##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R-4.3.0/bin/R CMD check --install=check:DIAlignR.install-out.txt --library=/home/biocbuild/R/R-4.3.0/site-library --timings DIAlignR_2.9.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.18-bioc/meat/DIAlignR.Rcheck’
* using R version 4.3.0 (2023-04-21)
* using platform: aarch64-unknown-linux-gnu (64-bit)
* R was compiled by
    gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
    GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
* running under: Ubuntu 22.04.2 LTS
* using session charset: UTF-8
* checking for file ‘DIAlignR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘DIAlignR’ version ‘2.9.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘DIAlignR’ can be installed ... OK
* used C++ compiler: ‘g++ (Ubuntu 11.3.0-1ubuntu1~22.04.1) 11.3.0’
* checking C++ specification ... NOTE
  Specified C++14: please drop specification unless essential
* checking installed package size ... NOTE
  installed size is 27.7Mb
  sub-directories of 1Mb or more:
    extdata   4.0Mb
    libs     16.8Mb
    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 R 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 ... OK
* 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-4.3.0/site-library/DIAlignR/libs/DIAlignR.so’:
  Found ‘_ZSt4cout’, possibly from ‘std::cout’ (C++)

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                    user system elapsed
alignTargetedRuns 10.121 12.168   7.136
* 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:
  ── 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_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 3 | SKIP 8 | PASS 629 ]
  Error: Test failures
  Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ...
  ‘DIAlignR-vignette.Rmd’ using ‘UTF-8’... OK
 NONE
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 1 ERROR, 4 NOTEs
See
  ‘/home/biocbuild/bbs-3.18-bioc/meat/DIAlignR.Rcheck/00check.log’
for details.

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R-4.3.0/bin/R CMD INSTALL DIAlignR
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/R/R-4.3.0/site-library’
* installing *source* package ‘DIAlignR’ ...
** using staged installation
** libs
using C++ compiler: ‘g++ (Ubuntu 11.3.0-1ubuntu1~22.04.1) 11.3.0’
using C++14
g++ -std=gnu++14 -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.3.0/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.3.0/site-library/RcppEigen/include' -I/usr/local/include    -fPIC  -g -O2  -c ChromatogramPeak.cpp -o ChromatogramPeak.o
g++ -std=gnu++14 -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.3.0/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.3.0/site-library/RcppEigen/include' -I/usr/local/include    -fPIC  -g -O2  -c DPosition.cpp -o DPosition.o
g++ -std=gnu++14 -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.3.0/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.3.0/site-library/RcppEigen/include' -I/usr/local/include    -fPIC  -g -O2  -c MSChromatogram.cpp -o MSChromatogram.o
g++ -std=gnu++14 -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.3.0/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.3.0/site-library/RcppEigen/include' -I/usr/local/include    -fPIC  -g -O2  -c PeakIntegrator.cpp -o PeakIntegrator.o
g++ -std=gnu++14 -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.3.0/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.3.0/site-library/RcppEigen/include' -I/usr/local/include    -fPIC  -g -O2  -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++14 -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.3.0/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.3.0/site-library/RcppEigen/include' -I/usr/local/include    -fPIC  -g -O2  -c Rmain.cpp -o Rmain.o
g++ -std=gnu++14 -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.3.0/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.3.0/site-library/RcppEigen/include' -I/usr/local/include    -fPIC  -g -O2  -c SavitzkyGolayFilter.cpp -o SavitzkyGolayFilter.o
g++ -std=gnu++14 -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.3.0/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.3.0/site-library/RcppEigen/include' -I/usr/local/include    -fPIC  -g -O2  -c affinealignment.cpp -o affinealignment.o
g++ -std=gnu++14 -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.3.0/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.3.0/site-library/RcppEigen/include' -I/usr/local/include    -fPIC  -g -O2  -c affinealignobj.cpp -o affinealignobj.o
g++ -std=gnu++14 -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.3.0/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.3.0/site-library/RcppEigen/include' -I/usr/local/include    -fPIC  -g -O2  -c alignment.cpp -o alignment.o
g++ -std=gnu++14 -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.3.0/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.3.0/site-library/RcppEigen/include' -I/usr/local/include    -fPIC  -g -O2  -c chromSimMatrix.cpp -o chromSimMatrix.o
g++ -std=gnu++14 -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.3.0/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.3.0/site-library/RcppEigen/include' -I/usr/local/include    -fPIC  -g -O2  -c constrainMat.cpp -o constrainMat.o
g++ -std=gnu++14 -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.3.0/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.3.0/site-library/RcppEigen/include' -I/usr/local/include    -fPIC  -g -O2  -c gapPenalty.cpp -o gapPenalty.o
g++ -std=gnu++14 -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.3.0/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.3.0/site-library/RcppEigen/include' -I/usr/local/include    -fPIC  -g -O2  -c integrateArea.cpp -o integrateArea.o
g++ -std=gnu++14 -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.3.0/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.3.0/site-library/RcppEigen/include' -I/usr/local/include    -fPIC  -g -O2  -c interface.cpp -o interface.o
g++ -std=gnu++14 -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.3.0/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.3.0/site-library/RcppEigen/include' -I/usr/local/include    -fPIC  -g -O2  -c miscell.cpp -o miscell.o
g++ -std=gnu++14 -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.3.0/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.3.0/site-library/RcppEigen/include' -I/usr/local/include    -fPIC  -g -O2  -c run_alignment.cpp -o run_alignment.o
g++ -std=gnu++14 -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.3.0/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.3.0/site-library/RcppEigen/include' -I/usr/local/include    -fPIC  -g -O2  -c simpleFcn.cpp -o simpleFcn.o
g++ -std=gnu++14 -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.3.0/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.3.0/site-library/RcppEigen/include' -I/usr/local/include    -fPIC  -g -O2  -c spline.cpp -o spline.o
g++ -std=gnu++14 -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.3.0/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.3.0/site-library/RcppEigen/include' -I/usr/local/include    -fPIC  -g -O2  -c utils.cpp -o utils.o
g++ -std=gnu++14 -shared -L/home/biocbuild/R/R-4.3.0/lib -L/usr/local/lib -o DIAlignR.so ChromatogramPeak.o DPosition.o MSChromatogram.o PeakIntegrator.o RcppExports.o Rmain.o SavitzkyGolayFilter.o affinealignment.o affinealignobj.o alignment.o chromSimMatrix.o constrainMat.o gapPenalty.o integrateArea.o interface.o miscell.o run_alignment.o simpleFcn.o spline.o utils.o -L/home/biocbuild/R/R-4.3.0/lib -lR
installing to /home/biocbuild/R/R-4.3.0/site-library/00LOCK-DIAlignR/00new/DIAlignR/libs
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (DIAlignR)

R version 4.3.0 (2023-04-21) -- "Already Tomorrow"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: aarch64-unknown-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(testthat)
> library(DIAlignR)
> 
> test_check("DIAlignR")
[1] "hroest_K120808_Strep10%PlasmaBiolRepl1_R03_SW_filt"
[2] "hroest_K120809_Strep0%PlasmaBiolRepl2_R04_SW_filt" 
[3] "hroest_K120809_Strep10%PlasmaBiolRepl2_R04_SW_filt"
Time difference of 0.05916858 secs
Time difference of 0.3479798 secs
Time difference of 0.1223497 secs
Time difference of 0.0318861 secs
Time difference of 0.01213098 secs
Time difference of 0.165904 secs
Time difference of 1.966341 secs
Time difference of 0.03749585 secs
Time difference of 0.4906647 secs
[1] "hroest_K120808_Strep10%PlasmaBiolRepl1_R03_SW_filt"
[2] "hroest_K120809_Strep0%PlasmaBiolRepl2_R04_SW_filt" 
Time difference of 0.01819038 secs
Time difference of 0.2715685 secs
Time difference of 0.1167879 secs
Time difference of 0.01816821 secs
Time difference of 0.007009029 secs
Time difference of 0.07749701 secs
Time difference of 1.14896 secs
Time difference of 0.009663105 secs
Time difference of 1.017108 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 0.01807761 secs
Time difference of 0.2754886 secs
Time difference of 0.1247718 secs
Time difference of 0.1013381 secs
Time difference of 0.01148772 secs
Time difference of 0.1222837 secs
Time difference of 2.035968 secs
Time difference of 0.02445269 secs
Time difference of 0.3957345 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 0.01904011 secs
Time difference of 0.01780748 secs
Time difference of 0.0005245209 secs
Time difference of 0.1010416 secs
Time difference of 0.0107739 secs
Time difference of 0.07313251 secs
Time difference of 0.02135134 secs
Time difference of 0.009456158 secs
Time difference of 0.1103399 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 0.009290695 secs
Time difference of 0.03824162 secs
Time difference of 0.01115322 secs
Time difference of 0.01486969 secs
Time difference of 0.009442329 secs
Time difference of 0.05880165 secs
Time difference of 0.1073518 secs
Time difference of 0.008580446 secs
Time difference of 0.2549739 secs
[1] "chludwig_K150309_004b_SW_1_16" "chludwig_K150309_008_SW_1_4"  
[3] "chludwig_K150309_013_SW_0"    
Time difference of 0.01212311 secs
Time difference of 0.01245952 secs
Time difference of 0.001211405 secs
Time difference of 0.01755452 secs
Time difference of 0.01323438 secs
Time difference of 0.07919621 secs
Time difference of 0.007542849 secs
Time difference of 0.02128839 secs
Time difference of 0.3191216 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 0.1028774 secs
Time difference of 0.0194366 secs
Time difference of 0.002475739 secs
Time difference of 0.01198602 secs
Time difference of 0.07816553 secs
Time difference of 0.02343965 secs
Time difference of 0.02040339 secs
Time difference of 0.1339445 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 0.03043532 secs
[1] "run0 run1\nrun2 run2"
Time difference of 0.322686 secs
Time difference of 0.118067 secs
Time difference of 0.01069307 secs
Time difference of 0.1126776 secs
Time difference of 1.939868 secs
Time difference of 0.01938128 secs
Time difference of 0.4152985 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 0.1142726 secs
Time difference of 1.149061 secs
Time difference of 6.498893 secs
Time difference of 0.5186548 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 0.1054785 secs
[1] "Written /home/biocbuild/R/R-4.3.0/site-library/DIAlignR/extdata/temp_prog1.RData"
[1] "Written /home/biocbuild/R/R-4.3.0/site-library/DIAlignR/extdata/temp_0_2.rds"
[1] "progTree1 is done."
Time difference of 1.712197 secs
Time difference of 0.4342122 secs
[1] "Written /home/biocbuild/R/R-4.3.0/site-library/DIAlignR/extdata/temp_1_2.rds"
Time difference of 0.8136246 secs
[1] "Written /home/biocbuild/R/R-4.3.0/site-library/DIAlignR/extdata/temp_2_2.rds"
Time difference of 0.3924961 secs
Time difference of 0.2471378 secs
[1] "Written /home/biocbuild/R/R-4.3.0/site-library/DIAlignR/extdata/temp_all_2.rds"
Time difference of 0.244108 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 0.1075161 secs
[1] "Written /home/biocbuild/R/R-4.3.0/site-library/DIAlignR/extdata/temp_prog1.RData"
[1] "Written /home/biocbuild/R/R-4.3.0/site-library/DIAlignR/extdata/temp_0_2.rds"
[1] "progTree1 is done."
Time difference of 1.598785 secs
Time difference of 0.435766 secs
[1] "Written /home/biocbuild/R/R-4.3.0/site-library/DIAlignR/extdata/temp_1_2.rds"
Time difference of 1.269665 secs
[1] "Written /home/biocbuild/R/R-4.3.0/site-library/DIAlignR/extdata/temp_2_2.rds"
Time difference of 0.3997681 secs
Time difference of 0.0152235 secs
[1] "Written /home/biocbuild/R/R-4.3.0/site-library/DIAlignR/extdata/temp_all_2.rds"
Error in reticulate::use_condaenv(condaEnv, required = TRUE) : 
  Unable to locate conda environment 'TricEnvr'.
Error in reticulate::use_condaenv(condaEnv, required = TRUE) : 
  Unable to locate conda environment 'TricEnvr'.
Error in reticulate::use_condaenv(condaEnv, required = TRUE) : 
  Unable to locate conda environment 'TricEnvr'.
[ FAIL 3 | WARN 3 | SKIP 8 | PASS 629 ]

══ Skipped tests ═══════════════════════════════════════════════════════════════
• empty test (5)
• ropenms not available for testing. A conda environment with name TricEnvr is MUST for testing. (3)

══ Failed tests ════════════════════════════════════════════════════════════════
── 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_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 3 | SKIP 8 | PASS 629 ]
Error: Test failures
Execution halted