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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 4.4.0 (2024-04-24)
* 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     19.2Mb
    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-4.4.0/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 9.947 10.502   6.561
* 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-4.4.0/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-4.4.0/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.4.0/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.4.0/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-4.4.0/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.4.0/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.4.0/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-4.4.0/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.4.0/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.4.0/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-4.4.0/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.4.0/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.4.0/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-4.4.0/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.4.0/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.4.0/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-4.4.0/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.4.0/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.4.0/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-4.4.0/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.4.0/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.4.0/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-4.4.0/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.4.0/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.4.0/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-4.4.0/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.4.0/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.4.0/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-4.4.0/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.4.0/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.4.0/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-4.4.0/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.4.0/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.4.0/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-4.4.0/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.4.0/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.4.0/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-4.4.0/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.4.0/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.4.0/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-4.4.0/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.4.0/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.4.0/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-4.4.0/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.4.0/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.4.0/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-4.4.0/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.4.0/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.4.0/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-4.4.0/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.4.0/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.4.0/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-4.4.0/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.4.0/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.4.0/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-4.4.0/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.4.0/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.4.0/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-4.4.0/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.4.0/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.4.0/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-4.4.0/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-4.4.0/lib -lR
installing to /home/biocbuild/R/R-4.4.0/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 4.4.0 (2024-04-24) -- "Puppy Cup"
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 0.05418777 secs
Time difference of 0.265146 secs
Time difference of 0.1877589 secs
Time difference of 0.02714205 secs
Time difference of 0.01078081 secs
Time difference of 0.1101372 secs
Time difference of 2.125286 secs
Time difference of 0.02753901 secs
Time difference of 0.4731436 secs
[1] "hroest_K120808_Strep10%PlasmaBiolRepl1_R03_SW_filt"
[2] "hroest_K120809_Strep0%PlasmaBiolRepl2_R04_SW_filt" 
Time difference of 0.01781559 secs
Time difference of 0.2526951 secs
Time difference of 0.1265695 secs
Time difference of 0.01968765 secs
Time difference of 0.008447409 secs
Time difference of 0.07148647 secs
Time difference of 1.16555 secs
Time difference of 0.01045513 secs
Time difference of 1.090132 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 0.01819754 secs
Time difference of 0.2653103 secs
Time difference of 0.1287537 secs
Time difference of 0.09843731 secs
Time difference of 0.01287603 secs
Time difference of 0.09472489 secs
Time difference of 1.581534 secs
Time difference of 0.02683401 secs
Time difference of 0.4393167 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 0.01872873 secs
Time difference of 0.01652884 secs
Time difference of 0.0005085468 secs
Time difference of 0.0950067 secs
Time difference of 0.01123142 secs
Time difference of 0.05517292 secs
Time difference of 0.0188458 secs
Time difference of 0.009296894 secs
Time difference of 0.1257477 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 0.01068139 secs
Time difference of 0.03736591 secs
Time difference of 0.01209426 secs
Time difference of 0.01360226 secs
Time difference of 0.01000047 secs
Time difference of 0.04754686 secs
Time difference of 0.1253953 secs
Time difference of 0.009252787 secs
Time difference of 0.2801425 secs
[1] "chludwig_K150309_004b_SW_1_16" "chludwig_K150309_008_SW_1_4"  
[3] "chludwig_K150309_013_SW_0"    
Time difference of 0.0152421 secs
Time difference of 0.01241398 secs
Time difference of 0.001348734 secs
Time difference of 0.02187824 secs
Time difference of 0.01488423 secs
Time difference of 0.08205056 secs
Time difference of 0.009015083 secs
Time difference of 0.02320218 secs
Time difference of 0.3148727 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 0.1120169 secs
Time difference of 0.01709628 secs
Time difference of 0.002396584 secs
Time difference of 0.01241779 secs
Time difference of 0.05590844 secs
Time difference of 0.0193975 secs
Time difference of 0.01838899 secs
Time difference of 0.1141777 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 0.02812719 secs
[1] "run0 run1\nrun2 run2"
Time difference of 0.2809207 secs
Time difference of 0.1248114 secs
Time difference of 0.01277661 secs
Time difference of 0.09902 secs
Time difference of 1.617634 secs
Time difference of 0.0183363 secs
Time difference of 0.4352915 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 0.1130309 secs
Time difference of 0.9877079 secs
Time difference of 6.606811 secs
Time difference of 0.522754 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 0.1038847 secs
[1] "Written /home/biocbuild/R/R-4.4.0/site-library/DIAlignR/extdata/temp_prog1.RData"
[1] "Written /home/biocbuild/R/R-4.4.0/site-library/DIAlignR/extdata/temp_0_2.rds"
[1] "progTree1 is done."
Time difference of 1.987756 secs
Time difference of 0.4216416 secs
[1] "Written /home/biocbuild/R/R-4.4.0/site-library/DIAlignR/extdata/temp_1_2.rds"
Time difference of 0.7661185 secs
[1] "Written /home/biocbuild/R/R-4.4.0/site-library/DIAlignR/extdata/temp_2_2.rds"
Time difference of 0.4270937 secs
Time difference of 0.2243474 secs
[1] "Written /home/biocbuild/R/R-4.4.0/site-library/DIAlignR/extdata/temp_all_2.rds"
Time difference of 0.2563276 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 0.1161399 secs
[1] "Written /home/biocbuild/R/R-4.4.0/site-library/DIAlignR/extdata/temp_prog1.RData"
[1] "Written /home/biocbuild/R/R-4.4.0/site-library/DIAlignR/extdata/temp_0_2.rds"
[1] "progTree1 is done."
Time difference of 1.455398 secs
Time difference of 0.3764389 secs
[1] "Written /home/biocbuild/R/R-4.4.0/site-library/DIAlignR/extdata/temp_1_2.rds"
Time difference of 0.6780548 secs
[1] "Written /home/biocbuild/R/R-4.4.0/site-library/DIAlignR/extdata/temp_2_2.rds"
Time difference of 0.3969371 secs
Time difference of 0.01581836 secs
[1] "Written /home/biocbuild/R/R-4.4.0/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