| Back to Build/check report for BioC 3.18: simplified long |
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This page was generated on 2023-05-10 10:04:29 -0000 (Wed, 10 May 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" | 6211 |
| 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 539/2194 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| DIAlignR 2.9.0 (landing page) Shubham Gupta
| kunpeng1 | Linux (Ubuntu 22.04.1 LTS) / aarch64 | OK | OK | ERROR | |||||||||
| Package: DIAlignR |
| Version: 2.9.0 |
| 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_2.9.0.tar.gz |
| StartedAt: 2023-05-09 14:27:42 -0000 (Tue, 09 May 2023) |
| EndedAt: 2023-05-09 14:31:42 -0000 (Tue, 09 May 2023) |
| EllapsedTime: 240.3 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_2.9.0.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 ‘2.9.0’
* 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) 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 9.813 11.411 6.862
* 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.
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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 0.05228877 secs
Time difference of 0.287807 secs
Time difference of 0.1291769 secs
Time difference of 0.02778602 secs
Time difference of 0.01011252 secs
Time difference of 0.1949153 secs
Time difference of 1.945696 secs
Time difference of 0.02947593 secs
Time difference of 0.4728012 secs
[1] "hroest_K120808_Strep10%PlasmaBiolRepl1_R03_SW_filt"
[2] "hroest_K120809_Strep0%PlasmaBiolRepl2_R04_SW_filt"
Time difference of 0.01787806 secs
Time difference of 0.2804036 secs
Time difference of 0.1127641 secs
Time difference of 0.01820803 secs
Time difference of 0.006877661 secs
Time difference of 0.07909274 secs
Time difference of 1.157445 secs
Time difference of 0.01010108 secs
Time difference of 1.060521 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 0.0173943 secs
Time difference of 0.3071113 secs
Time difference of 0.1211567 secs
Time difference of 0.1136861 secs
Time difference of 0.009602785 secs
Time difference of 0.093081 secs
Time difference of 1.6973 secs
Time difference of 0.0246439 secs
Time difference of 0.4113183 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 0.01838756 secs
Time difference of 0.01715374 secs
Time difference of 0.0004887581 secs
Time difference of 0.1127634 secs
Time difference of 0.009595156 secs
Time difference of 0.07048917 secs
Time difference of 0.02084851 secs
Time difference of 0.009616852 secs
Time difference of 0.1090753 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 0.009580135 secs
Time difference of 0.04164934 secs
Time difference of 0.01147938 secs
Time difference of 0.01554799 secs
Time difference of 0.009426355 secs
Time difference of 0.05908036 secs
Time difference of 0.1285551 secs
Time difference of 0.01010227 secs
Time difference of 0.2551746 secs
[1] "chludwig_K150309_004b_SW_1_16" "chludwig_K150309_008_SW_1_4"
[3] "chludwig_K150309_013_SW_0"
Time difference of 0.01233745 secs
Time difference of 0.01277328 secs
Time difference of 0.001240969 secs
Time difference of 0.01872706 secs
Time difference of 0.01415253 secs
Time difference of 0.07933211 secs
Time difference of 0.007964373 secs
Time difference of 0.02509236 secs
Time difference of 0.3493741 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 0.1009629 secs
Time difference of 0.01885653 secs
Time difference of 0.002526999 secs
Time difference of 0.01147604 secs
Time difference of 0.09440446 secs
Time difference of 0.02237988 secs
Time difference of 0.01968408 secs
Time difference of 0.1145825 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 0.02814794 secs
[1] "run0 run1\nrun2 run2"
Time difference of 0.3439527 secs
Time difference of 0.1567891 secs
Time difference of 0.01170397 secs
Time difference of 0.1009934 secs
Time difference of 1.87727 secs
Time difference of 0.0201385 secs
Time difference of 0.4603295 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 0.1208906 secs
Time difference of 1.079849 secs
Time difference of 6.590003 secs
Time difference of 0.5869398 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 0.1006694 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 1.831824 secs
Time difference of 0.4370224 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 0.7437248 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 0.388478 secs
Time difference of 0.2486978 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 0.2324629 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 0.1045535 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 1.50691 secs
Time difference of 0.3720238 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 0.6351318 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 0.3805513 secs
Time difference of 0.01646662 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 | 0.002 | 0.000 | 0.002 | |
| addFlankToLeft | 0.003 | 0.000 | 0.003 | |
| addFlankToRight | 0.001 | 0.000 | 0.001 | |
| addXIC | 0 | 0 | 0 | |
| alignChromatogramsCpp | 0.020 | 0.012 | 0.034 | |
| alignTargetedRuns | 9.813 | 11.411 | 6.862 | |
| alignToMaster | 2.414 | 0.154 | 2.567 | |
| alignToRef | 0.002 | 0.000 | 0.001 | |
| alignToRefMST | 0.000 | 0.001 | 0.001 | |
| alignedXIC | 0.096 | 0.002 | 0.097 | |
| analytesFromFeatures | 0.046 | 0.000 | 0.046 | |
| approxFill | 0.001 | 0.000 | 0.000 | |
| areaIntegrator | 0.004 | 0.000 | 0.004 | |
| blobXICs | 0.000 | 0.002 | 0.003 | |
| calculateIntensity | 0.002 | 0.001 | 0.003 | |
| checkOverlap | 0.001 | 0.000 | 0.000 | |
| checkParams | 0 | 0 | 0 | |
| childXIC | 0.096 | 0.000 | 0.097 | |
| childXICs | 0.652 | 0.004 | 0.656 | |
| constrainSimCpp | 0 | 0 | 0 | |
| createMZML | 0.004 | 0.000 | 0.004 | |
| createSqMass | 0.003 | 0.000 | 0.002 | |
| dialignrLoess | 0.001 | 0.000 | 0.000 | |
| doAffineAlignmentCpp | 0.001 | 0.000 | 0.001 | |
| doAlignmentCpp | 0.001 | 0.000 | 0.002 | |
| extractXIC_group | 0.945 | 0.000 | 0.959 | |
| extractXIC_group2 | 0.002 | 0.000 | 0.001 | |
| fetchAnalytesInfo | 0.01 | 0.00 | 0.01 | |
| fetchFeaturesFromRun | 0.006 | 0.003 | 0.008 | |
| fetchPeptidesInfo | 0.009 | 0.001 | 0.009 | |
| fetchPeptidesInfo2 | 0.009 | 0.000 | 0.008 | |
| fetchPrecursorsInfo | 0.001 | 0.000 | 0.002 | |
| fetchTransitionsFromRun | 0.009 | 0.000 | 0.009 | |
| filenamesFromMZML | 0.002 | 0.000 | 0.001 | |
| filenamesFromOSW | 0.002 | 0.000 | 0.001 | |
| getAlignObj | 0.026 | 0.000 | 0.025 | |
| getAlignObjs | 1.391 | 0.016 | 1.407 | |
| getAlignedFigs | 0.154 | 0.003 | 0.158 | |
| getAlignedIndices | 0.011 | 0.000 | 0.011 | |
| getAlignedTimes | 0.023 | 0.000 | 0.023 | |
| getAlignedTimesCpp | 0.005 | 0.004 | 0.009 | |
| getAlignedTimesFast | 0.018 | 0.000 | 0.019 | |
| getBaseGapPenaltyCpp | 0 | 0 | 0 | |
| getChildFeature | 0.048 | 0.000 | 0.048 | |
| getChildXICpp | 0.009 | 0.000 | 0.009 | |
| getChildXICs | 0.833 | 0.008 | 0.841 | |
| getChromSimMatCpp | 0.002 | 0.000 | 0.003 | |
| getChromatogramIndices | 0.141 | 0.000 | 0.140 | |
| getFeatures | 0.047 | 0.000 | 0.047 | |
| getGlobalAlignMaskCpp | 0.001 | 0.000 | 0.001 | |
| getGlobalAlignment | 0.008 | 0.000 | 0.009 | |
| getGlobalFits | 0.441 | 0.000 | 0.441 | |
| getLOESSfit | 0.004 | 0.000 | 0.004 | |
| getLinearfit | 0.006 | 0.003 | 0.008 | |
| getMST | 0.000 | 0.000 | 0.001 | |
| getMZMLpointers | 0.007 | 0.016 | 0.023 | |
| getMappedRT | 0.015 | 0.000 | 0.014 | |
| getMultipeptide | 1.891 | 0.028 | 1.919 | |
| getNativeIDs | 0.021 | 0.000 | 0.022 | |
| getNodeIDs | 0.000 | 0.000 | 0.001 | |
| getNodeRun | 0.584 | 0.009 | 0.592 | |
| getOswAnalytes | 0.010 | 0.000 | 0.009 | |
| getOswFiles | 0.006 | 0.003 | 0.010 | |
| getPeptideScores | 0.042 | 0.000 | 0.042 | |
| getPrecursorByID | 0.015 | 0.004 | 0.018 | |
| getPrecursorIndices | 0.056 | 0.004 | 0.060 | |
| getPrecursors | 0.025 | 0.004 | 0.028 | |
| getRSE | 0.003 | 0.000 | 0.004 | |
| getRTdf | 0.008 | 0.000 | 0.008 | |
| getRefExpFeatureMap | 0.411 | 0.008 | 0.419 | |
| getRefRun | 0.479 | 0.004 | 0.483 | |
| getRunNames | 0.012 | 0.000 | 0.012 | |
| getSeqSimMatCpp | 0.000 | 0.000 | 0.001 | |
| getTransitions | 0.153 | 0.009 | 0.159 | |
| getTree | 0.034 | 0.000 | 0.034 | |
| getXICs | 0.111 | 0.003 | 0.114 | |
| getXICs4AlignObj | 0.079 | 0.005 | 0.084 | |
| get_ropenms | 0 | 0 | 0 | |
| imputeChromatogram | 0.016 | 0.000 | 0.016 | |
| ipfReassignFDR | 0.001 | 0.000 | 0.001 | |
| mapIdxToTime | 0.001 | 0.000 | 0.001 | |
| mappedRTfromAlignObj | 0.004 | 0.000 | 0.004 | |
| mergeXIC | 0.003 | 0.000 | 0.004 | |
| mstAlignRuns | 3.032 | 0.072 | 3.104 | |
| mstScript1 | 0.530 | 0.261 | 0.553 | |
| mstScript2 | 2.994 | 0.641 | 3.325 | |
| nrDesc | 0.000 | 0.000 | 0.001 | |
| otherChildXICpp | 0.006 | 0.004 | 0.010 | |
| paramsDIAlignR | 0 | 0 | 0 | |
| perBatch | 0.002 | 0.000 | 0.002 | |
| pickNearestFeature | 0.004 | 0.000 | 0.004 | |
| plotAlignedAnalytes | 0.716 | 0.020 | 0.736 | |
| plotAlignmentPath | 0.467 | 0.012 | 0.479 | |
| plotAnalyteXICs | 0.505 | 0.007 | 0.512 | |
| plotXICgroup | 0.472 | 0.020 | 0.492 | |
| populateReferenceExperimentFeatureAlignmentMap | 0.013 | 0.000 | 0.014 | |
| progAlignRuns | 0.002 | 0.000 | 0.001 | |
| readMzMLHeader | 0.002 | 0.000 | 0.001 | |
| readSqMassHeader | 0.001 | 0.000 | 0.002 | |
| recalculateIntensity | 0.315 | 0.008 | 0.324 | |
| reduceXICs | 0.085 | 0.008 | 0.092 | |
| script1 | 0.792 | 1.004 | 1.002 | |
| script2 | 3.364 | 1.401 | 3.647 | |
| setAlignmentRank | 0.011 | 0.004 | 0.014 | |
| sgolayCpp | 0.004 | 0.000 | 0.003 | |
| sgolayFill | 0.001 | 0.000 | 0.001 | |
| smoothSingleXIC | 0.002 | 0.000 | 0.002 | |
| smoothXICs | 0.002 | 0.007 | 0.010 | |
| splineFill | 0.001 | 0.000 | 0.001 | |
| splineFillCpp | 0.004 | 0.000 | 0.004 | |
| traverseDown | 2.086 | 0.040 | 2.126 | |
| traverseMST | 0 | 0 | 0 | |
| traverseUp | 2.351 | 0.176 | 2.527 | |
| trfrParentFeature | 0.050 | 0.000 | 0.049 | |
| trimXICs | 0.003 | 0.000 | 0.002 | |
| uncompressVec | 0.007 | 0.000 | 0.006 | |
| updateFileInfo | 0.011 | 0.000 | 0.011 | |
| writeOutFeatureAlignmentMap | 0.005 | 0.000 | 0.005 | |
| writeTables | 0.004 | 0.000 | 0.003 | |