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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_2.16.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/DIAlignR.Rcheck’
* using R Under development (unstable) (2025-02-19 r87757)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
    aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0
    GNU Fortran (GCC) 14.2.0
* running under: openEuler 24.03 (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 ‘2.16.0’
* 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 ... WARNING
Found the following significant warnings:
  /home/biocbuild/R/R-devel_2025-02-19/site-library/RcppEigen/include/Eigen/src/Core/arch/NEON/PacketMath.h:1671:9: warning: ‘void* memcpy(void*, const void*, size_t)’ copying an object of non-trivial type ‘Eigen::internal::Packet4c’ {aka ‘struct Eigen::internal::eigen_packet_wrapper<int, 2>’} from an array of ‘const int8_t’ {aka ‘const signed char’} [-Wclass-memaccess]
  /home/biocbuild/R/R-devel_2025-02-19/site-library/RcppEigen/include/Eigen/src/Core/arch/NEON/PacketMath.h:1716:9: warning: ‘void* memcpy(void*, const void*, size_t)’ copying an object of non-trivial type ‘Eigen::internal::Packet4c’ {aka ‘struct Eigen::internal::eigen_packet_wrapper<int, 2>’} from an array of ‘const int8_t’ {aka ‘const signed char’} [-Wclass-memaccess]
See ‘/home/biocbuild/bbs-3.21-bioc/meat/DIAlignR.Rcheck/00install.out’ for details.
* used C++ compiler: ‘aarch64-unknown-linux-gnu-g++ (GCC) 14.2.0’
* checking C++ specification ... NOTE
  Specified C++14: please drop specification unless essential
* checking installed package size ... INFO
  installed size is 27.9Mb
  sub-directories of 1Mb or more:
    extdata   4.0Mb
    libs     17.0Mb
    metabo    4.1Mb
    ptms      1.5Mb
* checking package directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking whether startup messages can be suppressed ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
alignTargetedRuns: no visible binding for global variable ‘peptide_id’
alignTargetedRuns : <anonymous>: no visible global function definition
  for ‘.’
alignTargetedRuns: no visible binding for global variable ‘intensity’
alignToRoot4: no visible binding for global variable ‘trees’
alignToRoot4: no visible binding for global variable ‘precursors’
alignToRoot4: no visible binding for global variable ‘intensity’
childXICs: possible error in cummax(v = cummax(ifelse(is.na(x), -Inf,
  x))): unused argument (v = cummax(ifelse(is.na(x), -Inf, x)))
distMat.rSqrd : <anonymous> : <anonymous>: no visible binding for
  global variable ‘RT.ref’
distMat.rSqrd : <anonymous> : <anonymous>: no visible binding for
  global variable ‘RT.eXp’
fetchPrecursorsInfo: no visible binding for global variable
  ‘transition_id’
fetchPrecursorsInfo: no visible global function definition for ‘.’
fetchPrecursorsInfo: no visible binding for global variable
  ‘transition_group_id’
fetchTransitionsFromRun: no visible binding for global variable
  ‘intensity’
fetchTransitionsFromRun: no visible global function definition for ‘.’
fetchTransitionsFromRun: no visible binding for global variable
  ‘transition_group_id’
fetchTransitionsFromRun: no visible binding for global variable
  ‘peak_group_rank’
fetchTransitionsFromRun: no visible global function definition for
  ‘head’
getNativeIDs: no visible binding for global variable ‘peptide_id’
getPeptideScores: no visible binding for global variable ‘col2’
getPeptideScores: no visible binding for global variable ‘run’
getQuery: no visible binding for global variable
  ‘identifying.transitionPEPfilter’
getRTdf: no visible binding for global variable ‘peak_group_rank’
getRTdf: no visible binding for global variable ‘m_score’
getRTdf: no visible global function definition for ‘.’
getRTdf: no visible binding for global variable ‘transition_group_id’
getRTdf: no visible binding for global variable ‘RT’
getRefRun : <anonymous>: no visible binding for global variable
  ‘pvalue’
ipfReassignFDR: no visible binding for global variable ‘ref_run’
ipfReassignFDR: no visible binding for global variable ‘run’
ipfReassignFDR: no visible global function definition for ‘.’
ipfReassignFDR: no visible binding for global variable ‘i.to’
ipfReassignFDR: no visible binding for global variable ‘m_score_new’
ipfReassignFDR: no visible binding for global variable ‘ms2_m_score’
ipfReassignFDR: no visible binding for global variable ‘m_score’
mstAlignRuns: no visible binding for global variable ‘ropenms’
mstAlignRuns: no visible binding for global variable ‘peptide_id’
mstAlignRuns : <anonymous>: no visible global function definition for
  ‘.’
mstAlignRuns: no visible binding for global variable ‘intensity’
mstScript1: no visible binding for global variable ‘ropenms’
mstScript2: no visible binding for global variable ‘fileInfo’
mstScript2: no visible binding for global variable ‘peptide_id’
mstScript2: no visible binding for global variable ‘features’
mstScript2 : <anonymous>: no visible global function definition for ‘.’
mstScript2 : <anonymous>: no visible binding for global variable
  ‘features’
mstScript2: no visible binding for global variable ‘intensity’
populateReferenceExperimentFeatureAlignmentMap: no visible binding for
  global variable ‘run’
populateReferenceExperimentFeatureAlignmentMap: no visible binding for
  global variable ‘transition_group_id’
populateReferenceExperimentFeatureAlignmentMap: no visible binding for
  global variable ‘feature_id’
progAlignRuns: no visible binding for global variable ‘peptide_id’
progAlignRuns : <anonymous>: no visible global function definition for
  ‘.’
progAlignRuns: no visible binding for global variable ‘intensity’
progComb3: no visible binding for global variable ‘precursors’
progComb3: no visible binding for global variable ‘ropenms’
progSplit2: no visible binding for global variable ‘trees’
progSplit2: no visible binding for global variable ‘scoreFile’
progSplit2: no visible binding for global variable ‘precursors’
progSplit2 : <anonymous>: no visible global function definition for ‘.’
progSplit2: no visible binding for global variable ‘ropenms’
progSplit4: no visible binding for global variable ‘precursors’
progSplit4 : <anonymous>: no visible global function definition for ‘.’
progSplit4: no visible binding for global variable ‘intensity’
progTree1: no visible binding for global variable ‘ropenms’
progTree1: no visible binding for global variable ‘peptide_id’
reIntensity: no visible binding for global variable ‘run’
reIntensity: no visible binding for global variable ‘alignment_rank’
recalculateIntensity: no visible binding for global variable
  ‘peptide_id’
recalculateIntensity: no visible binding for global variable
  ‘chromatogramIndex’
script2: no visible binding for global variable ‘fileInfo’
script2: no visible binding for global variable ‘peptide_id’
script2 : <anonymous>: no visible global function definition for ‘.’
script2: no visible binding for global variable ‘features’
script2: no visible binding for global variable ‘globalFits’
script2: no visible binding for global variable ‘RSE’
script2: no visible binding for global variable ‘intensity’
setRootRank : <anonymous>: no visible global function definition for
  ‘.’
writeOutFeatureAlignmentMap: no visible binding for global variable
  ‘reference_feature_id’
writeOutFeatureAlignmentMap: no visible binding for global variable
  ‘experiment_feature_id’
writeOutFeatureAlignmentMap: no visible binding for global variable
  ‘ALIGNMENT_GROUP_ID’
writeOutFeatureAlignmentMap: no visible binding for global variable
  ‘REFERENCE’
writeOutFeatureAlignmentMap: no visible global function definition for
  ‘.’
writeOutFeatureAlignmentMap: no visible binding for global variable
  ‘i.to’
writeTables: no visible binding for global variable ‘peptide_id’
writeTables: no visible binding for global variable ‘run’
writeTables: no visible binding for global variable ‘precursor’
Undefined global functions or variables:
  . ALIGNMENT_GROUP_ID REFERENCE RSE RT RT.eXp RT.ref alignment_rank
  chromatogramIndex col2 experiment_feature_id feature_id features
  fileInfo globalFits head i.to identifying.transitionPEPfilter
  intensity m_score m_score_new ms2_m_score peak_group_rank peptide_id
  precursor precursors pvalue ref_run reference_feature_id ropenms run
  scoreFile transition_group_id transition_id trees
Consider adding
  importFrom("datasets", "trees")
  importFrom("utils", "head")
to your NAMESPACE file.
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... NOTE
Documented arguments not in \usage in Rd file 'alignToRef.Rd':
  ‘feature_alignment_mapping’

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

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

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

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

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

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

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

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

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

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
File ‘/home/biocbuild/R/R-devel_2025-02-19/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 9.833  9.399   6.408
* 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:
   2.   ├─testthat::compare(act$val, exp$val, ..., tolerance = tolerance)
   3.   └─testthat:::compare.default(act$val, exp$val, ..., tolerance = tolerance)
   4.     ├─base::all.equal(x, y, ...)
   5.     └─data.table:::all.equal.data.table(x, y, ...)
   6.       ├─base::all.equal(x, y, tolerance = tolerance, ..., check.attributes = check.attributes)
   7.       └─bit64::all.equal.integer64(...)
   8.         ├─base::is.na(current)
   9.         └─bit64::is.na.integer64(current)
  ── 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 10 | WARN 3 | SKIP 8 | PASS 622 ]
  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, 1 WARNING, 4 NOTEs
See
  ‘/home/biocbuild/bbs-3.21-bioc/meat/DIAlignR.Rcheck/00check.log’
for details.

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD INSTALL DIAlignR
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/R/R-devel_2025-02-19/site-library’
* installing *source* package ‘DIAlignR’ ...
** this is package ‘DIAlignR’ version ‘2.16.0’
** using staged installation
** libs
using C++ compiler: ‘aarch64-unknown-linux-gnu-g++ (GCC) 14.2.0’
using C++14
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++14 -I"/home/biocbuild/R/R/include" -DNDEBUG  -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/Rcpp/include' -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/RcppEigen/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -Werror=format-security  -c ChromatogramPeak.cpp -o ChromatogramPeak.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++14 -I"/home/biocbuild/R/R/include" -DNDEBUG  -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/Rcpp/include' -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/RcppEigen/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -Werror=format-security  -c DPosition.cpp -o DPosition.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++14 -I"/home/biocbuild/R/R/include" -DNDEBUG  -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/Rcpp/include' -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/RcppEigen/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -Werror=format-security  -c MSChromatogram.cpp -o MSChromatogram.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++14 -I"/home/biocbuild/R/R/include" -DNDEBUG  -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/Rcpp/include' -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/RcppEigen/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -Werror=format-security  -c PeakIntegrator.cpp -o PeakIntegrator.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++14 -I"/home/biocbuild/R/R/include" -DNDEBUG  -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/Rcpp/include' -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/RcppEigen/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -Werror=format-security  -c RcppExports.cpp -o RcppExports.o
In file included from /home/biocbuild/R/R-devel_2025-02-19/site-library/RcppEigen/include/Eigen/Core:214,
                 from /home/biocbuild/R/R-devel_2025-02-19/site-library/RcppEigen/include/Eigen/Dense:1,
                 from /home/biocbuild/R/R-devel_2025-02-19/site-library/RcppEigen/include/RcppEigenForward.h:28,
                 from /home/biocbuild/R/R-devel_2025-02-19/site-library/RcppEigen/include/RcppEigen.h:25,
                 from RcppExports.cpp:4:
/home/biocbuild/R/R-devel_2025-02-19/site-library/RcppEigen/include/Eigen/src/Core/arch/NEON/PacketMath.h: In function ‘Packet Eigen::internal::pload(const typename unpacket_traits<T>::type*) [with Packet = eigen_packet_wrapper<int, 2>; typename unpacket_traits<T>::type = signed char]’:
/home/biocbuild/R/R-devel_2025-02-19/site-library/RcppEigen/include/Eigen/src/Core/arch/NEON/PacketMath.h:1671:9: warning: ‘void* memcpy(void*, const void*, size_t)’ copying an object of non-trivial type ‘Eigen::internal::Packet4c’ {aka ‘struct Eigen::internal::eigen_packet_wrapper<int, 2>’} from an array of ‘const int8_t’ {aka ‘const signed char’} [-Wclass-memaccess]
 1671 |   memcpy(&res, from, sizeof(Packet4c));
      |   ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /home/biocbuild/R/R-devel_2025-02-19/site-library/RcppEigen/include/Eigen/Core:172:
/home/biocbuild/R/R-devel_2025-02-19/site-library/RcppEigen/include/Eigen/src/Core/GenericPacketMath.h:159:8: note: ‘Eigen::internal::Packet4c’ {aka ‘struct Eigen::internal::eigen_packet_wrapper<int, 2>’} declared here
  159 | struct eigen_packet_wrapper
      |        ^~~~~~~~~~~~~~~~~~~~
/home/biocbuild/R/R-devel_2025-02-19/site-library/RcppEigen/include/Eigen/src/Core/arch/NEON/PacketMath.h: In function ‘Packet Eigen::internal::ploadu(const typename unpacket_traits<T>::type*) [with Packet = eigen_packet_wrapper<int, 2>; typename unpacket_traits<T>::type = signed char]’:
/home/biocbuild/R/R-devel_2025-02-19/site-library/RcppEigen/include/Eigen/src/Core/arch/NEON/PacketMath.h:1716:9: warning: ‘void* memcpy(void*, const void*, size_t)’ copying an object of non-trivial type ‘Eigen::internal::Packet4c’ {aka ‘struct Eigen::internal::eigen_packet_wrapper<int, 2>’} from an array of ‘const int8_t’ {aka ‘const signed char’} [-Wclass-memaccess]
 1716 |   memcpy(&res, from, sizeof(Packet4c));
      |   ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/home/biocbuild/R/R-devel_2025-02-19/site-library/RcppEigen/include/Eigen/src/Core/GenericPacketMath.h:159:8: note: ‘Eigen::internal::Packet4c’ {aka ‘struct Eigen::internal::eigen_packet_wrapper<int, 2>’} declared here
  159 | struct eigen_packet_wrapper
      |        ^~~~~~~~~~~~~~~~~~~~
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++14 -I"/home/biocbuild/R/R/include" -DNDEBUG  -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/Rcpp/include' -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/RcppEigen/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -Werror=format-security  -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:
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(bd_type, double, bd_type, double, bool)’ defined but not used [-Wunused-function]
  261 |   void spline::set_boundary(spline::bd_type left, double left_value,
      |        ^~~~~~
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++14 -I"/home/biocbuild/R/R/include" -DNDEBUG  -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/Rcpp/include' -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/RcppEigen/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -Werror=format-security  -c SavitzkyGolayFilter.cpp -o SavitzkyGolayFilter.o
In file included from /home/biocbuild/R/R-devel_2025-02-19/site-library/RcppEigen/include/Eigen/Core:214,
                 from /home/biocbuild/R/R-devel_2025-02-19/site-library/RcppEigen/include/Eigen/Dense:1,
                 from /home/biocbuild/R/R-devel_2025-02-19/site-library/RcppEigen/include/RcppEigenForward.h:28,
                 from /home/biocbuild/R/R-devel_2025-02-19/site-library/RcppEigen/include/RcppEigen.h:25,
                 from SavitzkyGolayFilter.cpp:1:
/home/biocbuild/R/R-devel_2025-02-19/site-library/RcppEigen/include/Eigen/src/Core/arch/NEON/PacketMath.h: In function ‘Packet Eigen::internal::pload(const typename unpacket_traits<T>::type*) [with Packet = eigen_packet_wrapper<int, 2>; typename unpacket_traits<T>::type = signed char]’:
/home/biocbuild/R/R-devel_2025-02-19/site-library/RcppEigen/include/Eigen/src/Core/arch/NEON/PacketMath.h:1671:9: warning: ‘void* memcpy(void*, const void*, size_t)’ copying an object of non-trivial type ‘Eigen::internal::Packet4c’ {aka ‘struct Eigen::internal::eigen_packet_wrapper<int, 2>’} from an array of ‘const int8_t’ {aka ‘const signed char’} [-Wclass-memaccess]
 1671 |   memcpy(&res, from, sizeof(Packet4c));
      |   ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /home/biocbuild/R/R-devel_2025-02-19/site-library/RcppEigen/include/Eigen/Core:172:
/home/biocbuild/R/R-devel_2025-02-19/site-library/RcppEigen/include/Eigen/src/Core/GenericPacketMath.h:159:8: note: ‘Eigen::internal::Packet4c’ {aka ‘struct Eigen::internal::eigen_packet_wrapper<int, 2>’} declared here
  159 | struct eigen_packet_wrapper
      |        ^~~~~~~~~~~~~~~~~~~~
/home/biocbuild/R/R-devel_2025-02-19/site-library/RcppEigen/include/Eigen/src/Core/arch/NEON/PacketMath.h: In function ‘Packet Eigen::internal::ploadu(const typename unpacket_traits<T>::type*) [with Packet = eigen_packet_wrapper<int, 2>; typename unpacket_traits<T>::type = signed char]’:
/home/biocbuild/R/R-devel_2025-02-19/site-library/RcppEigen/include/Eigen/src/Core/arch/NEON/PacketMath.h:1716:9: warning: ‘void* memcpy(void*, const void*, size_t)’ copying an object of non-trivial type ‘Eigen::internal::Packet4c’ {aka ‘struct Eigen::internal::eigen_packet_wrapper<int, 2>’} from an array of ‘const int8_t’ {aka ‘const signed char’} [-Wclass-memaccess]
 1716 |   memcpy(&res, from, sizeof(Packet4c));
      |   ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/home/biocbuild/R/R-devel_2025-02-19/site-library/RcppEigen/include/Eigen/src/Core/GenericPacketMath.h:159:8: note: ‘Eigen::internal::Packet4c’ {aka ‘struct Eigen::internal::eigen_packet_wrapper<int, 2>’} declared here
  159 | struct eigen_packet_wrapper
      |        ^~~~~~~~~~~~~~~~~~~~
In file included from /home/biocbuild/R/R-devel_2025-02-19/site-library/RcppEigen/include/Eigen/Core:341:
/home/biocbuild/R/R-devel_2025-02-19/site-library/RcppEigen/include/Eigen/src/Core/products/TriangularMatrixVector.h: In function ‘static void Eigen::internal::trmv_selector<Mode, 1>::run(const Lhs&, const Rhs&, Dest&, const typename Dest::Scalar&) [with Lhs = Eigen::Transpose<const Eigen::Block<const Eigen::Block<Eigen::Matrix<double, -1, -1>, -1, -1, false>, -1, -1, false> >; Rhs = Eigen::Transpose<const Eigen::CwiseBinaryOp<Eigen::internal::scalar_product_op<double, double>, const Eigen::CwiseNullaryOp<Eigen::internal::scalar_constant_op<double>, const Eigen::Matrix<double, 1, -1> >, const Eigen::Transpose<const Eigen::Block<const Eigen::Block<const Eigen::Block<Eigen::Matrix<double, -1, -1>, -1, -1, false>, -1, 1, true>, -1, 1, false> > > >; Dest = Eigen::Transpose<Eigen::Block<Eigen::Block<Eigen::Matrix<double, -1, -1, 1, -1, -1>, 1, -1, true>, 1, -1, false> >; int Mode = 6]’:
/home/biocbuild/R/R-devel_2025-02-19/site-library/RcppEigen/include/Eigen/src/Core/products/TriangularMatrixVector.h:332:12: warning: ‘result’ may be used uninitialized [-Wmaybe-uninitialized]
  327 |     internal::triangular_matrix_vector_product
      |     ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  328 |       <Index,Mode,
      |       ~~~~~~~~~~~~
  329 |        LhsScalar, LhsBlasTraits::NeedToConjugate,
      |        ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  330 |        RhsScalar, RhsBlasTraits::NeedToConjugate,
      |        ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  331 |        RowMajor>
      |        ~~~~~~~~~
  332 |       ::run(actualLhs.rows(),actualLhs.cols(),
      |       ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  333 |             actualLhs.data(),actualLhs.outerStride(),
      |             ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  334 |             actualRhsPtr,1,
      |             ~~~~~~~~~~~~~~~
  335 |             dest.data(),dest.innerStride(),
      |             ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  336 |             actualAlpha);
      |             ~~~~~~~~~~~~
/home/biocbuild/R/R-devel_2025-02-19/site-library/RcppEigen/include/Eigen/src/Core/products/TriangularMatrixVector.h:105:24: note: by argument 5 of type ‘const double*’ to ‘static void Eigen::internal::triangular_matrix_vector_product<Index, Mode, LhsScalar, ConjLhs, RhsScalar, ConjRhs, 1, Version>::run(Index, Index, const LhsScalar*, Index, const RhsScalar*, Index, ResScalar*, Index, const ResScalar&) [with Index = long int; int Mode = 6; LhsScalar = double; bool ConjLhs = false; RhsScalar = double; bool ConjRhs = false; int Version = 0]’ declared here
  105 | EIGEN_DONT_INLINE void triangular_matrix_vector_product<Index,Mode,LhsScalar,ConjLhs,RhsScalar,ConjRhs,RowMajor,Version>
      |                        ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++14 -I"/home/biocbuild/R/R/include" -DNDEBUG  -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/Rcpp/include' -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/RcppEigen/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -Werror=format-security  -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:484:16: warning: ‘MaxRowIndex’ may be used uninitialized [-Wmaybe-uninitialized]
  484 |   OlapStartRow = MaxRowIndex;
      |   ~~~~~~~~~~~~~^~~~~~~~~~~~~
affinealignment.cpp:436:7: note: ‘MaxRowIndex’ was declared here
  436 |   int MaxRowIndex, MaxColIndex;
      |       ^~~~~~~~~~~
affinealignment.cpp:485:16: warning: ‘MaxColIndex’ may be used uninitialized [-Wmaybe-uninitialized]
  485 |   OlapStartCol = MaxColIndex;
      |   ~~~~~~~~~~~~~^~~~~~~~~~~~~
affinealignment.cpp:436:20: note: ‘MaxColIndex’ was declared here
  436 |   int MaxRowIndex, MaxColIndex;
      |                    ^~~~~~~~~~~
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++14 -I"/home/biocbuild/R/R/include" -DNDEBUG  -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/Rcpp/include' -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/RcppEigen/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -Werror=format-security  -c affinealignobj.cpp -o affinealignobj.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++14 -I"/home/biocbuild/R/R/include" -DNDEBUG  -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/Rcpp/include' -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/RcppEigen/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -Werror=format-security  -c alignment.cpp -o alignment.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++14 -I"/home/biocbuild/R/R/include" -DNDEBUG  -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/Rcpp/include' -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/RcppEigen/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -Werror=format-security  -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++){
      |                    ~~^~~~~~~~~~~~~
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++14 -I"/home/biocbuild/R/R/include" -DNDEBUG  -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/Rcpp/include' -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/RcppEigen/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -Werror=format-security  -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;
      |          ^~~~~~
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++14 -I"/home/biocbuild/R/R/include" -DNDEBUG  -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/Rcpp/include' -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/RcppEigen/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -Werror=format-security  -c gapPenalty.cpp -o gapPenalty.o
gapPenalty.cpp: In function ‘double DIAlign::getGapPenalty(const SimMatrix&, double, std::string)’:
gapPenalty.cpp:6:10: warning: ‘gapPenalty’ may be used uninitialized [-Wmaybe-uninitialized]
    6 |   double gapPenalty;
      |          ^~~~~~~~~~
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++14 -I"/home/biocbuild/R/R/include" -DNDEBUG  -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/Rcpp/include' -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/RcppEigen/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -Werror=format-security  -c integrateArea.cpp -o integrateArea.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++14 -I"/home/biocbuild/R/R/include" -DNDEBUG  -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/Rcpp/include' -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/RcppEigen/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -Werror=format-security  -c interface.cpp -o interface.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++14 -I"/home/biocbuild/R/R/include" -DNDEBUG  -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/Rcpp/include' -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/RcppEigen/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -Werror=format-security  -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(bd_type, double, bd_type, double, bool)’ defined but not used [-Wunused-function]
  261 |   void spline::set_boundary(spline::bd_type left, double left_value,
      |        ^~~~~~
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++14 -I"/home/biocbuild/R/R/include" -DNDEBUG  -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/Rcpp/include' -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/RcppEigen/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -Werror=format-security  -c run_alignment.cpp -o run_alignment.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++14 -I"/home/biocbuild/R/R/include" -DNDEBUG  -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/Rcpp/include' -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/RcppEigen/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -Werror=format-security  -c simpleFcn.cpp -o simpleFcn.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++14 -I"/home/biocbuild/R/R/include" -DNDEBUG  -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/Rcpp/include' -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/RcppEigen/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -Werror=format-security  -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(bd_type, double, bd_type, double, bool)’ defined but not used [-Wunused-function]
  261 |   void spline::set_boundary(spline::bd_type left, double left_value,
      |        ^~~~~~
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++14 -I"/home/biocbuild/R/R/include" -DNDEBUG  -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/Rcpp/include' -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/RcppEigen/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -Werror=format-security  -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);
      |         ^~~
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++14 -shared -L/home/biocbuild/R/R/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/lib -lR
installing to /home/biocbuild/R/R-devel_2025-02-19/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
Warning in fun(libname, pkgname) :
  Package 'DIAlignR' is deprecated and will be removed from Bioconductor
  version 3.22
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
Warning in fun(libname, pkgname) :
  Package 'DIAlignR' is deprecated and will be removed from Bioconductor
  version 3.22
** testing if installed package keeps a record of temporary installation path
* DONE (DIAlignR)

R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: aarch64-unknown-linux-gnu

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> library(testthat)
> library(DIAlignR)
Warning message:
In fun(libname, pkgname) :
  Package 'DIAlignR' is deprecated and will be removed from Bioconductor
  version 3.22
> 
> test_check("DIAlignR")
[1] "hroest_K120808_Strep10%PlasmaBiolRepl1_R03_SW_filt"
[2] "hroest_K120809_Strep0%PlasmaBiolRepl2_R04_SW_filt" 
[3] "hroest_K120809_Strep10%PlasmaBiolRepl2_R04_SW_filt"
Time difference of 0.08029628 secs
Time difference of 0.2359161 secs
Time difference of 0.2193158 secs
Time difference of 0.02765489 secs
Time difference of 0.009436369 secs
Time difference of 0.1128039 secs
Time difference of 1.950838 secs
Time difference of 0.02820086 secs
Time difference of 0.4779787 secs
[1] "hroest_K120808_Strep10%PlasmaBiolRepl1_R03_SW_filt"
[2] "hroest_K120809_Strep0%PlasmaBiolRepl2_R04_SW_filt" 
Time difference of 0.0173707 secs
Time difference of 0.2312324 secs
Time difference of 0.1462471 secs
Time difference of 0.01809335 secs
Time difference of 0.006570578 secs
Time difference of 0.0681951 secs
Time difference of 0.9547496 secs
Time difference of 0.009933233 secs
Time difference of 1.027155 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 0.0180285 secs
Time difference of 0.2484281 secs
Time difference of 0.1515994 secs
Time difference of 0.09784746 secs
Time difference of 0.009609222 secs
Time difference of 0.09309053 secs
Time difference of 1.351277 secs
Time difference of 0.02548909 secs
Time difference of 0.4028208 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 0.0187161 secs
Time difference of 0.01670313 secs
Time difference of 0.0004093647 secs
Time difference of 0.09766936 secs
Time difference of 0.009796619 secs
Time difference of 0.05678797 secs
Time difference of 0.01696539 secs
Time difference of 0.009955168 secs
Time difference of 0.1243095 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 0.01031542 secs
Time difference of 0.03645587 secs
Time difference of 0.01464748 secs
Time difference of 0.01270723 secs
Time difference of 0.01130342 secs
Time difference of 0.06244755 secs
Time difference of 0.08965707 secs
Time difference of 0.009232044 secs
Time difference of 0.2499671 secs
[1] "chludwig_K150309_004b_SW_1_16" "chludwig_K150309_008_SW_1_4"  
[3] "chludwig_K150309_013_SW_0"    
Time difference of 0.01542091 secs
Time difference of 0.01514149 secs
Time difference of 0.00143218 secs
Time difference of 0.02021432 secs
Time difference of 0.01240468 secs
Time difference of 0.06577206 secs
Time difference of 0.006301641 secs
Time difference of 0.02270055 secs
Time difference of 0.3211262 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.>
<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 0.0987463 secs
Time difference of 0.01705718 secs
Time difference of 0.002685308 secs
Time difference of 0.009685993 secs
Time difference of 0.05601597 secs
Time difference of 0.01763606 secs
Time difference of 0.01957631 secs
Time difference of 0.1124067 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 0.02679396 secs
[1] "run0 run1\nrun2 run2"
Time difference of 0.2584655 secs
Time difference of 0.205997 secs
Time difference of 0.0112772 secs
Time difference of 0.08511972 secs
Time difference of 1.695217 secs
Time difference of 0.01872373 secs
Time difference of 0.398921 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 0.1184371 secs
Time difference of 0.8994873 secs
Time difference of 5.411219 secs
Time difference of 0.5170641 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 0.1008971 secs
[1] "Written /home/biocbuild/R/R-devel_2025-02-19/site-library/DIAlignR/extdata/temp_prog1.RData"
[1] "Written /home/biocbuild/R/R-devel_2025-02-19/site-library/DIAlignR/extdata/temp_0_2.rds"
[1] "progTree1 is done."
Time difference of 1.448759 secs
Time difference of 0.4258683 secs
[1] "Written /home/biocbuild/R/R-devel_2025-02-19/site-library/DIAlignR/extdata/temp_1_2.rds"
Time difference of 0.7056844 secs
[1] "Written /home/biocbuild/R/R-devel_2025-02-19/site-library/DIAlignR/extdata/temp_2_2.rds"
Time difference of 0.3936777 secs
Time difference of 0.2480621 secs
[1] "Written /home/biocbuild/R/R-devel_2025-02-19/site-library/DIAlignR/extdata/temp_all_2.rds"
Time difference of 0.2159073 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 0.1015558 secs
[1] "Written /home/biocbuild/R/R-devel_2025-02-19/site-library/DIAlignR/extdata/temp_prog1.RData"
[1] "Written /home/biocbuild/R/R-devel_2025-02-19/site-library/DIAlignR/extdata/temp_0_2.rds"
[1] "progTree1 is done."
Time difference of 1.314077 secs
Time difference of 0.3692243 secs
[1] "Written /home/biocbuild/R/R-devel_2025-02-19/site-library/DIAlignR/extdata/temp_1_2.rds"
Time difference of 0.6313436 secs
[1] "Written /home/biocbuild/R/R-devel_2025-02-19/site-library/DIAlignR/extdata/temp_2_2.rds"
Time difference of 0.4024091 secs
Time difference of 0.01731014 secs
[1] "Written /home/biocbuild/R/R-devel_2025-02-19/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 10 | WARN 3 | SKIP 8 | PASS 622 ]

══ 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_align_dia_runs.R:122:3'): test_getAlignObjs ──────────────────
outData[[2]][["4618"]][["run1_run2"]][["ref"]] not equal to lapply(...).
Component 1: Attributes: < Component 2: Component 2: 2 string mismatches >
Component 2: Attributes: < Component 2: Component 2: 2 string mismatches >
Component 3: Attributes: < Component 2: Component 2: 2 string mismatches >
Component 4: Attributes: < Component 2: Component 2: 2 string mismatches >
Component 5: Attributes: < Component 2: Component 2: 2 string mismatches >
Component 6: Attributes: < Component 2: Component 2: 2 string mismatches >
── Failure ('test_align_dia_runs.R:124:3'): test_getAlignObjs ──────────────────
outData[[2]][["4618"]][["run1_run2"]][["eXp"]] not equal to lapply(...).
Component 1: Attributes: < Component 2: Component 2: 2 string mismatches >
Component 2: Attributes: < Component 2: Component 2: 2 string mismatches >
Component 3: Attributes: < Component 2: Component 2: 2 string mismatches >
Component 4: Attributes: < Component 2: Component 2: 2 string mismatches >
Component 5: Attributes: < Component 2: Component 2: 2 string mismatches >
Component 6: Attributes: < Component 2: Component 2: 2 string mismatches >
── Failure ('test_get_global_fit.R:21:3'): test_dialignrLoess ──────────────────
outData$pars$span not equal to 0.8.
1/1 mismatches
[1] 0.4 - 0.8 == -0.4
── Failure ('test_get_global_fit.R:22:3'): test_dialignrLoess ──────────────────
predict(outData, newdata = data.frame(RT.ref = 13.5))[[1]] not equal to 5.5.
1/1 mismatches
[1] 2.75 - 5.5 == -2.75
── Failure ('test_get_peaks_chromatograms.R:48:3'): test_getXICs4AlignObj ──────
outData[["hroest_K120808_Strep10%PlasmaBiolRepl1_R03_SW_filt"]][["4618"]] not equal to lapply(XICs[[runs[["run0"]]]][["4618"]], as.matrix).
Component 1: Attributes: < Component 2: Component 2: 2 string mismatches >
Component 2: Attributes: < Component 2: Component 2: 2 string mismatches >
Component 3: Attributes: < Component 2: Component 2: 2 string mismatches >
Component 4: Attributes: < Component 2: Component 2: 2 string mismatches >
Component 5: Attributes: < Component 2: Component 2: 2 string mismatches >
Component 6: Attributes: < Component 2: Component 2: 2 string mismatches >
── Failure ('test_get_peaks_chromatograms.R:49:3'): test_getXICs4AlignObj ──────
outData[["hroest_K120809_Strep0%PlasmaBiolRepl2_R04_SW_filt"]][["4618"]] not equal to lapply(XICs[[runs[["run1"]]]][["4618"]], as.matrix).
Component 1: Attributes: < Component 2: Component 2: 2 string mismatches >
Component 2: Attributes: < Component 2: Component 2: 2 string mismatches >
Component 3: Attributes: < Component 2: Component 2: 2 string mismatches >
Component 4: Attributes: < Component 2: Component 2: 2 string mismatches >
Component 5: Attributes: < Component 2: Component 2: 2 string mismatches >
Component 6: Attributes: < Component 2: Component 2: 2 string mismatches >
── Failure ('test_get_peaks_chromatograms.R:68:3'): test_getXICs ───────────────
outData[["hroest_K120808_Strep10%PlasmaBiolRepl1_R03_SW_filt"]][["4618"]] not equal to lapply(...).
Component 1: Attributes: < Component 2: Component 2: 2 string mismatches >
Component 2: Attributes: < Component 2: Component 2: 2 string mismatches >
Component 3: Attributes: < Component 2: Component 2: 2 string mismatches >
Component 4: Attributes: < Component 2: Component 2: 2 string mismatches >
Component 5: Attributes: < Component 2: Component 2: 2 string mismatches >
Component 6: Attributes: < Component 2: Component 2: 2 string mismatches >
── Failure ('test_get_peaks_chromatograms.R:70:3'): test_getXICs ───────────────
outData[["hroest_K120809_Strep10%PlasmaBiolRepl2_R04_SW_filt"]][["4618"]] not equal to lapply(...).
Component 1: Attributes: < Component 2: Component 2: 2 string mismatches >
Component 2: Attributes: < Component 2: Component 2: 2 string mismatches >
Component 3: Attributes: < Component 2: Component 2: 2 string mismatches >
Component 4: Attributes: < Component 2: Component 2: 2 string mismatches >
Component 5: Attributes: < Component 2: Component 2: 2 string mismatches >
Component 6: Attributes: < Component 2: Component 2: 2 string mismatches >
── Error ('test_utils.R:76:13'): test_getRefExpFeatureMap ──────────────────────
Error in `is.na.integer64(current)`: REAL() can only be applied to a 'numeric', not a 'integer'
Backtrace:
    ▆
 1. └─testthat::expect_equal(outData[[1]], expData, tolerance = 1e-04) at test_utils.R:76:13
 2.   ├─testthat::compare(act$val, exp$val, ..., tolerance = tolerance)
 3.   └─testthat:::compare.default(act$val, exp$val, ..., tolerance = tolerance)
 4.     ├─base::all.equal(x, y, ...)
 5.     └─data.table:::all.equal.data.table(x, y, ...)
 6.       ├─base::all.equal(x, y, tolerance = tolerance, ..., check.attributes = check.attributes)
 7.       └─bit64::all.equal.integer64(...)
 8.         ├─base::is.na(current)
 9.         └─bit64::is.na.integer64(current)
── 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 10 | WARN 3 | SKIP 8 | PASS 622 ]
Error: Test failures
Execution halted