| Back to Build/check report for BioC 3.18: simplified long |
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This page was generated on 2023-06-06 11:00:30 -0000 (Tue, 06 Jun 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | 4.3.0 (2023-04-21) -- "Already Tomorrow" | 4366 |
| Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X | ||||
|
To the developers/maintainers of the DIAlignR package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/DIAlignR.git to reflect on this report. See Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. Note: If "R CMD check" recently failed on the Linux builder over a missing dependency, add the missing dependency to "Suggests" in your DESCRIPTION file. See the Renviron.bioc for details. |
| Package 541/2199 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| DIAlignR 2.9.0 (landing page) Shubham Gupta
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | ERROR | |||||||||
| Package: DIAlignR |
| Version: 2.9.0 |
| 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 |
| StartedAt: 2023-06-05 21:16:35 -0000 (Mon, 05 Jun 2023) |
| EndedAt: 2023-06-05 21:20:38 -0000 (Mon, 05 Jun 2023) |
| EllapsedTime: 243.3 seconds |
| RetCode: 1 |
| Status: ERROR |
| CheckDir: DIAlignR.Rcheck |
| Warnings: NA |
##############################################################################
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###
### 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 (GCC) 10.3.1
GNU Fortran (GCC) 10.3.1
* running under: openEuler 22.03 (LTS-SP1)
* 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++ (GCC) 10.3.1’
* checking C++ specification ... NOTE
Specified C++14: please drop specification unless essential
* checking installed package size ... NOTE
installed size is 31.0Mb
sub-directories of 1Mb or more:
extdata 4.0Mb
libs 20.0Mb
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 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 10.017 10.150 6.449
script2 3.398 1.641 3.924
* 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.
DIAlignR.Rcheck/00install.out
############################################################################## ############################################################################## ### ### 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++ (GCC) 10.3.1’ 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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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)
DIAlignR.Rcheck/tests/testthat.Rout.fail
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 0.05486846 secs
Time difference of 0.3140121 secs
Time difference of 0.1187608 secs
Time difference of 0.02790999 secs
Time difference of 0.01038718 secs
Time difference of 0.1494765 secs
Time difference of 2.077386 secs
Time difference of 0.0379951 secs
Time difference of 0.5723503 secs
[1] "hroest_K120808_Strep10%PlasmaBiolRepl1_R03_SW_filt"
[2] "hroest_K120809_Strep0%PlasmaBiolRepl2_R04_SW_filt"
Time difference of 0.0177815 secs
Time difference of 0.300648 secs
Time difference of 0.1260006 secs
Time difference of 0.01927233 secs
Time difference of 0.007798672 secs
Time difference of 0.08931398 secs
Time difference of 1.253295 secs
Time difference of 0.01074982 secs
Time difference of 1.12912 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 0.01795101 secs
Time difference of 0.3171709 secs
Time difference of 0.1336331 secs
Time difference of 0.1015589 secs
Time difference of 0.01140261 secs
Time difference of 0.1214111 secs
Time difference of 2.133569 secs
Time difference of 0.0270679 secs
Time difference of 0.4306443 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 0.01900983 secs
Time difference of 0.01874185 secs
Time difference of 0.0005903244 secs
Time difference of 0.09937811 secs
Time difference of 0.01228571 secs
Time difference of 0.07726192 secs
Time difference of 0.02376199 secs
Time difference of 0.01047254 secs
Time difference of 0.1187458 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 0.01075268 secs
Time difference of 0.04394817 secs
Time difference of 0.0121305 secs
Time difference of 0.01384091 secs
Time difference of 0.009788513 secs
Time difference of 0.06390309 secs
Time difference of 0.1210616 secs
Time difference of 0.009412766 secs
Time difference of 0.2735264 secs
[1] "chludwig_K150309_004b_SW_1_16" "chludwig_K150309_008_SW_1_4"
[3] "chludwig_K150309_013_SW_0"
Time difference of 0.01541424 secs
Time difference of 0.01484919 secs
Time difference of 0.001379013 secs
Time difference of 0.02174926 secs
Time difference of 0.01437521 secs
Time difference of 0.08579183 secs
Time difference of 0.00854969 secs
Time difference of 0.02460837 secs
Time difference of 0.3474388 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 0.09792376 secs
Time difference of 0.01836538 secs
Time difference of 0.002408028 secs
Time difference of 0.01248479 secs
Time difference of 0.07829642 secs
Time difference of 0.02432585 secs
Time difference of 0.02096057 secs
Time difference of 0.1331651 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 0.02764726 secs
[1] "run0 run1\nrun2 run2"
Time difference of 0.3226244 secs
Time difference of 0.1272154 secs
Time difference of 0.01252604 secs
Time difference of 0.1420655 secs
Time difference of 1.953252 secs
Time difference of 0.0205462 secs
Time difference of 0.430491 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 0.1128724 secs
Time difference of 0.994282 secs
Time difference of 6.523702 secs
Time difference of 0.5809398 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 0.1033647 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 1.85905 secs
Time difference of 0.439662 secs
[1] "Written /home/biocbuild/R/R-4.3.0/site-library/DIAlignR/extdata/temp_1_2.rds"
Time difference of 0.8860548 secs
[1] "Written /home/biocbuild/R/R-4.3.0/site-library/DIAlignR/extdata/temp_2_2.rds"
Time difference of 0.4083135 secs
Time difference of 0.253479 secs
[1] "Written /home/biocbuild/R/R-4.3.0/site-library/DIAlignR/extdata/temp_all_2.rds"
Time difference of 0.2443545 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 0.1027019 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 1.608514 secs
Time difference of 0.4218447 secs
[1] "Written /home/biocbuild/R/R-4.3.0/site-library/DIAlignR/extdata/temp_1_2.rds"
Time difference of 1.16342 secs
[1] "Written /home/biocbuild/R/R-4.3.0/site-library/DIAlignR/extdata/temp_2_2.rds"
Time difference of 0.4025528 secs
Time difference of 0.0161736 secs
[1] "Written /home/biocbuild/R/R-4.3.0/site-library/DIAlignR/extdata/temp_all_2.rds"
Error : Unable to find conda binary. Is Anaconda installed?
Error : Unable to find conda binary. Is Anaconda installed?
Error : Unable to find conda binary. Is Anaconda installed?
[ 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
DIAlignR.Rcheck/DIAlignR-Ex.timings
| name | user | system | elapsed | |
| MSTperBatch | 0.001 | 0.000 | 0.001 | |
| addFlankToLeft | 0.002 | 0.000 | 0.003 | |
| addFlankToRight | 0.001 | 0.000 | 0.001 | |
| addXIC | 0 | 0 | 0 | |
| alignChromatogramsCpp | 0.028 | 0.000 | 0.028 | |
| alignTargetedRuns | 10.017 | 10.150 | 6.449 | |
| alignToMaster | 2.594 | 0.228 | 2.827 | |
| alignToRef | 0.001 | 0.000 | 0.001 | |
| alignToRefMST | 0.001 | 0.000 | 0.001 | |
| alignedXIC | 0.100 | 0.003 | 0.103 | |
| analytesFromFeatures | 0.044 | 0.003 | 0.047 | |
| approxFill | 0.001 | 0.000 | 0.001 | |
| areaIntegrator | 0.000 | 0.004 | 0.003 | |
| blobXICs | 0.002 | 0.000 | 0.002 | |
| calculateIntensity | 0.003 | 0.000 | 0.002 | |
| checkOverlap | 0 | 0 | 0 | |
| checkParams | 0.001 | 0.000 | 0.000 | |
| childXIC | 0.093 | 0.000 | 0.093 | |
| childXICs | 0.680 | 0.007 | 0.689 | |
| constrainSimCpp | 0.001 | 0.001 | 0.001 | |
| createMZML | 0.003 | 0.000 | 0.003 | |
| createSqMass | 0.002 | 0.000 | 0.002 | |
| dialignrLoess | 0.001 | 0.000 | 0.000 | |
| doAffineAlignmentCpp | 0.002 | 0.000 | 0.001 | |
| doAlignmentCpp | 0.001 | 0.000 | 0.001 | |
| extractXIC_group | 0.913 | 0.007 | 0.925 | |
| extractXIC_group2 | 0.001 | 0.001 | 0.001 | |
| fetchAnalytesInfo | 0.01 | 0.00 | 0.01 | |
| fetchFeaturesFromRun | 0.009 | 0.000 | 0.009 | |
| fetchPeptidesInfo | 0.009 | 0.000 | 0.008 | |
| fetchPeptidesInfo2 | 0.009 | 0.000 | 0.009 | |
| fetchPrecursorsInfo | 0.001 | 0.000 | 0.001 | |
| fetchTransitionsFromRun | 0.009 | 0.000 | 0.009 | |
| filenamesFromMZML | 0.001 | 0.000 | 0.001 | |
| filenamesFromOSW | 0.000 | 0.001 | 0.001 | |
| getAlignObj | 0.022 | 0.003 | 0.024 | |
| getAlignObjs | 1.437 | 0.000 | 1.441 | |
| getAlignedFigs | 0.155 | 0.003 | 0.158 | |
| getAlignedIndices | 0.01 | 0.00 | 0.01 | |
| getAlignedTimes | 0.031 | 0.003 | 0.035 | |
| getAlignedTimesCpp | 0.008 | 0.000 | 0.008 | |
| getAlignedTimesFast | 0.017 | 0.001 | 0.017 | |
| getBaseGapPenaltyCpp | 0 | 0 | 0 | |
| getChildFeature | 0.041 | 0.003 | 0.045 | |
| getChildXICpp | 0.008 | 0.000 | 0.008 | |
| getChildXICs | 0.809 | 0.012 | 0.822 | |
| getChromSimMatCpp | 0.000 | 0.001 | 0.002 | |
| getChromatogramIndices | 0.134 | 0.006 | 0.139 | |
| getFeatures | 0.039 | 0.003 | 0.043 | |
| getGlobalAlignMaskCpp | 0.000 | 0.000 | 0.001 | |
| getGlobalAlignment | 0.007 | 0.000 | 0.008 | |
| getGlobalFits | 0.435 | 0.000 | 0.435 | |
| getLOESSfit | 0.003 | 0.000 | 0.004 | |
| getLinearfit | 0.004 | 0.000 | 0.003 | |
| getMST | 0.001 | 0.000 | 0.001 | |
| getMZMLpointers | 0.019 | 0.000 | 0.018 | |
| getMappedRT | 0.012 | 0.000 | 0.012 | |
| getMultipeptide | 2.189 | 0.018 | 2.212 | |
| getNativeIDs | 0.017 | 0.005 | 0.021 | |
| getNodeIDs | 0 | 0 | 0 | |
| getNodeRun | 0.516 | 0.031 | 0.549 | |
| getOswAnalytes | 0.009 | 0.000 | 0.009 | |
| getOswFiles | 0.009 | 0.000 | 0.009 | |
| getPeptideScores | 0.04 | 0.00 | 0.04 | |
| getPrecursorByID | 0.018 | 0.000 | 0.018 | |
| getPrecursorIndices | 0.056 | 0.000 | 0.056 | |
| getPrecursors | 0.027 | 0.000 | 0.027 | |
| getRSE | 0.003 | 0.000 | 0.003 | |
| getRTdf | 0.004 | 0.004 | 0.007 | |
| getRefExpFeatureMap | 0.362 | 0.004 | 0.366 | |
| getRefRun | 0.456 | 0.019 | 0.476 | |
| getRunNames | 0.008 | 0.004 | 0.011 | |
| getSeqSimMatCpp | 0.001 | 0.000 | 0.001 | |
| getTransitions | 0.152 | 0.000 | 0.150 | |
| getTree | 0.360 | 0.036 | 0.398 | |
| getXICs | 0.104 | 0.016 | 0.119 | |
| getXICs4AlignObj | 0.083 | 0.000 | 0.083 | |
| get_ropenms | 0.000 | 0.000 | 0.001 | |
| imputeChromatogram | 0.012 | 0.004 | 0.016 | |
| ipfReassignFDR | 0 | 0 | 0 | |
| mapIdxToTime | 0.001 | 0.000 | 0.000 | |
| mappedRTfromAlignObj | 0.003 | 0.000 | 0.002 | |
| mergeXIC | 0.002 | 0.000 | 0.003 | |
| mstAlignRuns | 2.523 | 0.107 | 2.638 | |
| mstScript1 | 0.510 | 0.296 | 0.576 | |
| mstScript2 | 3.153 | 0.645 | 3.503 | |
| nrDesc | 0.001 | 0.000 | 0.000 | |
| otherChildXICpp | 0.006 | 0.004 | 0.010 | |
| paramsDIAlignR | 0.000 | 0.000 | 0.001 | |
| perBatch | 0.001 | 0.000 | 0.001 | |
| pickNearestFeature | 0.003 | 0.000 | 0.003 | |
| plotAlignedAnalytes | 0.748 | 0.036 | 0.785 | |
| plotAlignmentPath | 0.449 | 0.032 | 0.481 | |
| plotAnalyteXICs | 0.550 | 0.016 | 0.567 | |
| plotXICgroup | 0.456 | 0.010 | 0.468 | |
| populateReferenceExperimentFeatureAlignmentMap | 0.009 | 0.004 | 0.012 | |
| progAlignRuns | 0.001 | 0.001 | 0.001 | |
| readMzMLHeader | 0.000 | 0.001 | 0.001 | |
| readSqMassHeader | 0.000 | 0.001 | 0.001 | |
| recalculateIntensity | 0.333 | 0.008 | 0.341 | |
| reduceXICs | 0.105 | 0.000 | 0.105 | |
| script1 | 0.775 | 1.027 | 1.012 | |
| script2 | 3.398 | 1.641 | 3.924 | |
| setAlignmentRank | 0.013 | 0.000 | 0.013 | |
| sgolayCpp | 0.003 | 0.000 | 0.003 | |
| sgolayFill | 0.002 | 0.000 | 0.002 | |
| smoothSingleXIC | 0.002 | 0.000 | 0.002 | |
| smoothXICs | 0.009 | 0.000 | 0.009 | |
| splineFill | 0.001 | 0.000 | 0.001 | |
| splineFillCpp | 0.000 | 0.004 | 0.004 | |
| traverseDown | 2.102 | 0.123 | 2.229 | |
| traverseMST | 0.001 | 0.000 | 0.000 | |
| traverseUp | 2.261 | 0.088 | 2.353 | |
| trfrParentFeature | 0.051 | 0.000 | 0.051 | |
| trimXICs | 0.002 | 0.000 | 0.002 | |
| uncompressVec | 0.007 | 0.000 | 0.007 | |
| updateFileInfo | 0.009 | 0.004 | 0.013 | |
| writeOutFeatureAlignmentMap | 0.001 | 0.004 | 0.005 | |
| writeTables | 0.002 | 0.000 | 0.003 | |