Back to Multiple platform build/check report for BioC 3.19: simplified long |
|
This page was generated on 2024-07-24 09:05 -0400 (Wed, 24 Jul 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4747 |
palomino7 | Windows Server 2022 Datacenter | x64 | 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" | 4489 |
merida1 | macOS 12.7.5 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4518 |
kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4467 |
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 |
Package 567/2300 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
DIAlignR 2.12.0 (landing page) Shubham Gupta
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | ![]() | ||||||||
palomino7 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | ![]() | ||||||||
merida1 | macOS 12.7.5 Monterey / x86_64 | OK | OK | OK | OK | ![]() | ||||||||
kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | OK | ERROR | OK | |||||||||
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. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
Package: DIAlignR |
Version: 2.12.0 |
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:DIAlignR.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings DIAlignR_2.12.0.tar.gz |
StartedAt: 2024-07-22 03:57:55 -0400 (Mon, 22 Jul 2024) |
EndedAt: 2024-07-22 04:05:36 -0400 (Mon, 22 Jul 2024) |
EllapsedTime: 461.0 seconds |
RetCode: 0 |
Status: OK |
CheckDir: DIAlignR.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:DIAlignR.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings DIAlignR_2.12.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.19-bioc/meat/DIAlignR.Rcheck’ * using R version 4.4.1 (2024-06-14) * using platform: x86_64-apple-darwin20 * R was compiled by Apple clang version 14.0.0 (clang-1400.0.29.202) GNU Fortran (GCC) 12.2.0 * running under: macOS Monterey 12.7.5 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘DIAlignR/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘DIAlignR’ version ‘2.12.0’ * 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: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’ * used SDK: ‘MacOSX11.3.sdk’ * checking C++ specification ... NOTE Specified C++14: please drop specification unless essential * checking installed package size ... NOTE installed size is 11.5Mb sub-directories of 1Mb or more: extdata 4.0Mb metabo 4.1Mb ptms 1.5Mb * checking package directory ... OK * checking DESCRIPTION meta-information ... OK * checking top-level files ... OK * checking for left-over files ... OK * checking index information ... OK * checking package subdirectories ... OK * checking code files for non-ASCII characters ... OK * checking R files for syntax errors ... OK * checking whether the package can be loaded ... OK * checking whether the package can be loaded with stated dependencies ... OK * checking whether the package can be unloaded cleanly ... OK * checking whether the namespace can be loaded with stated dependencies ... OK * checking whether the namespace can be unloaded cleanly ... OK * checking dependencies in R code ... OK * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... NOTE alignTargetedRuns: no visible binding for global variable ‘peptide_id’ alignTargetedRuns : <anonymous>: no visible global function definition for ‘.’ alignTargetedRuns: no visible binding for global variable ‘intensity’ alignToRoot4: no visible binding for global variable ‘trees’ alignToRoot4: no visible binding for global variable ‘precursors’ alignToRoot4: no visible binding for global variable ‘intensity’ childXICs: possible error in cummax(v = cummax(ifelse(is.na(x), -Inf, x))): unused argument (v = cummax(ifelse(is.na(x), -Inf, x))) distMat.rSqrd : <anonymous> : <anonymous>: no visible binding for global variable ‘RT.ref’ distMat.rSqrd : <anonymous> : <anonymous>: no visible binding for global variable ‘RT.eXp’ fetchPrecursorsInfo: no visible binding for global variable ‘transition_id’ fetchPrecursorsInfo: no visible global function definition for ‘.’ fetchPrecursorsInfo: no visible binding for global variable ‘transition_group_id’ fetchTransitionsFromRun: no visible binding for global variable ‘intensity’ fetchTransitionsFromRun: no visible global function definition for ‘.’ fetchTransitionsFromRun: no visible binding for global variable ‘transition_group_id’ fetchTransitionsFromRun: no visible binding for global variable ‘peak_group_rank’ fetchTransitionsFromRun: no visible global function definition for ‘head’ getNativeIDs: no visible binding for global variable ‘peptide_id’ getPeptideScores: no visible binding for global variable ‘col2’ getPeptideScores: no visible binding for global variable ‘run’ getQuery: no visible binding for global variable ‘identifying.transitionPEPfilter’ getRTdf: no visible binding for global variable ‘peak_group_rank’ getRTdf: no visible binding for global variable ‘m_score’ getRTdf: no visible global function definition for ‘.’ getRTdf: no visible binding for global variable ‘transition_group_id’ getRTdf: no visible binding for global variable ‘RT’ getRefRun : <anonymous>: no visible binding for global variable ‘pvalue’ ipfReassignFDR: no visible binding for global variable ‘ref_run’ ipfReassignFDR: no visible binding for global variable ‘run’ ipfReassignFDR: no visible global function definition for ‘.’ ipfReassignFDR: no visible binding for global variable ‘i.to’ ipfReassignFDR: no visible binding for global variable ‘m_score_new’ ipfReassignFDR: no visible binding for global variable ‘ms2_m_score’ ipfReassignFDR: no visible binding for global variable ‘m_score’ mstAlignRuns: no visible binding for global variable ‘ropenms’ mstAlignRuns: no visible binding for global variable ‘peptide_id’ mstAlignRuns : <anonymous>: no visible global function definition for ‘.’ mstAlignRuns: no visible binding for global variable ‘intensity’ mstScript1: no visible binding for global variable ‘ropenms’ mstScript2: no visible binding for global variable ‘fileInfo’ mstScript2: no visible binding for global variable ‘peptide_id’ mstScript2: no visible binding for global variable ‘features’ mstScript2 : <anonymous>: no visible global function definition for ‘.’ mstScript2 : <anonymous>: no visible binding for global variable ‘features’ mstScript2: no visible binding for global variable ‘intensity’ populateReferenceExperimentFeatureAlignmentMap: no visible binding for global variable ‘run’ populateReferenceExperimentFeatureAlignmentMap: no visible binding for global variable ‘transition_group_id’ populateReferenceExperimentFeatureAlignmentMap: no visible binding for global variable ‘feature_id’ progAlignRuns: no visible binding for global variable ‘peptide_id’ progAlignRuns : <anonymous>: no visible global function definition for ‘.’ progAlignRuns: no visible binding for global variable ‘intensity’ progComb3: no visible binding for global variable ‘precursors’ progComb3: no visible binding for global variable ‘ropenms’ progSplit2: no visible binding for global variable ‘trees’ progSplit2: no visible binding for global variable ‘scoreFile’ progSplit2: no visible binding for global variable ‘precursors’ progSplit2 : <anonymous>: no visible global function definition for ‘.’ progSplit2: no visible binding for global variable ‘ropenms’ progSplit4: no visible binding for global variable ‘precursors’ progSplit4 : <anonymous>: no visible global function definition for ‘.’ progSplit4: no visible binding for global variable ‘intensity’ progTree1: no visible binding for global variable ‘ropenms’ progTree1: no visible binding for global variable ‘peptide_id’ reIntensity: no visible binding for global variable ‘run’ reIntensity: no visible binding for global variable ‘alignment_rank’ recalculateIntensity: no visible binding for global variable ‘peptide_id’ recalculateIntensity: no visible binding for global variable ‘chromatogramIndex’ script2: no visible binding for global variable ‘fileInfo’ script2: no visible binding for global variable ‘peptide_id’ script2 : <anonymous>: no visible global function definition for ‘.’ script2: no visible binding for global variable ‘features’ script2: no visible binding for global variable ‘globalFits’ script2: no visible binding for global variable ‘RSE’ script2: no visible binding for global variable ‘intensity’ setRootRank : <anonymous>: no visible global function definition for ‘.’ writeOutFeatureAlignmentMap: no visible binding for global variable ‘reference_feature_id’ writeOutFeatureAlignmentMap: no visible binding for global variable ‘experiment_feature_id’ writeOutFeatureAlignmentMap: no visible binding for global variable ‘ALIGNMENT_GROUP_ID’ writeOutFeatureAlignmentMap: no visible binding for global variable ‘REFERENCE’ writeOutFeatureAlignmentMap: no visible global function definition for ‘.’ writeOutFeatureAlignmentMap: no visible binding for global variable ‘i.to’ writeTables: no visible binding for global variable ‘peptide_id’ writeTables: no visible binding for global variable ‘run’ writeTables: no visible binding for global variable ‘precursor’ Undefined global functions or variables: . ALIGNMENT_GROUP_ID REFERENCE RSE RT RT.eXp RT.ref alignment_rank chromatogramIndex col2 experiment_feature_id feature_id features fileInfo globalFits head i.to identifying.transitionPEPfilter intensity m_score m_score_new ms2_m_score peak_group_rank peptide_id precursor precursors pvalue ref_run reference_feature_id ropenms run scoreFile transition_group_id transition_id trees Consider adding importFrom("datasets", "trees") importFrom("utils", "head") to your NAMESPACE file. * checking Rd files ... OK * checking Rd metadata ... OK * checking Rd cross-references ... OK * checking for missing documentation entries ... OK * checking for code/documentation mismatches ... OK * checking Rd \usage sections ... NOTE Documented arguments not in \usage in Rd file 'alignToRef.Rd': ‘feature_alignment_mapping’ Documented arguments not in \usage in Rd file 'blobXICs.Rd': ‘nativeId’ Documented arguments not in \usage in Rd file 'extractXIC_group2.Rd': ‘mz’ Documented arguments not in \usage in Rd file 'getOswAnalytes.Rd': ‘dataPath’ ‘filenames’ Documented arguments not in \usage in Rd file 'getOswFiles.Rd': ‘dataPath’ ‘filenames’ Documented arguments not in \usage in Rd file 'perBatch.Rd': ‘rownum’ Documented arguments not in \usage in Rd file 'readSqMassHeader.Rd': ‘mzmlName’ Documented arguments not in \usage in Rd file 'setAlignmentRank.Rd': ‘XICs.eXp’ Documented arguments not in \usage in Rd file 'traverseDown.Rd': ‘analytes’ Documented arguments not in \usage in Rd file 'writeTables.Rd': ‘filename’ Functions with \usage entries need to have the appropriate \alias entries, and all their arguments documented. The \usage entries must correspond to syntactically valid R code. See chapter ‘Writing R documentation files’ in the ‘Writing R Extensions’ manual. * checking Rd contents ... OK * checking for unstated dependencies in examples ... OK * checking contents of ‘data’ directory ... OK * checking data for non-ASCII characters ... OK * checking data for ASCII and uncompressed saves ... OK * checking line endings in C/C++/Fortran sources/headers ... OK * checking compiled code ... NOTE Note: information on .o files is not available File ‘/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/DIAlignR/libs/DIAlignR.so’: Found ‘__ZNSt3__14coutE’, 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 21.226 22.499 16.489 script2 5.530 1.979 7.431 mstScript2 4.895 0.866 6.653 mstAlignRuns 4.017 0.123 5.216 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘testthat.R’ OK * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking running R code from vignettes ... SKIPPED * checking re-building of vignette outputs ... SKIPPED * checking PDF version of manual ... OK * DONE Status: 5 NOTEs See ‘/Users/biocbuild/bbs-3.19-bioc/meat/DIAlignR.Rcheck/00check.log’ for details.
DIAlignR.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL DIAlignR ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library’ * installing *source* package ‘DIAlignR’ ... ** using staged installation ** libs using C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’ using C++14 using SDK: ‘MacOSX11.3.sdk’ clang++ -arch x86_64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppEigen/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c ChromatogramPeak.cpp -o ChromatogramPeak.o clang++ -arch x86_64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppEigen/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c DPosition.cpp -o DPosition.o clang++ -arch x86_64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppEigen/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c MSChromatogram.cpp -o MSChromatogram.o clang++ -arch x86_64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppEigen/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c PeakIntegrator.cpp -o PeakIntegrator.o clang++ -arch x86_64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppEigen/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c RcppExports.cpp -o RcppExports.o clang++ -arch x86_64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppEigen/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c Rmain.cpp -o Rmain.o In file included from Rmain.cpp:19: ./miscell.h:14:19: warning: unused function 'detect_end_na' [-Wunused-function] static bool const detect_end_na(double a, double b); ^ ./miscell.h:16:19: warning: unused function 'detect_start_na' [-Wunused-function] static bool const detect_start_na(double a, double b); ^ ./miscell.h:18:19: warning: unused function 'lessZero' [-Wunused-function] static bool const lessZero(double a); ^ 3 warnings generated. clang++ -arch x86_64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppEigen/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c SavitzkyGolayFilter.cpp -o SavitzkyGolayFilter.o clang++ -arch x86_64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppEigen/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c affinealignment.cpp -o affinealignment.o clang++ -arch x86_64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppEigen/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c affinealignobj.cpp -o affinealignobj.o clang++ -arch x86_64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppEigen/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c alignment.cpp -o alignment.o clang++ -arch x86_64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppEigen/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c chromSimMatrix.cpp -o chromSimMatrix.o clang++ -arch x86_64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppEigen/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c constrainMat.cpp -o constrainMat.o constrainMat.cpp:78:10: warning: unused variable 'mapped' [-Wunused-variable] double mapped = 0.0; ^ 1 warning generated. clang++ -arch x86_64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppEigen/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c gapPenalty.cpp -o gapPenalty.o clang++ -arch x86_64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppEigen/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c integrateArea.cpp -o integrateArea.o clang++ -arch x86_64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppEigen/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c interface.cpp -o interface.o clang++ -arch x86_64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppEigen/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c miscell.cpp -o miscell.o miscell.cpp:53:19: warning: unused function 'lessZero' [-Wunused-function] static bool const lessZero(double a){ ^ 1 warning generated. clang++ -arch x86_64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppEigen/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c run_alignment.cpp -o run_alignment.o clang++ -arch x86_64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppEigen/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c simpleFcn.cpp -o simpleFcn.o clang++ -arch x86_64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppEigen/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c spline.cpp -o spline.o clang++ -arch x86_64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppEigen/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c utils.cpp -o utils.o utils.cpp:48:9: warning: unused variable 'idx' [-Wunused-variable] int idx = n*(1-p); ^ 1 warning generated. clang++ -arch x86_64 -std=gnu++14 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/x86_64/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 -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation installing to /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/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
R version 4.4.1 (2024-06-14) -- "Race for Your Life" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: x86_64-apple-darwin20 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 0.1244118 secs Time difference of 0.601877 secs Time difference of 0.3537869 secs Time difference of 0.06286716 secs Time difference of 0.01689696 secs Time difference of 0.22158 secs Time difference of 3.983427 secs Time difference of 0.06387997 secs Time difference of 0.9463341 secs [1] "hroest_K120808_Strep10%PlasmaBiolRepl1_R03_SW_filt" [2] "hroest_K120809_Strep0%PlasmaBiolRepl2_R04_SW_filt" Time difference of 0.035429 secs Time difference of 0.5126929 secs Time difference of 0.2689261 secs Time difference of 0.04251003 secs Time difference of 0.01161289 secs Time difference of 0.1458011 secs Time difference of 2.349059 secs Time difference of 0.01937008 secs Time difference of 2.112781 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 0.04077601 secs Time difference of 0.588784 secs Time difference of 0.272815 secs Time difference of 0.2228291 secs Time difference of 0.021662 secs Time difference of 0.1759632 secs Time difference of 3.410787 secs Time difference of 0.05147505 secs Time difference of 0.8311629 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 0.04622602 secs Time difference of 0.03318596 secs Time difference of 0.0009410381 secs Time difference of 0.2300551 secs Time difference of 0.01890397 secs Time difference of 0.1074989 secs Time difference of 0.04427791 secs Time difference of 0.02060795 secs Time difference of 0.2373621 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 0.021873 secs Time difference of 0.07794905 secs Time difference of 0.02009201 secs Time difference of 0.03518486 secs Time difference of 0.01514792 secs Time difference of 0.08270884 secs Time difference of 0.246695 secs Time difference of 0.01806307 secs Time difference of 0.4399731 secs [1] "chludwig_K150309_004b_SW_1_16" "chludwig_K150309_008_SW_1_4" [3] "chludwig_K150309_013_SW_0" Time difference of 0.02171612 secs Time difference of 0.03013706 secs Time difference of 0.004559994 secs Time difference of 0.04176211 secs Time difference of 0.02349091 secs Time difference of 0.1430929 secs Time difference of 0.01733994 secs Time difference of 0.05213094 secs Time difference of 0.5800898 secs <simpleWarning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, drop.square = drop.square, normalize = normalize, statistics = control$statistics, surface = control$surface, cell = control$cell, iterations = iterations, iterTrace = control$iterTrace, trace.hat = control$trace.hat): span too small. fewer data values than degrees of freedom.> <simpleWarning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, drop.square = drop.square, normalize = normalize, statistics = control$statistics, surface = control$surface, cell = control$cell, iterations = iterations, iterTrace = control$iterTrace, trace.hat = control$trace.hat): span too small. fewer data values than degrees of freedom.> <simpleWarning in sqrt(sum.squares/one.delta): NaNs produced> <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 0.2577469 secs Time difference of 0.03471994 secs Time difference of 0.005545855 secs Time difference of 0.01992393 secs Time difference of 0.113198 secs Time difference of 0.04663396 secs Time difference of 0.04100204 secs Time difference of 0.2293789 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 0.06813502 secs [1] "run0 run1\nrun2 run2" Time difference of 0.6046841 secs Time difference of 0.2803819 secs Time difference of 0.01994014 secs Time difference of 0.1709521 secs Time difference of 3.675802 secs Time difference of 0.03973699 secs Time difference of 0.8350589 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 0.2812011 secs Time difference of 2.36105 secs Time difference of 15.33769 secs Time difference of 1.370583 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 0.256 secs [1] "Written /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/DIAlignR/extdata/temp_prog1.RData" [1] "Written /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/DIAlignR/extdata/temp_0_2.rds" [1] "progTree1 is done." Time difference of 3.483202 secs Time difference of 0.8285429 secs [1] "Written /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/DIAlignR/extdata/temp_1_2.rds" Time difference of 1.618134 secs [1] "Written /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/DIAlignR/extdata/temp_2_2.rds" Time difference of 0.838788 secs Time difference of 0.519146 secs [1] "Written /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/DIAlignR/extdata/temp_all_2.rds" Time difference of 0.5383608 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 0.22823 secs [1] "Written /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/DIAlignR/extdata/temp_prog1.RData" [1] "Written /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/DIAlignR/extdata/temp_0_2.rds" [1] "progTree1 is done." Time difference of 3.106667 secs Time difference of 0.8151069 secs [1] "Written /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/DIAlignR/extdata/temp_1_2.rds" Time difference of 1.555383 secs [1] "Written /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/DIAlignR/extdata/temp_2_2.rds" Time difference of 0.8027611 secs Time difference of 0.03866482 secs [1] "Written /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/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 0 | WARN 0 | SKIP 8 | PASS 632 ] ══ Skipped tests (8) ═══════════════════════════════════════════════════════════ • empty test (5): 'test_get_filenames.R:77:1', 'test_get_filenames.R:82:1', 'test_utils.R:200:1', 'test_utils.R:203:1', 'test_utils.R:206:1' • ropenms not available for testing. A conda environment with name TricEnvr is MUST for testing. (3): 'test_pyopenms.R:4:3', 'test_pyopenms.R:8:3', 'test_pyopenms.R:27:3' [ FAIL 0 | WARN 0 | SKIP 8 | PASS 632 ] > > proc.time() user system elapsed 128.751 16.381 135.001
DIAlignR.Rcheck/DIAlignR-Ex.timings
name | user | system | elapsed | |
MSTperBatch | 0.002 | 0.001 | 0.007 | |
addFlankToLeft | 0.003 | 0.001 | 0.004 | |
addFlankToRight | 0.002 | 0.001 | 0.008 | |
addXIC | 0.000 | 0.001 | 0.001 | |
alignChromatogramsCpp | 0.044 | 0.009 | 0.064 | |
alignTargetedRuns | 21.226 | 22.499 | 16.489 | |
alignToMaster | 3.640 | 0.136 | 4.889 | |
alignToRef | 0.002 | 0.001 | 0.003 | |
alignToRefMST | 0.001 | 0.000 | 0.003 | |
alignedXIC | 0.156 | 0.009 | 0.215 | |
analytesFromFeatures | 0.072 | 0.009 | 0.102 | |
approxFill | 0.001 | 0.001 | 0.002 | |
areaIntegrator | 0.005 | 0.002 | 0.007 | |
blobXICs | 0.004 | 0.003 | 0.008 | |
calculateIntensity | 0.004 | 0.001 | 0.006 | |
checkOverlap | 0.001 | 0.001 | 0.001 | |
checkParams | 0.000 | 0.001 | 0.001 | |
childXIC | 0.155 | 0.005 | 0.197 | |
childXICs | 1.089 | 0.035 | 1.404 | |
constrainSimCpp | 0.001 | 0.002 | 0.005 | |
createMZML | 0.005 | 0.003 | 0.012 | |
createSqMass | 0.004 | 0.002 | 0.007 | |
dialignrLoess | 0.001 | 0.001 | 0.002 | |
doAffineAlignmentCpp | 0.002 | 0.002 | 0.005 | |
doAlignmentCpp | 0.002 | 0.003 | 0.005 | |
extractXIC_group | 1.739 | 0.055 | 2.252 | |
extractXIC_group2 | 0.002 | 0.001 | 0.003 | |
fetchAnalytesInfo | 0.016 | 0.002 | 0.020 | |
fetchFeaturesFromRun | 0.014 | 0.002 | 0.018 | |
fetchPeptidesInfo | 0.014 | 0.002 | 0.022 | |
fetchPeptidesInfo2 | 0.015 | 0.002 | 0.021 | |
fetchPrecursorsInfo | 0.002 | 0.001 | 0.005 | |
fetchTransitionsFromRun | 0.014 | 0.002 | 0.026 | |
filenamesFromMZML | 0.002 | 0.001 | 0.003 | |
filenamesFromOSW | 0.002 | 0.001 | 0.004 | |
getAlignObj | 0.036 | 0.003 | 0.044 | |
getAlignObjs | 2.322 | 0.053 | 2.968 | |
getAlignedFigs | 0.246 | 0.011 | 0.319 | |
getAlignedIndices | 0.017 | 0.003 | 0.024 | |
getAlignedTimes | 0.032 | 0.009 | 0.052 | |
getAlignedTimesCpp | 0.010 | 0.002 | 0.014 | |
getAlignedTimesFast | 0.025 | 0.010 | 0.043 | |
getBaseGapPenaltyCpp | 0.001 | 0.000 | 0.001 | |
getChildFeature | 0.076 | 0.010 | 0.108 | |
getChildXICpp | 0.011 | 0.002 | 0.016 | |
getChildXICs | 1.459 | 0.045 | 1.871 | |
getChromSimMatCpp | 0.004 | 0.005 | 0.009 | |
getChromatogramIndices | 0.193 | 0.007 | 0.258 | |
getFeatures | 0.072 | 0.009 | 0.111 | |
getGlobalAlignMaskCpp | 0.001 | 0.003 | 0.005 | |
getGlobalAlignment | 0.013 | 0.001 | 0.017 | |
getGlobalFits | 0.815 | 0.018 | 1.029 | |
getLOESSfit | 0.006 | 0.002 | 0.009 | |
getLinearfit | 0.005 | 0.001 | 0.009 | |
getMST | 0.001 | 0.001 | 0.002 | |
getMZMLpointers | 0.030 | 0.004 | 0.045 | |
getMappedRT | 0.020 | 0.003 | 0.026 | |
getMultipeptide | 3.627 | 0.098 | 4.671 | |
getNativeIDs | 0.036 | 0.002 | 0.046 | |
getNodeIDs | 0.000 | 0.000 | 0.002 | |
getNodeRun | 0.876 | 0.027 | 1.135 | |
getOswAnalytes | 0.015 | 0.004 | 0.022 | |
getOswFiles | 0.014 | 0.001 | 0.019 | |
getPeptideScores | 0.069 | 0.007 | 0.091 | |
getPrecursorByID | 0.025 | 0.004 | 0.033 | |
getPrecursorIndices | 0.088 | 0.009 | 0.116 | |
getPrecursors | 0.045 | 0.006 | 0.059 | |
getRSE | 0.006 | 0.002 | 0.008 | |
getRTdf | 0.011 | 0.002 | 0.016 | |
getRefExpFeatureMap | 0.652 | 0.021 | 0.851 | |
getRefRun | 0.691 | 0.021 | 0.884 | |
getRunNames | 0.017 | 0.003 | 0.031 | |
getSeqSimMatCpp | 0.001 | 0.001 | 0.002 | |
getTransitions | 0.273 | 0.018 | 0.360 | |
getTree | 0.056 | 0.004 | 0.071 | |
getXICs | 0.163 | 0.009 | 0.206 | |
getXICs4AlignObj | 0.114 | 0.006 | 0.151 | |
get_ropenms | 0.001 | 0.000 | 0.000 | |
imputeChromatogram | 0.029 | 0.003 | 0.042 | |
ipfReassignFDR | 0.000 | 0.001 | 0.001 | |
mapIdxToTime | 0.000 | 0.001 | 0.002 | |
mappedRTfromAlignObj | 0.004 | 0.002 | 0.007 | |
mergeXIC | 0.005 | 0.001 | 0.006 | |
mstAlignRuns | 4.017 | 0.123 | 5.216 | |
mstScript1 | 0.770 | 0.501 | 0.986 | |
mstScript2 | 4.895 | 0.866 | 6.653 | |
nrDesc | 0.001 | 0.001 | 0.001 | |
otherChildXICpp | 0.012 | 0.003 | 0.020 | |
paramsDIAlignR | 0.001 | 0.000 | 0.000 | |
perBatch | 0.002 | 0.000 | 0.003 | |
pickNearestFeature | 0.005 | 0.002 | 0.009 | |
plotAlignedAnalytes | 1.180 | 0.040 | 1.534 | |
plotAlignmentPath | 0.711 | 0.056 | 0.967 | |
plotAnalyteXICs | 0.820 | 0.032 | 1.096 | |
plotXICgroup | 0.736 | 0.018 | 0.923 | |
populateReferenceExperimentFeatureAlignmentMap | 0.020 | 0.004 | 0.026 | |
progAlignRuns | 0.003 | 0.001 | 0.003 | |
readMzMLHeader | 0.002 | 0.001 | 0.005 | |
readSqMassHeader | 0.002 | 0.001 | 0.003 | |
recalculateIntensity | 0.523 | 0.017 | 0.662 | |
reduceXICs | 0.153 | 0.008 | 0.216 | |
script1 | 1.456 | 1.588 | 1.941 | |
script2 | 5.530 | 1.979 | 7.431 | |
setAlignmentRank | 0.021 | 0.004 | 0.032 | |
sgolayCpp | 0.005 | 0.002 | 0.006 | |
sgolayFill | 0.001 | 0.001 | 0.003 | |
smoothSingleXIC | 0.004 | 0.002 | 0.007 | |
smoothXICs | 0.016 | 0.003 | 0.026 | |
splineFill | 0.001 | 0.001 | 0.002 | |
splineFillCpp | 0.007 | 0.002 | 0.011 | |
traverseDown | 3.476 | 0.068 | 4.437 | |
traverseMST | 0.001 | 0.000 | 0.001 | |
traverseUp | 3.434 | 0.053 | 4.350 | |
trfrParentFeature | 0.079 | 0.011 | 0.117 | |
trimXICs | 0.003 | 0.002 | 0.008 | |
uncompressVec | 0.009 | 0.002 | 0.011 | |
updateFileInfo | 0.017 | 0.003 | 0.025 | |
writeOutFeatureAlignmentMap | 0.007 | 0.002 | 0.011 | |
writeTables | 0.005 | 0.002 | 0.010 | |