^~~~~~~~~~~~~~
miscell.cpp: In function ‘std::vector<int> DIAlign::getSkip(const std::vector<int>&, const std::vector<int>&)’:
miscell.cpp:164:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  164 |   for(int i = 0; i < index.size(); i++){
      |                  ~~^~~~~~~~~~~~~~
miscell.cpp: In function ‘void DIAlign::mergeIntensity(std::vector<std::vector<double> >&, std::vector<std::vector<double> >&, double)’:
miscell.cpp:221:19: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::vector<double> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  221 |   for(int i = 0; i< A.size(); i++){
      |                  ~^~~~~~~~~~
miscell.cpp: In function ‘void DIAlign::addFlankToLeft(const std::vector<double>&, std::vector<double>&, std::vector<double>&, const std::vector<std::vector<double> >&, std::vector<std::vector<double> >&, std::vector<int>&)’:
miscell.cpp:250:19: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::vector<double> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  250 |   for(int i = 0; i< intenN.size(); i++){
      |                  ~^~~~~~~~~~~~~~~
miscell.cpp: In function ‘void DIAlign::addFlankToRight(const std::vector<double>&, std::vector<double>&, std::vector<double>&, const std::vector<std::vector<double> >&, std::vector<std::vector<double> >&, std::vector<int>&)’:
miscell.cpp:277:19: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::vector<double> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  277 |   for(int i = 0; i< intenN.size(); i++){
      |                  ~^~~~~~~~~~~~~~~
miscell.cpp: In function ‘void DIAlign::addFlankToLeft1(const std::vector<std::vector<double> >&, std::vector<std::vector<double> >&, std::vector<int>&)’:
miscell.cpp:288:19: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::vector<double> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  288 |   for(int i = 0; i< intenN.size(); i++){
      |                  ~^~~~~~~~~~~~~~~
miscell.cpp: In function ‘void DIAlign::addFlankToRight1(const std::vector<std::vector<double> >&, std::vector<std::vector<double> >&, std::vector<int>&)’:
miscell.cpp:307:19: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::vector<double> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  307 |   for(int i = 0; i< intenN.size(); i++){
      |                  ~^~~~~~~~~~~~~~~
miscell.cpp: In function ‘std::vector<int> DIAlign::getMatchingIdx(const std::vector<double>&, const std::vector<double>&)’:
miscell.cpp:318:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  318 |   for(int i =0, j=0; i< tMain.size(); i++){
      |                      ~^~~~~~~~~~~~~~
miscell.cpp:320:12: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  320 |     for(; j<t.size();){
      |           ~^~~~~~~~~
miscell.cpp: In function ‘std::vector<std::vector<double> > DIAlign::imputeChromatogram1(const std::vector<std::vector<double> >&, const std::vector<int>&, const std::vector<double>&, const std::vector<double>&)’:
miscell.cpp:337:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::vector<double> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  337 |   for(int j = 0; j <A.size(); j++){
      |                  ~~^~~~~~~~~
miscell.cpp:339:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  339 |     for(int i = 0; i < temp.size(); i++){
      |                    ~~^~~~~~~~~~~~~
miscell.cpp:353:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  353 |   for(int i =0; i< middle.size(); i++){
      |                 ~^~~~~~~~~~~~~~~
miscell.cpp:358:19: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::vector<double> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  358 |   for(int i =0; i < intensity.size(); i++){
      |                 ~~^~~~~~~~~~~~~~~~~~
miscell.cpp:360:19: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  360 |     for(int j=0; j<result.size(); j++){
      |                  ~^~~~~~~~~~~~~~
miscell.cpp: At global scope:
miscell.cpp:53:19: warning: ‘const bool DIAlign::lessZero(double)’ defined but not used [-Wunused-function]
   53 | static bool const lessZero(double a){
      |                   ^~~~~~~~
In file included from miscell.h:9,
                 from miscell.cpp:3:
spline.h:390:10: warning: ‘double DIAlign::{anonymous}::tk::spline::deriv(int, double) const’ defined but not used [-Wunused-function]
  390 |   double spline::deriv(int order, double x) const
      |          ^~~~~~
spline.h:364:10: warning: ‘double DIAlign::{anonymous}::tk::spline::operator()(double) const’ defined but not used [-Wunused-function]
  364 |   double spline::operator() (double x) const
      |          ^~~~~~
spline.h:273:8: warning: ‘void DIAlign::{anonymous}::tk::spline::set_points(const std::vector<double>&, const std::vector<double>&, bool)’ defined but not used [-Wunused-function]
  273 |   void spline::set_points(const std::vector<double>& x,
      |        ^~~~~~
spline.h:261:8: warning: ‘void DIAlign::{anonymous}::tk::spline::set_boundary(DIAlign::{anonymous}::tk::spline::bd_type, double, DIAlign::{anonymous}::tk::spline::bd_type, double, bool)’ defined but not used [-Wunused-function]
  261 |   void spline::set_boundary(spline::bd_type left, double left_value,
      |        ^~~~~~
g++ -std=gnu++14 -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.4.1/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.4.1/site-library/RcppEigen/include' -I/usr/local/include    -fPIC  -g -O2  -Wall  -c run_alignment.cpp -o run_alignment.o
g++ -std=gnu++14 -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.4.1/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.4.1/site-library/RcppEigen/include' -I/usr/local/include    -fPIC  -g -O2  -Wall  -c simpleFcn.cpp -o simpleFcn.o
g++ -std=gnu++14 -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.4.1/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.4.1/site-library/RcppEigen/include' -I/usr/local/include    -fPIC  -g -O2  -Wall  -c spline.cpp -o spline.o
In file included from spline.cpp:1:
spline.h:390:10: warning: ‘double DIAlign::{anonymous}::tk::spline::deriv(int, double) const’ defined but not used [-Wunused-function]
  390 |   double spline::deriv(int order, double x) const
      |          ^~~~~~
spline.h:261:8: warning: ‘void DIAlign::{anonymous}::tk::spline::set_boundary(DIAlign::{anonymous}::tk::spline::bd_type, double, DIAlign::{anonymous}::tk::spline::bd_type, double, bool)’ defined but not used [-Wunused-function]
  261 |   void spline::set_boundary(spline::bd_type left, double left_value,
      |        ^~~~~~
g++ -std=gnu++14 -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.4.1/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.4.1/site-library/RcppEigen/include' -I/usr/local/include    -fPIC  -g -O2  -Wall  -c utils.cpp -o utils.o
utils.cpp: In function ‘double DIAlign::Utils::getQuantile(std::vector<double>, double)’:
utils.cpp:48:9: warning: unused variable ‘idx’ [-Wunused-variable]
   48 |     int idx = n*(1-p);
      |         ^~~
g++ -std=gnu++14 -shared -L/home/biocbuild/R/R-4.4.1/lib -L/usr/local/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 -L/home/biocbuild/R/R-4.4.1/lib -lR
installing to /home/biocbuild/R/R-4.4.1/site-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
** 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 (DIAlignR)

R version 4.4.1 (2024-06-14) -- "Race for Your Life"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: aarch64-unknown-linux-gnu

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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)
> 
> 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 0.05464005 secs
Time difference of 0.2653599 secs
Time difference of 0.1856048 secs
Time difference of 0.02732563 secs
Time difference of 0.01044846 secs
Time difference of 0.1103787 secs
Time difference of 2.31847 secs
Time difference of 0.03904843 secs
Time difference of 0.5489693 secs
[1] "hroest_K120808_Strep10%PlasmaBiolRepl1_R03_SW_filt"
[2] "hroest_K120809_Strep0%PlasmaBiolRepl2_R04_SW_filt" 
Time difference of 0.01864624 secs
Time difference of 0.2464025 secs
Time difference of 0.1216872 secs
Time difference of 0.01869321 secs
Time difference of 0.007911444 secs
Time difference of 0.07258058 secs
Time difference of 1.110754 secs
Time difference of 0.01009011 secs
Time difference of 1.170406 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 0.01874232 secs
Time difference of 0.2730577 secs
Time difference of 0.1304076 secs
Time difference of 0.0990169 secs
Time difference of 0.01207232 secs
Time difference of 0.1010914 secs
Time difference of 1.684893 secs
Time difference of 0.02872634 secs
Time difference of 0.4685035 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 0.02146173 secs
Time difference of 0.02164221 secs
Time difference of 0.0007286072 secs
Time difference of 0.1104059 secs
Time difference of 0.01306772 secs
Time difference of 0.06297874 secs
Time difference of 0.02142978 secs
Time difference of 0.01070833 secs
Time difference of 0.156698 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 0.01061845 secs
Time difference of 0.03910041 secs
Time difference of 0.01263356 secs
Time difference of 0.0161128 secs
Time difference of 0.01564097 secs
Time difference of 0.04823494 secs
Time difference of 0.1238742 secs
Time difference of 0.009225368 secs
Time difference of 0.2804515 secs
[1] "chludwig_K150309_004b_SW_1_16" "chludwig_K150309_008_SW_1_4"  
[3] "chludwig_K150309_013_SW_0"    
Time difference of 0.01597619 secs
Time difference of 0.01291752 secs
Time difference of 0.001315594 secs
Time difference of 0.02342868 secs
Time difference of 0.01599479 secs
Time difference of 0.08354259 secs
Time difference of 0.008497238 secs
Time difference of 0.02568436 secs
Time difference of 0.3499105 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 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$trace.hat): Chernobyl! trL>n 10>
<simpleError in simpleLoess(y, x, w, span, degree = degree, parametric = parametric,     drop.square = drop.square, normalize = normalize, statistics = control$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 0.116822 secs
Time difference of 0.01817584 secs
Time difference of 0.002552271 secs
Time difference of 0.01275301 secs
Time difference of 0.06159115 secs
Time difference of 0.02139854 secs
Time difference of 0.02049279 secs
Time difference of 0.1231248 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 0.02942562 secs
[1] "run0 run1\nrun2 run2"
Time difference of 0.2979662 secs
Time difference of 0.1405005 secs
Time difference of 0.01490068 secs
Time difference of 0.1179383 secs
Time difference of 1.729015 secs
Time difference of 0.02286077 secs
Time difference of 0.4746277 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 0.129251 secs
Time difference of 1.085188 secs
Time difference of 6.628751 secs
Time difference of 0.5790215 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 0.1156278 secs
[1] "Written /home/biocbuild/R/R-4.4.1/site-library/DIAlignR/extdata/temp_prog1.RData"
[1] "Written /home/biocbuild/R/R-4.4.1/site-library/DIAlignR/extdata/temp_0_2.rds"
[1] "progTree1 is done."
Time difference of 2.227431 secs
Time difference of 0.4265914 secs
[1] "Written /home/biocbuild/R/R-4.4.1/site-library/DIAlignR/extdata/temp_1_2.rds"
Time difference of 0.8251114 secs
[1] "Written /home/biocbuild/R/R-4.4.1/site-library/DIAlignR/extdata/temp_2_2.rds"
Time difference of 0.4293871 secs
Time difference of 0.2350204 secs
[1] "Written /home/biocbuild/R/R-4.4.1/site-library/DIAlignR/extdata/temp_all_2.rds"
Time difference of 0.2703259 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 0.1152644 secs
[1] "Written /home/biocbuild/R/R-4.4.1/site-library/DIAlignR/extdata/temp_prog1.RData"
[1] "Written /home/biocbuild/R/R-4.4.1/site-library/DIAlignR/extdata/temp_0_2.rds"
[1] "progTree1 is done."
Time difference of 1.554145 secs
Time difference of 0.4084964 secs
[1] "Written /home/biocbuild/R/R-4.4.1/site-library/DIAlignR/extdata/temp_1_2.rds"
Time difference of 0.7182784 secs
[1] "Written /home/biocbuild/R/R-4.4.1/site-library/DIAlignR/extdata/temp_2_2.rds"
Time difference of 0.399648 secs
Time difference of 0.0159955 secs
[1] "Written /home/biocbuild/R/R-4.4.1/site-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 ════════════════════════════════════════════════════════════════
── Failure ('test_utils.R:276:3'): test_ipfReassignFDR ─────────────────────────
`finalTbl` not equal to `expData`.
Column 'RT': 'is.NA' value mismatch: 2 in current 0 in target

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