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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_2.14.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/DIAlignR.Rcheck’
* using R version 4.4.1 (2024-06-14)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
    gcc (GCC) 12.2.1 20220819 (openEuler 12.2.1-14)
    GNU Fortran (GCC) 10.3.1
* running under: openEuler 22.03 (LTS-SP1)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘DIAlignR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘DIAlignR’ version ‘2.14.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘DIAlignR’ can be installed ... WARNING
Found the following significant warnings:
  /home/biocbuild/R/R-4.4.1/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-4.4.1/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-3.20-bioc/meat/DIAlignR.Rcheck/00install.out’ for details.
* used C++ compiler: ‘g++ (conda-forge gcc 14.2.0-1) 14.2.0’
* checking C++ specification ... NOTE
  Specified C++14: please drop specification unless essential
* checking installed package size ... NOTE
  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 dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
alignTargetedRuns: no visible binding for global variable ‘peptide_id’
alignTargetedRuns : <anonymous>: no visible global function definition
  for ‘.’
alignTargetedRuns: no visible binding for global variable ‘intensity’
alignToRoot4: no visible binding for global variable ‘trees’
alignToRoot4: no visible binding for global variable ‘precursors’
alignToRoot4: no visible binding for global variable ‘intensity’
childXICs: possible error in cummax(v = cummax(ifelse(is.na(x), -Inf,
  x))): unused argument (v = cummax(ifelse(is.na(x), -Inf, x)))
distMat.rSqrd : <anonymous> : <anonymous>: no visible binding for
  global variable ‘RT.ref’
distMat.rSqrd : <anonymous> : <anonymous>: no visible binding for
  global variable ‘RT.eXp’
fetchPrecursorsInfo: no visible binding for global variable
  ‘transition_id’
fetchPrecursorsInfo: no visible global function definition for ‘.’
fetchPrecursorsInfo: no visible binding for global variable
  ‘transition_group_id’
fetchTransitionsFromRun: no visible binding for global variable
  ‘intensity’
fetchTransitionsFromRun: no visible global function definition for ‘.’
fetchTransitionsFromRun: no visible binding for global variable
  ‘transition_group_id’
fetchTransitionsFromRun: no visible binding for global variable
  ‘peak_group_rank’
fetchTransitionsFromRun: no visible global function definition for
  ‘head’
getNativeIDs: no visible binding for global variable ‘peptide_id’
getPeptideScores: no visible binding for global variable ‘col2’
getPeptideScores: no visible binding for global variable ‘run’
getQuery: no visible binding for global variable
  ‘identifying.transitionPEPfilter’
getRTdf: no visible binding for global variable ‘peak_group_rank’
getRTdf: no visible binding for global variable ‘m_score’
getRTdf: no visible global function definition for ‘.’
getRTdf: no visible binding for global variable ‘transition_group_id’
getRTdf: no visible binding for global variable ‘RT’
getRefRun : <anonymous>: no visible binding for global variable
  ‘pvalue’
ipfReassignFDR: no visible binding for global variable ‘ref_run’
ipfReassignFDR: no visible binding for global variable ‘run’
ipfReassignFDR: no visible global function definition for ‘.’
ipfReassignFDR: no visible binding for global variable ‘i.to’
ipfReassignFDR: no visible binding for global variable ‘m_score_new’
ipfReassignFDR: no visible binding for global variable ‘ms2_m_score’
ipfReassignFDR: no visible binding for global variable ‘m_score’
mstAlignRuns: no visible binding for global variable ‘ropenms’
mstAlignRuns: no visible binding for global variable ‘peptide_id’
mstAlignRuns : <anonymous>: no visible global function definition for
  ‘.’
mstAlignRuns: no visible binding for global variable ‘intensity’
mstScript1: no visible binding for global variable ‘ropenms’
mstScript2: no visible binding for global variable ‘fileInfo’
mstScript2: no visible binding for global variable ‘peptide_id’
mstScript2: no visible binding for global variable ‘features’
mstScript2 : <anonymous>: no visible global function definition for ‘.’
mstScript2 : <anonymous>: no visible binding for global variable
  ‘features’
mstScript2: no visible binding for global variable ‘intensity’
populateReferenceExperimentFeatureAlignmentMap: no visible binding for
  global variable ‘run’
populateReferenceExperimentFeatureAlignmentMap: no visible binding for
  global variable ‘transition_group_id’
populateReferenceExperimentFeatureAlignmentMap: no visible binding for
  global variable ‘feature_id’
progAlignRuns: no visible binding for global variable ‘peptide_id’
progAlignRuns : <anonymous>: no visible global function definition for
  ‘.’
progAlignRuns: no visible binding for global variable ‘intensity’
progComb3: no visible binding for global variable ‘precursors’
progComb3: no visible binding for global variable ‘ropenms’
progSplit2: no visible binding for global variable ‘trees’
progSplit2: no visible binding for global variable ‘scoreFile’
progSplit2: no visible binding for global variable ‘precursors’
progSplit2 : <anonymous>: no visible global function definition for ‘.’
progSplit2: no visible binding for global variable ‘ropenms’
progSplit4: no visible binding for global variable ‘precursors’
progSplit4 : <anonymous>: no visible global function definition for ‘.’
progSplit4: no visible binding for global variable ‘intensity’
progTree1: no visible binding for global variable ‘ropenms’
progTree1: no visible binding for global variable ‘peptide_id’
reIntensity: no visible binding for global variable ‘run’
reIntensity: no visible binding for global variable ‘alignment_rank’
recalculateIntensity: no visible binding for global variable
  ‘peptide_id’
recalculateIntensity: no visible binding for global variable
  ‘chromatogramIndex’
script2: no visible binding for global variable ‘fileInfo’
script2: no visible binding for global variable ‘peptide_id’
script2 : <anonymous>: no visible global function definition for ‘.’
script2: no visible binding for global variable ‘features’
script2: no visible binding for global variable ‘globalFits’
script2: no visible binding for global variable ‘RSE’
script2: no visible binding for global variable ‘intensity’
setRootRank : <anonymous>: no visible global function definition for
  ‘.’
writeOutFeatureAlignmentMap: no visible binding for global variable
  ‘reference_feature_id’
writeOutFeatureAlignmentMap: no visible binding for global variable
  ‘experiment_feature_id’
writeOutFeatureAlignmentMap: no visible binding for global variable
  ‘ALIGNMENT_GROUP_ID’
writeOutFeatureAlignmentMap: no visible binding for global variable
  ‘REFERENCE’
writeOutFeatureAlignmentMap: no visible global function definition for
  ‘.’
writeOutFeatureAlignmentMap: no visible binding for global variable
  ‘i.to’
writeTables: no visible binding for global variable ‘peptide_id’
writeTables: no visible binding for global variable ‘run’
writeTables: no visible binding for global variable ‘precursor’
Undefined global functions or variables:
  . ALIGNMENT_GROUP_ID REFERENCE RSE RT RT.eXp RT.ref alignment_rank
  chromatogramIndex col2 experiment_feature_id feature_id features
  fileInfo globalFits head i.to identifying.transitionPEPfilter
  intensity m_score m_score_new ms2_m_score peak_group_rank peptide_id
  precursor precursors pvalue ref_run reference_feature_id ropenms run
  scoreFile transition_group_id transition_id trees
Consider adding
  importFrom("datasets", "trees")
  importFrom("utils", "head")
to your NAMESPACE file.
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... NOTE
Documented arguments not in \usage in Rd file 'alignToRef.Rd':
  ‘feature_alignment_mapping’

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

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

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

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

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

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

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

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

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

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
File ‘/home/biocbuild/R/R-4.4.1/site-library/DIAlignR/libs/DIAlignR.so’:
  Found ‘_ZSt4cout’, possibly from ‘std::cout’ (C++)

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs nor [v]sprintf. The detected symbols are linked into
the code but might come from libraries and not actually be called.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                    user system elapsed
alignTargetedRuns 10.046 10.704   6.798
* 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 3 | WARN 0 | SKIP 8 | PASS 629 ]
  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, 5 NOTEs
See
  ‘/home/biocbuild/bbs-3.20-bioc/meat/DIAlignR.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD INSTALL DIAlignR
###
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* installing to library ‘/home/biocbuild/R/R-4.4.1/site-library’
* installing *source* package ‘DIAlignR’ ...
** using staged installation
** libs
using C++ compiler: ‘g++ (conda-forge gcc 14.2.0-1) 14.2.0’
using C++14
g++ -std=gnu++14 -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.4.1/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.4.1/site-library/RcppEigen/include' -I/usr/local/include    -fPIC  -g -O2  -Wall  -c ChromatogramPeak.cpp -o ChromatogramPeak.o
g++ -std=gnu++14 -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.4.1/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.4.1/site-library/RcppEigen/include' -I/usr/local/include    -fPIC  -g -O2  -Wall  -c DPosition.cpp -o DPosition.o
g++ -std=gnu++14 -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.4.1/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.4.1/site-library/RcppEigen/include' -I/usr/local/include    -fPIC  -g -O2  -Wall  -c MSChromatogram.cpp -o MSChromatogram.o
g++ -std=gnu++14 -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.4.1/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.4.1/site-library/RcppEigen/include' -I/usr/local/include    -fPIC  -g -O2  -Wall  -c PeakIntegrator.cpp -o PeakIntegrator.o
g++ -std=gnu++14 -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.4.1/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.4.1/site-library/RcppEigen/include' -I/usr/local/include    -fPIC  -g -O2  -Wall  -c RcppExports.cpp -o RcppExports.o
In file included from /home/biocbuild/R/R-4.4.1/site-library/RcppEigen/include/Eigen/Core:214,
                 from /home/biocbuild/R/R-4.4.1/site-library/RcppEigen/include/Eigen/Dense:1,
                 from /home/biocbuild/R/R-4.4.1/site-library/RcppEigen/include/RcppEigenForward.h:28,
                 from /home/biocbuild/R/R-4.4.1/site-library/RcppEigen/include/RcppEigen.h:25,
                 from RcppExports.cpp:4:
/home/biocbuild/R/R-4.4.1/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-4.4.1/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-4.4.1/site-library/RcppEigen/include/Eigen/Core:172:
/home/biocbuild/R/R-4.4.1/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-4.4.1/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-4.4.1/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-4.4.1/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
      |        ^~~~~~~~~~~~~~~~~~~~
g++ -std=gnu++14 -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.4.1/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.4.1/site-library/RcppEigen/include' -I/usr/local/include    -fPIC  -g -O2  -Wall  -c Rmain.cpp -o Rmain.o
Rmain.cpp: In function 'Rcpp::NumericVector areaIntegrator(Rcpp::List, Rcpp::List, double, double, std::string, std::string, bool, bool, int, int)':
Rmain.cpp:273:21: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<std::vector<double> >::size_type' {aka 'long unsigned int'} [-Wsign-compare]
  273 |     for(int i = 0; i<vov2.size(); i++) sgolay.smoothChroms(vov2[i]);
      |                    ~^~~~~~~~~~~~
Rmain.cpp: In function 'Rcpp::NumericMatrix sgolayCpp(Rcpp::NumericMatrix, int, int)':
Rmain.cpp:305:19: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<double>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
  305 |   for(int i = 0; i<d.size(); i++){
      |                  ~^~~~~~~~~
Rmain.cpp: In function 'Rcpp::NumericMatrix getAlignedTimesCpp(Rcpp::List, Rcpp::List, int, int, std::string, double, std::string, std::string, const std::vector<double>&, double, double, double, bool, double, double, int, bool, double)':
Rmain.cpp:368:21: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<std::vector<double> >::size_type' {aka 'long unsigned int'} [-Wsign-compare]
  368 |     for(int i = 0; i<intensity1.size(); i++){
      |                    ~^~~~~~~~~~~~~~~~~~
Rmain.cpp: In function 'Rcpp::List getChildXICpp(Rcpp::List, Rcpp::List, int, int, std::string, double, std::string, std::string, const std::vector<double>&, double, double, double, bool, double, double, int, bool, double, double, std::string, std::string, bool)':
Rmain.cpp:771:21: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<std::vector<double> >::size_type' {aka 'long unsigned int'} [-Wsign-compare]
  771 |     for(int i = 0; i<intensity1.size(); i++){
      |                    ~^~~~~~~~~~~~~~~~~~
Rmain.cpp:818:20: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<int>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
  818 |   for(int i = 0; i < keep.size(); i++){
      |                  ~~^~~~~~~~~~~~~
Rmain.cpp:824:20: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<std::vector<double> >::size_type' {aka 'long unsigned int'} [-Wsign-compare]
  824 |   for(int j = 0; j <intensity1NN.size(); j++){
      |                  ~~^~~~~~~~~~~~~~~~~~~~
Rmain.cpp:827:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<int>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
  827 |     for(int i = 0; i < keep.size(); i++){
      |                    ~~^~~~~~~~~~~~~
Rmain.cpp:837:20: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<int>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
  837 |   for(int i = 0; i < keep.size(); i++) alignedChildTime[keep[i]] = t1NN[i];
      |                  ~~^~~~~~~~~~~~~
Rmain.cpp:862:21: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<std::vector<double> >::size_type' {aka 'long unsigned int'} [-Wsign-compare]
  862 |   for (int i = 0; i < intensity1NN.size(); i++){
      |                   ~~^~~~~~~~~~~~~~~~~~~~~
Rmain.cpp:873:28: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<double>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
  873 |     for(int i =0, j = 0; i < alignedChildTime.size(); i++){
      |                          ~~^~~~~~~~~~~~~~~~~~~~~~~~~
Rmain.cpp: In function 'Rcpp::List otherChildXICpp(Rcpp::List, Rcpp::List, int, int, Rcpp::NumericMatrix, std::vector<double>, double, std::string)':
Rmain.cpp:944:21: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<std::vector<double> >::size_type' {aka 'long unsigned int'} [-Wsign-compare]
  944 |     for(int i = 0; i<intensity1.size(); i++){
      |                    ~^~~~~~~~~~~~~~~~~~
Rmain.cpp:972:20: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<std::vector<double> >::size_type' {aka 'long unsigned int'} [-Wsign-compare]
  972 |   for(int j = 0; j <intensity1NN.size(); j++){
      |                  ~~^~~~~~~~~~~~~~~~~~~~
Rmain.cpp:975:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<int>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
  975 |     for(int i = 0; i < keep.size(); i++){
      |                    ~~^~~~~~~~~~~~~
Rmain.cpp:1008:21: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<std::vector<double> >::size_type' {aka 'long unsigned int'} [-Wsign-compare]
 1008 |   for (int i = 0; i < intensity1NN.size(); i++){
      |                   ~~^~~~~~~~~~~~~~~~~~~~~
In file included from Rmain.cpp:19:
miscell.h: At global scope:
miscell.h:14:19: warning: 'const bool DIAlign::detect_end_na(double, double)' declared 'static' but never defined [-Wunused-function]
   14 | static bool const detect_end_na(double a, double b);
      |                   ^~~~~~~~~~~~~
miscell.h:16:19: warning: 'const bool DIAlign::detect_start_na(double, double)' declared 'static' but never defined [-Wunused-function]
   16 | static bool const detect_start_na(double a, double b);
      |                   ^~~~~~~~~~~~~~~
miscell.h:18:19: warning: 'const bool DIAlign::lessZero(double)' declared 'static' but never defined [-Wunused-function]
   18 | static bool const lessZero(double a);
      |                   ^~~~~~~~
In file included from miscell.h:9:
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,
      |        ^~~~~~
g++ -std=gnu++14 -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.4.1/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.4.1/site-library/RcppEigen/include' -I/usr/local/include    -fPIC  -g -O2  -Wall  -c SavitzkyGolayFilter.cpp -o SavitzkyGolayFilter.o
In file included from /home/biocbuild/R/R-4.4.1/site-library/RcppEigen/include/Eigen/Core:214,
                 from /home/biocbuild/R/R-4.4.1/site-library/RcppEigen/include/Eigen/Dense:1,
                 from /home/biocbuild/R/R-4.4.1/site-library/RcppEigen/include/RcppEigenForward.h:28,
                 from /home/biocbuild/R/R-4.4.1/site-library/RcppEigen/include/RcppEigen.h:25,
                 from SavitzkyGolayFilter.cpp:1:
/home/biocbuild/R/R-4.4.1/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-4.4.1/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-4.4.1/site-library/RcppEigen/include/Eigen/Core:172:
/home/biocbuild/R/R-4.4.1/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-4.4.1/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-4.4.1/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-4.4.1/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-4.4.1/site-library/RcppEigen/include/Eigen/Core:341:
/home/biocbuild/R/R-4.4.1/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-4.4.1/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-4.4.1/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>
      |                        ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
g++ -std=gnu++14 -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.4.1/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.4.1/site-library/RcppEigen/include' -I/usr/local/include    -fPIC  -g -O2  -Wall  -c affinealignment.cpp -o affinealignment.o
affinealignment.cpp: In function 'double DIAlign::AffineAlignment::getOlapAffineAlignStartIndices(double*, double*, double*, int, int, int&, int&, DIAlign::Traceback::tbJump&)':
affinealignment.cpp: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;
      |                    ^~~~~~~~~~~
g++ -std=gnu++14 -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.4.1/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.4.1/site-library/RcppEigen/include' -I/usr/local/include    -fPIC  -g -O2  -Wall  -c affinealignobj.cpp -o affinealignobj.o
g++ -std=gnu++14 -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.4.1/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.4.1/site-library/RcppEigen/include' -I/usr/local/include    -fPIC  -g -O2  -Wall  -c alignment.cpp -o alignment.o
g++ -std=gnu++14 -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.4.1/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.4.1/site-library/RcppEigen/include' -I/usr/local/include    -fPIC  -g -O2  -Wall  -c chromSimMatrix.cpp -o chromSimMatrix.o
chromSimMatrix.cpp: In function 'std::vector<double> DIAlign::SimilarityMatrix::perSampleEucLenVecOfVec(const std::vector<std::vector<double> >&)':
chromSimMatrix.cpp:32:21: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<double>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
   32 |   for (int i = 0; i < mag.size(); i++){
      |                   ~~^~~~~~~~~~~~
chromSimMatrix.cpp: In function 'std::vector<double> DIAlign::SimilarityMatrix::perSampleSqrSumVecOfVec(const std::vector<std::vector<double> >&)':
chromSimMatrix.cpp:45:21: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<double>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
   45 |   for (int i = 0; i < mag.size(); i++){
      |                   ~~^~~~~~~~~~~~
chromSimMatrix.cpp: In function 'std::vector<double> DIAlign::SimilarityMatrix::perSampleMeanVecOfVec(const std::vector<std::vector<double> >&)':
chromSimMatrix.cpp:57:21: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<double>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
   57 |   for (int i = 0; i < mean.size(); i++){
      |                   ~~^~~~~~~~~~~~~
chromSimMatrix.cpp: In function 'std::vector<double> DIAlign::SimilarityMatrix::perSampleSumVecOfVec(const std::vector<std::vector<double> >&)':
chromSimMatrix.cpp:70:21: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<double>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
   70 |   for (int i = 0; i < sum.size(); i++){
      |                   ~~^~~~~~~~~~~~
chromSimMatrix.cpp: In function 'DIAlign::SimMatrix DIAlign::SimilarityMatrix::getSimilarityMatrix(const std::vector<std::vector<double> >&, const std::vector<std::vector<double> >&, std::string, std::string, double, double, int)':
chromSimMatrix.cpp:414:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<double>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
  414 |     for(int i = 0; i < MASK.size(); i++){
      |                    ~~^~~~~~~~~~~~~
g++ -std=gnu++14 -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.4.1/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.4.1/site-library/RcppEigen/include' -I/usr/local/include    -fPIC  -g -O2  -Wall  -c constrainMat.cpp -o constrainMat.o
constrainMat.cpp: In function 'void DIAlign::ConstrainMatrix::calcNoBeefMask2(DIAlign::SimMatrix&, std::vector<double>, std::vector<double>, std::vector<double>, int, bool)':
constrainMat.cpp:78:10: warning: unused variable 'mapped' [-Wunused-variable]
   78 |   double mapped = 0.0;
      |          ^~~~~~
g++ -std=gnu++14 -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.4.1/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.4.1/site-library/RcppEigen/include' -I/usr/local/include    -fPIC  -g -O2  -Wall  -c gapPenalty.cpp -o gapPenalty.o
gapPenalty.cpp: In function 'double DIAlign::getGapPenalty(const SimMatrix&, double, std::string)':
gapPenalty.cpp:6:10: warning: 'gapPenalty' may be used uninitialized [-Wmaybe-uninitialized]
    6 |   double gapPenalty;
      |          ^~~~~~~~~~
g++ -std=gnu++14 -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.4.1/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.4.1/site-library/RcppEigen/include' -I/usr/local/include    -fPIC  -g -O2  -Wall  -c integrateArea.cpp -o integrateArea.o
g++ -std=gnu++14 -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.4.1/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.4.1/site-library/RcppEigen/include' -I/usr/local/include    -fPIC  -g -O2  -Wall  -c interface.cpp -o interface.o
g++ -std=gnu++14 -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.4.1/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.4.1/site-library/RcppEigen/include' -I/usr/local/include    -fPIC  -g -O2  -Wall  -c miscell.cpp -o miscell.o
miscell.cpp: In function 'void DIAlign::xicIntersect(std::vector<std::vector<double> >&, std::vector<std::vector<double> >&)':
miscell.cpp:10:30: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare]
   10 |   for (unsigned int i = 0; i < len; i++){
      |                            ~~^~~~~
miscell.cpp:15:29: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare]
   15 |   for(unsigned int i = 0; i < len; i++){
      |                           ~~^~~~~
miscell.cpp:26:30: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare]
   26 |   for (unsigned int i = 0; i < len; i++){
      |                            ~~^~~~~
miscell.cpp:39:30: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare]
   39 |   for (unsigned int i = 0; i < len; i++) len2[i] = intensity[i].size();
      |                            ~~^~~~~
miscell.cpp: In function 'std::vector<std::vector<double> > DIAlign::imputeChromatogram(const std::vector<std::vector<double> >&, const std::vector<double>&, const std::vector<int>&)':
miscell.cpp:125:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<int>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
  125 |   for(int i =0; i< middle.size(); i++){
      |                 ~^~~~~~~~~~~~~~~
miscell.cpp:131:19: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<std::vector<double> >::size_type' {aka 'long unsigned int'} [-Wsign-compare]
  131 |   for(int i =0; i < (Anew.size()-1); i++){
      |                 ~~^~~~~~~~~~~~~~~~~
miscell.cpp:139:19: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<double>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
  139 |     for(int j=0; j<result.size(); j++){
      |                  ~^~~~~~~~~~~~~~
miscell.cpp: In function 'std::vector<int> DIAlign::getSkip(const std::vector<int>&, const std::vector<int>&)':
miscell.cpp:164:20: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<int>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
  164 |   for(int i = 0; i < index.size(); i++){
      |                  ~~^~~~~~~~~~~~~~
miscell.cpp: In function 'void DIAlign::mergeIntensity(std::vector<std::vector<double> >&, std::vector<std::vector<double> >&, double)':
miscell.cpp:221:19: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<std::vector<double> >::size_type' {aka 'long unsigned int'} [-Wsign-compare]
  221 |   for(int i = 0; i< A.size(); i++){
      |                  ~^~~~~~~~~~
miscell.cpp: In function 'void DIAlign::addFlankToLeft(const std::vector<double>&, std::vector<double>&, std::vector<double>&, const std::vector<std::vector<double> >&, std::vector<std::vector<double> >&, std::vector<int>&)':
miscell.cpp:250:19: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<std::vector<double> >::size_type' {aka 'long unsigned int'} [-Wsign-compare]
  250 |   for(int i = 0; i< intenN.size(); i++){
      |                  ~^~~~~~~~~~~~~~~
miscell.cpp: In function 'void DIAlign::addFlankToRight(const std::vector<double>&, std::vector<double>&, std::vector<double>&, const std::vector<std::vector<double> >&, std::vector<std::vector<double> >&, std::vector<int>&)':
miscell.cpp:277:19: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<std::vector<double> >::size_type' {aka 'long unsigned int'} [-Wsign-compare]
  277 |   for(int i = 0; i< intenN.size(); i++){
      |                  ~^~~~~~~~~~~~~~~
miscell.cpp: In function 'void DIAlign::addFlankToLeft1(const std::vector<std::vector<double> >&, std::vector<std::vector<double> >&, std::vector<int>&)':
miscell.cpp:288:19: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<std::vector<double> >::size_type' {aka 'long unsigned int'} [-Wsign-compare]
  288 |   for(int i = 0; i< intenN.size(); i++){
      |                  ~^~~~~~~~~~~~~~~
miscell.cpp: In function 'void DIAlign::addFlankToRight1(const std::vector<std::vector<double> >&, std::vector<std::vector<double> >&, std::vector<int>&)':
miscell.cpp:307:19: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<std::vector<double> >::size_type' {aka 'long unsigned int'} [-Wsign-compare]
  307 |   for(int i = 0; i< intenN.size(); i++){
      |                  ~^~~~~~~~~~~~~~~
miscell.cpp: In function 'std::vector<int> DIAlign::getMatchingIdx(const std::vector<double>&, const std::vector<double>&)':
miscell.cpp:318:23: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<double>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
  318 |   for(int i =0, j=0; i< tMain.size(); i++){
      |                      ~^~~~~~~~~~~~~~
miscell.cpp:320:12: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<double>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
  320 |     for(; j<t.size();){
      |           ~^~~~~~~~~
miscell.cpp: In function 'std::vector<std::vector<double> > DIAlign::imputeChromatogram1(const std::vector<std::vector<double> >&, const std::vector<int>&, const std::vector<double>&, const std::vector<double>&)':
miscell.cpp:337:20: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<std::vector<double> >::size_type' {aka 'long unsigned int'} [-Wsign-compare]
  337 |   for(int j = 0; j <A.size(); j++){
      |                  ~~^~~~~~~~~
miscell.cpp:339:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<double>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
  339 |     for(int i = 0; i < temp.size(); i++){
      |                    ~~^~~~~~~~~~~~~
miscell.cpp:353:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<int>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
  353 |   for(int i =0; i< middle.size(); i++){
      |                 ~^~~~~~~~~~~~~~~
miscell.cpp:358:19: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<std::vector<double> >::size_type' {aka 'long unsigned int'} [-Wsign-compare]
  358 |   for(int i =0; i < intensity.size(); i++){
      |                 ~~^~~~~~~~~~~~~~~~~~
miscell.cpp:360:19: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<double>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
  360 |     for(int j=0; j<result.size(); j++){
      |                  ~^~~~~~~~~~~~~~
miscell.cpp: At global scope:
miscell.cpp:53:19: warning: 'const bool DIAlign::lessZero(double)' defined but not used [-Wunused-function]
   53 | static bool const lessZero(double a){
      |                   ^~~~~~~~
In file included from miscell.h:9,
                 from miscell.cpp:3:
spline.h:390:10: warning: 'double DIAlign::{anonymous}::tk::spline::deriv(int, double) const' defined but not used [-Wunused-function]
  390 |   double spline::deriv(int order, double x) const
      |          ^~~~~~
spline.h:364:10: warning: 'double DIAlign::{anonymous}::tk::spline::operator()(double) const' defined but not used [-Wunused-function]
  364 |   double spline::operator() (double x) const
      |          ^~~~~~
spline.h:273:8: warning: 'void DIAlign::{anonymous}::tk::spline::set_points(const std::vector<double>&, const std::vector<double>&, bool)' defined but not used [-Wunused-function]
  273 |   void spline::set_points(const std::vector<double>& x,
      |        ^~~~~~
spline.h:261:8: warning: 'void DIAlign::{anonymous}::tk::spline::set_boundary(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,
      |        ^~~~~~
g++ -std=gnu++14 -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.4.1/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.4.1/site-library/RcppEigen/include' -I/usr/local/include    -fPIC  -g -O2  -Wall  -c run_alignment.cpp -o run_alignment.o
g++ -std=gnu++14 -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.4.1/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.4.1/site-library/RcppEigen/include' -I/usr/local/include    -fPIC  -g -O2  -Wall  -c simpleFcn.cpp -o simpleFcn.o
g++ -std=gnu++14 -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.4.1/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.4.1/site-library/RcppEigen/include' -I/usr/local/include    -fPIC  -g -O2  -Wall  -c spline.cpp -o spline.o
In file included from spline.cpp:1:
spline.h:390:10: warning: 'double DIAlign::{anonymous}::tk::spline::deriv(int, double) const' defined but not used [-Wunused-function]
  390 |   double spline::deriv(int order, double x) const
      |          ^~~~~~
spline.h:261:8: warning: 'void DIAlign::{anonymous}::tk::spline::set_boundary(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,
      |        ^~~~~~
g++ -std=gnu++14 -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.4.1/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.4.1/site-library/RcppEigen/include' -I/usr/local/include    -fPIC  -g -O2  -Wall  -c utils.cpp -o utils.o
utils.cpp: In function 'double DIAlign::Utils::getQuantile(std::vector<double>, double)':
utils.cpp:48:9: warning: unused variable 'idx' [-Wunused-variable]
   48 |     int idx = n*(1-p);
      |         ^~~
g++ -std=gnu++14 -shared -L/home/biocbuild/R/R-4.4.1/lib -L/usr/local/lib -o DIAlignR.so ChromatogramPeak.o DPosition.o MSChromatogram.o PeakIntegrator.o RcppExports.o Rmain.o SavitzkyGolayFilter.o affinealignment.o affinealignobj.o alignment.o chromSimMatrix.o constrainMat.o gapPenalty.o integrateArea.o interface.o miscell.o run_alignment.o simpleFcn.o spline.o utils.o -L/home/biocbuild/R/R-4.4.1/lib -lR
installing to /home/biocbuild/R/R-4.4.1/site-library/00LOCK-DIAlignR/00new/DIAlignR/libs
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (DIAlignR)

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

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> 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 0.05527544 secs
Time difference of 0.2677643 secs
Time difference of 0.2086103 secs
Time difference of 0.02864122 secs
Time difference of 0.01158881 secs
Time difference of 0.1186497 secs
Time difference of 2.070365 secs
Time difference of 0.03171563 secs
Time difference of 0.5020163 secs
[1] "hroest_K120808_Strep10%PlasmaBiolRepl1_R03_SW_filt"
[2] "hroest_K120809_Strep0%PlasmaBiolRepl2_R04_SW_filt" 
Time difference of 0.01880646 secs
Time difference of 0.2526319 secs
Time difference of 0.1340637 secs
Time difference of 0.01870322 secs
Time difference of 0.007979631 secs
Time difference of 0.07149458 secs
Time difference of 1.022045 secs
Time difference of 0.01035881 secs
Time difference of 1.143661 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 0.019032 secs
Time difference of 0.2749212 secs
Time difference of 0.1366768 secs
Time difference of 0.100724 secs
Time difference of 0.01276946 secs
Time difference of 0.09693003 secs
Time difference of 1.523315 secs
Time difference of 0.02951384 secs
Time difference of 0.415307 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 0.020154 secs
Time difference of 0.01802373 secs
Time difference of 0.0004656315 secs
Time difference of 0.1005378 secs
Time difference of 0.01235485 secs
Time difference of 0.06154609 secs
Time difference of 0.01835585 secs
Time difference of 0.01082945 secs
Time difference of 0.1448328 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 0.01112056 secs
Time difference of 0.03885722 secs
Time difference of 0.01336241 secs
Time difference of 0.01406765 secs
Time difference of 0.00993228 secs
Time difference of 0.04906464 secs
Time difference of 0.1120772 secs
Time difference of 0.01026678 secs
Time difference of 0.2772548 secs
[1] "chludwig_K150309_004b_SW_1_16" "chludwig_K150309_008_SW_1_4"  
[3] "chludwig_K150309_013_SW_0"    
Time difference of 0.0153842 secs
Time difference of 0.0126195 secs
Time difference of 0.001271486 secs
Time difference of 0.02177262 secs
Time difference of 0.01394534 secs
Time difference of 0.07883406 secs
Time difference of 0.009028912 secs
Time difference of 0.02505636 secs
Time difference of 0.315695 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 0.1042597 secs
Time difference of 0.01733088 secs
Time difference of 0.002530575 secs
Time difference of 0.0122416 secs
Time difference of 0.05890846 secs
Time difference of 0.01838326 secs
Time difference of 0.02060723 secs
Time difference of 0.1232736 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 0.03084636 secs
[1] "run0 run1\nrun2 run2"
Time difference of 0.2745662 secs
Time difference of 0.1442394 secs
Time difference of 0.01444888 secs
Time difference of 0.1038175 secs
Time difference of 1.60457 secs
Time difference of 0.02276945 secs
Time difference of 0.4800875 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 0.1242568 secs
Time difference of 0.8263083 secs
Time difference of 6.473869 secs
Time difference of 0.5492332 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 0.1057963 secs
[1] "Written /home/biocbuild/R/R-4.4.1/site-library/DIAlignR/extdata/temp_prog1.RData"
[1] "Written /home/biocbuild/R/R-4.4.1/site-library/DIAlignR/extdata/temp_0_2.rds"
[1] "progTree1 is done."
Time difference of 1.408071 secs
Time difference of 0.4045238 secs
[1] "Written /home/biocbuild/R/R-4.4.1/site-library/DIAlignR/extdata/temp_1_2.rds"
Time difference of 0.7205589 secs
[1] "Written /home/biocbuild/R/R-4.4.1/site-library/DIAlignR/extdata/temp_2_2.rds"
Time difference of 0.3861959 secs
Time difference of 0.2385285 secs
[1] "Written /home/biocbuild/R/R-4.4.1/site-library/DIAlignR/extdata/temp_all_2.rds"
Time difference of 0.208895 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 0.09794521 secs
[1] "Written /home/biocbuild/R/R-4.4.1/site-library/DIAlignR/extdata/temp_prog1.RData"
[1] "Written /home/biocbuild/R/R-4.4.1/site-library/DIAlignR/extdata/temp_0_2.rds"
[1] "progTree1 is done."
Time difference of 1.259684 secs
Time difference of 0.3951583 secs
[1] "Written /home/biocbuild/R/R-4.4.1/site-library/DIAlignR/extdata/temp_1_2.rds"
Time difference of 0.5862463 secs
[1] "Written /home/biocbuild/R/R-4.4.1/site-library/DIAlignR/extdata/temp_2_2.rds"
Time difference of 0.4050374 secs
Time difference of 0.01734209 secs
[1] "Written /home/biocbuild/R/R-4.4.1/site-library/DIAlignR/extdata/temp_all_2.rds"
Error in reticulate::use_condaenv(condaEnv, required = TRUE) : 
  Unable to locate conda environment 'TricEnvr'.
Error in reticulate::use_condaenv(condaEnv, required = TRUE) : 
  Unable to locate conda environment 'TricEnvr'.
Error in reticulate::use_condaenv(condaEnv, required = TRUE) : 
  Unable to locate conda environment 'TricEnvr'.
[ FAIL 3 | WARN 0 | SKIP 8 | PASS 629 ]

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

══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test_utils.R:61:3'): test_getMultipeptide ───────────────────────────
Error in `sum.integer64(structure(c(8.12925173103238e+105, 7.07020651020428e+62, 
2.87322374279237e+166, 3.16623447292931e-138, 2.73500684933996e-275, 
3.15239881785171e+291, 4.67202095363214e+123, 8.27712377546863e-298, 
264730160634500, 4.29832987800134e+292, 1.24545021916353e-79, 
6.68432480390972e-210, 5.77682771166528e-16, 7.69829720567834e+172, 
1.44901952004469e-19, 4.589273630966e+269, 1.43016762562436e-297
), class = "integer64"), na.rm = FALSE)`: (converted from warning) NAs produced by integer64 overflow
Backtrace:
    ▆
 1. └─testthat::expect_equal(outData[[1]], expData, tolerance = 1e-04) at test_utils.R:61:3
 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(...)
── 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 3 | WARN 0 | SKIP 8 | PASS 629 ]
Error: Test failures
Execution halted