| Back to Build/check report for BioC 3.17: simplified long |
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This page was generated on 2023-03-27 05:50:33 -0000 (Mon, 27 Mar 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| kunpeng1 | Linux (Ubuntu 22.04.1 LTS) | aarch64 | R Under development (unstable) (2023-03-12 r83975) -- "Unsuffered Consequences" | 6083 |
| 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: - Please 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 How and When does the builder pull? When will my changes propagate? for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 538/2195 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| DIAlignR 2.7.0 (landing page) Shubham Gupta
| kunpeng1 | Linux (Ubuntu 22.04.1 LTS) / aarch64 | OK | OK | ERROR | |||||||||
| Package: DIAlignR |
| Version: 2.7.0 |
| Command: /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:DIAlignR.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/site-library --timings DIAlignR_2.7.0.tar.gz |
| StartedAt: 2023-03-25 01:12:58 -0000 (Sat, 25 Mar 2023) |
| EndedAt: 2023-03-25 01:17:10 -0000 (Sat, 25 Mar 2023) |
| EllapsedTime: 251.9 seconds |
| RetCode: 1 |
| Status: ERROR |
| CheckDir: DIAlignR.Rcheck |
| Warnings: NA |
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### Running command:
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### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:DIAlignR.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/site-library --timings DIAlignR_2.7.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/DIAlignR.Rcheck’
* using R Under development (unstable) (2023-03-12 r83975)
* 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 ‘2.7.0’
* 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) 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 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/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/site-library/DIAlignR/libs/DIAlignR.so’:
Found ‘_ZSt4cout’, possibly from ‘std::cout’ (C++)
Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs nor [v]sprintf. The detected symbols are linked into
the code but might come from libraries and not actually be called.
See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
alignTargetedRuns 9.550 10.918 6.676
script2 3.566 1.452 3.943
* 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-3.17-bioc/meat/DIAlignR.Rcheck/00check.log’
for details.
DIAlignR.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL DIAlignR ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/site-library’ * installing *source* package ‘DIAlignR’ ... ** using staged installation ** libs using C++ compiler: ‘g++ (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0’ using C++14 g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/library/RcppEigen/include' -I/usr/local/include -fPIC -g -O2 -c ChromatogramPeak.cpp -o ChromatogramPeak.o g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/library/RcppEigen/include' -I/usr/local/include -fPIC -g -O2 -c DPosition.cpp -o DPosition.o g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/library/RcppEigen/include' -I/usr/local/include -fPIC -g -O2 -c MSChromatogram.cpp -o MSChromatogram.o g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/library/RcppEigen/include' -I/usr/local/include -fPIC -g -O2 -c PeakIntegrator.cpp -o PeakIntegrator.o g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/library/RcppEigen/include' -I/usr/local/include -fPIC -g -O2 -c RcppExports.cpp -o RcppExports.o g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/library/RcppEigen/include' -I/usr/local/include -fPIC -g -O2 -c Rmain.cpp -o Rmain.o g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/library/RcppEigen/include' -I/usr/local/include -fPIC -g -O2 -c SavitzkyGolayFilter.cpp -o SavitzkyGolayFilter.o g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/library/RcppEigen/include' -I/usr/local/include -fPIC -g -O2 -c affinealignment.cpp -o affinealignment.o g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/library/RcppEigen/include' -I/usr/local/include -fPIC -g -O2 -c affinealignobj.cpp -o affinealignobj.o g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/library/RcppEigen/include' -I/usr/local/include -fPIC -g -O2 -c alignment.cpp -o alignment.o g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/library/RcppEigen/include' -I/usr/local/include -fPIC -g -O2 -c chromSimMatrix.cpp -o chromSimMatrix.o g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/library/RcppEigen/include' -I/usr/local/include -fPIC -g -O2 -c constrainMat.cpp -o constrainMat.o g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/library/RcppEigen/include' -I/usr/local/include -fPIC -g -O2 -c gapPenalty.cpp -o gapPenalty.o g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/library/RcppEigen/include' -I/usr/local/include -fPIC -g -O2 -c integrateArea.cpp -o integrateArea.o g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/library/RcppEigen/include' -I/usr/local/include -fPIC -g -O2 -c interface.cpp -o interface.o g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/library/RcppEigen/include' -I/usr/local/include -fPIC -g -O2 -c miscell.cpp -o miscell.o g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/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/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/library/RcppEigen/include' -I/usr/local/include -fPIC -g -O2 -c simpleFcn.cpp -o simpleFcn.o g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/library/RcppEigen/include' -I/usr/local/include -fPIC -g -O2 -c spline.cpp -o spline.o g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/library/RcppEigen/include' -I/usr/local/include -fPIC -g -O2 -c utils.cpp -o utils.o g++ -std=gnu++14 -shared -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 installing to /home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/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 Under development (unstable) (2023-03-12 r83975) -- "Unsuffered Consequences"
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.
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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 0.0586884 secs
Time difference of 0.3049912 secs
Time difference of 0.1361227 secs
Time difference of 0.06285429 secs
Time difference of 0.01494908 secs
Time difference of 0.2229011 secs
Time difference of 2.030854 secs
Time difference of 0.02846241 secs
Time difference of 0.4822543 secs
[1] "hroest_K120808_Strep10%PlasmaBiolRepl1_R03_SW_filt"
[2] "hroest_K120809_Strep0%PlasmaBiolRepl2_R04_SW_filt"
Time difference of 0.02083325 secs
Time difference of 0.2897623 secs
Time difference of 0.118468 secs
Time difference of 0.05224085 secs
Time difference of 0.007015705 secs
Time difference of 0.08322167 secs
Time difference of 1.165034 secs
Time difference of 0.01000524 secs
Time difference of 1.057202 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 0.02393746 secs
Time difference of 1.443007 secs
Time difference of 2.298246 secs
Time difference of 0.1815765 secs
Time difference of 0.01454496 secs
Time difference of 0.115972 secs
Time difference of 2.004171 secs
Time difference of 0.02903485 secs
Time difference of 0.4987299 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 0.02068949 secs
Time difference of 0.01803589 secs
Time difference of 0.0005056858 secs
Time difference of 0.1183462 secs
Time difference of 0.009506941 secs
Time difference of 0.07188892 secs
Time difference of 0.02049255 secs
Time difference of 0.009535789 secs
Time difference of 0.1256559 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 0.01007056 secs
Time difference of 0.04253983 secs
Time difference of 0.01308537 secs
Time difference of 0.01450086 secs
Time difference of 0.00949645 secs
Time difference of 0.06225228 secs
Time difference of 0.1266921 secs
Time difference of 0.009438515 secs
Time difference of 0.2421265 secs
[1] "chludwig_K150309_004b_SW_1_16" "chludwig_K150309_008_SW_1_4"
[3] "chludwig_K150309_013_SW_0"
Time difference of 0.01153016 secs
Time difference of 0.01240373 secs
Time difference of 0.001239538 secs
Time difference of 0.01758599 secs
Time difference of 0.0141387 secs
Time difference of 0.07544708 secs
Time difference of 0.008173227 secs
Time difference of 0.02306485 secs
Time difference of 0.3522005 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 0.09840345 secs
Time difference of 0.01819062 secs
Time difference of 0.002368927 secs
Time difference of 0.01050687 secs
Time difference of 0.08735228 secs
Time difference of 0.02121878 secs
Time difference of 0.01881742 secs
Time difference of 0.1079977 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 0.02696228 secs
[1] "run0 run1\nrun2 run2"
Time difference of 0.3295693 secs
Time difference of 0.1499569 secs
Time difference of 0.01013064 secs
Time difference of 0.09210944 secs
Time difference of 1.83005 secs
Time difference of 0.01951575 secs
Time difference of 0.443753 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 0.123137 secs
Time difference of 1.146786 secs
Time difference of 6.127575 secs
Time difference of 0.6336706 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 0.1103001 secs
[1] "Written /home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/site-library/DIAlignR/extdata/temp_prog1.RData"
[1] "Written /home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/site-library/DIAlignR/extdata/temp_0_2.rds"
[1] "progTree1 is done."
Time difference of 1.821302 secs
Time difference of 0.4267168 secs
[1] "Written /home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/site-library/DIAlignR/extdata/temp_1_2.rds"
Time difference of 0.799294 secs
[1] "Written /home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/site-library/DIAlignR/extdata/temp_2_2.rds"
Time difference of 0.4078183 secs
Time difference of 0.2708704 secs
[1] "Written /home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/site-library/DIAlignR/extdata/temp_all_2.rds"
Time difference of 0.2421854 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 0.1017854 secs
[1] "Written /home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/site-library/DIAlignR/extdata/temp_prog1.RData"
[1] "Written /home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/site-library/DIAlignR/extdata/temp_0_2.rds"
[1] "progTree1 is done."
Time difference of 1.630733 secs
Time difference of 0.3972216 secs
[1] "Written /home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/site-library/DIAlignR/extdata/temp_1_2.rds"
Time difference of 0.6865704 secs
[1] "Written /home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/site-library/DIAlignR/extdata/temp_2_2.rds"
Time difference of 0.4074678 secs
Time difference of 0.01675177 secs
[1] "Written /home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/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
DIAlignR.Rcheck/DIAlignR-Ex.timings
| name | user | system | elapsed | |
| MSTperBatch | 0.001 | 0.000 | 0.001 | |
| addFlankToLeft | 0.003 | 0.000 | 0.003 | |
| addFlankToRight | 0.002 | 0.000 | 0.001 | |
| addXIC | 0 | 0 | 0 | |
| alignChromatogramsCpp | 0.014 | 0.016 | 0.030 | |
| alignTargetedRuns | 9.550 | 10.918 | 6.676 | |
| alignToMaster | 2.462 | 0.171 | 2.633 | |
| alignToRef | 0.001 | 0.000 | 0.001 | |
| alignToRefMST | 0.001 | 0.000 | 0.001 | |
| alignedXIC | 0.088 | 0.007 | 0.095 | |
| analytesFromFeatures | 0.041 | 0.005 | 0.045 | |
| approxFill | 0.000 | 0.000 | 0.001 | |
| areaIntegrator | 0.003 | 0.000 | 0.003 | |
| blobXICs | 0.002 | 0.000 | 0.002 | |
| calculateIntensity | 0.000 | 0.003 | 0.002 | |
| checkOverlap | 0 | 0 | 0 | |
| checkParams | 0 | 0 | 0 | |
| childXIC | 0.088 | 0.007 | 0.095 | |
| childXICs | 0.608 | 0.004 | 0.612 | |
| constrainSimCpp | 0.000 | 0.001 | 0.001 | |
| createMZML | 0.002 | 0.001 | 0.003 | |
| createSqMass | 0.001 | 0.001 | 0.002 | |
| dialignrLoess | 0.000 | 0.001 | 0.001 | |
| doAffineAlignmentCpp | 0.000 | 0.001 | 0.001 | |
| doAlignmentCpp | 0.001 | 0.000 | 0.001 | |
| extractXIC_group | 0.903 | 0.013 | 0.925 | |
| extractXIC_group2 | 0.001 | 0.000 | 0.001 | |
| fetchAnalytesInfo | 0.01 | 0.00 | 0.01 | |
| fetchFeaturesFromRun | 0.009 | 0.000 | 0.009 | |
| fetchPeptidesInfo | 0.009 | 0.000 | 0.008 | |
| fetchPeptidesInfo2 | 0.008 | 0.000 | 0.008 | |
| fetchPrecursorsInfo | 0.001 | 0.000 | 0.001 | |
| fetchTransitionsFromRun | 0.008 | 0.000 | 0.008 | |
| filenamesFromMZML | 0.001 | 0.000 | 0.001 | |
| filenamesFromOSW | 0.001 | 0.000 | 0.001 | |
| getAlignObj | 0.024 | 0.000 | 0.024 | |
| getAlignObjs | 1.327 | 0.023 | 1.350 | |
| getAlignedFigs | 0.170 | 0.000 | 0.169 | |
| getAlignedIndices | 0.010 | 0.000 | 0.011 | |
| getAlignedTimes | 0.019 | 0.004 | 0.023 | |
| getAlignedTimesCpp | 0.005 | 0.004 | 0.008 | |
| getAlignedTimesFast | 0.018 | 0.000 | 0.017 | |
| getBaseGapPenaltyCpp | 0.001 | 0.000 | 0.000 | |
| getChildFeature | 0.047 | 0.000 | 0.046 | |
| getChildXICpp | 0.009 | 0.000 | 0.009 | |
| getChildXICs | 0.800 | 0.020 | 0.821 | |
| getChromSimMatCpp | 0.003 | 0.000 | 0.003 | |
| getChromatogramIndices | 0.137 | 0.000 | 0.137 | |
| getFeatures | 0.044 | 0.000 | 0.044 | |
| getGlobalAlignMaskCpp | 0.001 | 0.000 | 0.001 | |
| getGlobalAlignment | 0.008 | 0.000 | 0.008 | |
| getGlobalFits | 0.432 | 0.007 | 0.438 | |
| getLOESSfit | 0.004 | 0.000 | 0.003 | |
| getLinearfit | 0.004 | 0.000 | 0.003 | |
| getMST | 0.001 | 0.000 | 0.000 | |
| getMZMLpointers | 0.019 | 0.000 | 0.019 | |
| getMappedRT | 0.005 | 0.008 | 0.012 | |
| getMultipeptide | 1.851 | 0.028 | 1.879 | |
| getNativeIDs | 0.018 | 0.003 | 0.021 | |
| getNodeIDs | 0 | 0 | 0 | |
| getNodeRun | 0.568 | 0.008 | 0.577 | |
| getOswAnalytes | 0.009 | 0.000 | 0.009 | |
| getOswFiles | 0.009 | 0.000 | 0.009 | |
| getPeptideScores | 0.04 | 0.00 | 0.04 | |
| getPrecursorByID | 0.017 | 0.000 | 0.017 | |
| getPrecursorIndices | 0.054 | 0.000 | 0.053 | |
| getPrecursors | 0.023 | 0.004 | 0.027 | |
| getRSE | 0.003 | 0.000 | 0.003 | |
| getRTdf | 0.007 | 0.000 | 0.007 | |
| getRefExpFeatureMap | 0.357 | 0.004 | 0.361 | |
| getRefRun | 0.486 | 0.003 | 0.488 | |
| getRunNames | 0.011 | 0.000 | 0.011 | |
| getSeqSimMatCpp | 0.001 | 0.000 | 0.001 | |
| getTransitions | 0.491 | 0.012 | 0.501 | |
| getTree | 0.031 | 0.000 | 0.031 | |
| getXICs | 0.11 | 0.00 | 0.11 | |
| getXICs4AlignObj | 0.077 | 0.000 | 0.077 | |
| get_ropenms | 0 | 0 | 0 | |
| imputeChromatogram | 0.015 | 0.000 | 0.015 | |
| ipfReassignFDR | 0 | 0 | 0 | |
| mapIdxToTime | 0.001 | 0.000 | 0.000 | |
| mappedRTfromAlignObj | 0.003 | 0.000 | 0.003 | |
| mergeXIC | 0.003 | 0.000 | 0.003 | |
| mstAlignRuns | 2.485 | 0.043 | 2.528 | |
| mstScript1 | 0.521 | 0.257 | 0.539 | |
| mstScript2 | 3.159 | 0.585 | 3.439 | |
| nrDesc | 0.001 | 0.000 | 0.001 | |
| otherChildXICpp | 0.01 | 0.00 | 0.01 | |
| paramsDIAlignR | 0.001 | 0.000 | 0.000 | |
| perBatch | 0.001 | 0.000 | 0.002 | |
| pickNearestFeature | 0.003 | 0.000 | 0.004 | |
| plotAlignedAnalytes | 0.684 | 0.016 | 0.699 | |
| plotAlignmentPath | 0.440 | 0.028 | 0.468 | |
| plotAnalyteXICs | 0.488 | 0.000 | 0.488 | |
| plotXICgroup | 0.447 | 0.004 | 0.451 | |
| populateReferenceExperimentFeatureAlignmentMap | 0.009 | 0.004 | 0.013 | |
| progAlignRuns | 0.000 | 0.001 | 0.001 | |
| readMzMLHeader | 0.000 | 0.001 | 0.002 | |
| readSqMassHeader | 0.001 | 0.000 | 0.001 | |
| recalculateIntensity | 0.303 | 0.000 | 0.303 | |
| reduceXICs | 0.089 | 0.003 | 0.092 | |
| script1 | 0.808 | 0.867 | 0.953 | |
| script2 | 3.566 | 1.452 | 3.943 | |
| setAlignmentRank | 0.013 | 0.000 | 0.012 | |
| sgolayCpp | 0.003 | 0.000 | 0.003 | |
| sgolayFill | 0.001 | 0.000 | 0.001 | |
| smoothSingleXIC | 0.002 | 0.000 | 0.002 | |
| smoothXICs | 0.008 | 0.000 | 0.008 | |
| splineFill | 0.000 | 0.000 | 0.001 | |
| splineFillCpp | 0.000 | 0.003 | 0.004 | |
| traverseDown | 1.951 | 0.008 | 1.959 | |
| traverseMST | 0.001 | 0.000 | 0.000 | |
| traverseUp | 1.951 | 0.016 | 1.967 | |
| trfrParentFeature | 0.044 | 0.004 | 0.048 | |
| trimXICs | 0.002 | 0.000 | 0.002 | |
| uncompressVec | 0.006 | 0.000 | 0.005 | |
| updateFileInfo | 0.01 | 0.00 | 0.01 | |
| writeOutFeatureAlignmentMap | 0.005 | 0.000 | 0.004 | |
| writeTables | 0.000 | 0.003 | 0.003 | |