Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-06-28 11:39 -0400 (Fri, 28 Jun 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.0 RC (2024-04-16 r86468) -- "Puppy Cup" | 4693 |
palomino6 | Windows Server 2022 Datacenter | x64 | 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" | 4089 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.1 RC (2024-06-06 r86719) -- "Race for Your Life" | 4407 |
kjohnson3 | macOS 13.6.5 Ventura | arm64 | 4.4.1 RC (2024-06-06 r86719) -- "Race for Your Life" | 4356 |
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 554/2243 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
DIAlignR 2.13.0 (landing page) Shubham Gupta
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | ![]() | ||||||||
palomino6 | Windows Server 2022 Datacenter / x64 | OK | ERROR | skipped | skipped | |||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | ![]() | ||||||||
kjohnson3 | macOS 13.6.5 Ventura / arm64 | OK | OK | ERROR | OK | |||||||||
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | see weekly results here | ||||||||||||
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: 2.13.0 |
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_2.13.0.tar.gz |
StartedAt: 2024-06-27 19:54:11 -0400 (Thu, 27 Jun 2024) |
EndedAt: 2024-06-27 19:57:35 -0400 (Thu, 27 Jun 2024) |
EllapsedTime: 203.9 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_2.13.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/DIAlignR.Rcheck’ * using R version 4.4.1 RC (2024-06-06 r86719) * 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 12.7.1 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘DIAlignR/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘DIAlignR’ version ‘2.13.0’ * 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 12.646 12.045 8.593 * 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-3.20-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 RC (2024-06-06 r86719) -- "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 0.05198312 secs Time difference of 0.2343318 secs Time difference of 0.1671431 secs Time difference of 0.02855802 secs Time difference of 0.01173401 secs Time difference of 0.110883 secs Time difference of 1.698947 secs Time difference of 0.02493691 secs Time difference of 0.3477681 secs [1] "hroest_K120808_Strep10%PlasmaBiolRepl1_R03_SW_filt" [2] "hroest_K120809_Strep0%PlasmaBiolRepl2_R04_SW_filt" Time difference of 0.01873398 secs Time difference of 0.1799901 secs Time difference of 0.1034551 secs Time difference of 0.02727795 secs Time difference of 0.01087689 secs Time difference of 0.08073997 secs Time difference of 0.8988478 secs Time difference of 0.006295919 secs Time difference of 0.8897529 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 0.01696706 secs Time difference of 0.201473 secs Time difference of 0.08978391 secs Time difference of 0.104949 secs Time difference of 0.01042581 secs Time difference of 0.07937098 secs Time difference of 1.112971 secs Time difference of 0.01871896 secs Time difference of 0.3026762 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 0.01825118 secs Time difference of 0.01656008 secs Time difference of 0.000371933 secs Time difference of 0.09533405 secs Time difference of 0.009418964 secs Time difference of 0.04576397 secs Time difference of 0.01205206 secs Time difference of 0.01020908 secs Time difference of 0.09348011 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 0.006780863 secs Time difference of 0.02768803 secs Time difference of 0.008405924 secs Time difference of 0.0156889 secs Time difference of 0.006525993 secs Time difference of 0.04226303 secs Time difference of 0.09034586 secs Time difference of 0.005516052 secs Time difference of 0.2010388 secs [1] "chludwig_K150309_004b_SW_1_16" "chludwig_K150309_008_SW_1_4" [3] "chludwig_K150309_013_SW_0" Time difference of 0.01113081 secs Time difference of 0.01129103 secs Time difference of 0.001173019 secs Time difference of 0.01857996 secs Time difference of 0.01238394 secs Time difference of 0.07936716 secs Time difference of 0.007040977 secs Time difference of 0.01850104 secs Time difference of 0.1919069 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 0.1165009 secs Time difference of 0.01613903 secs Time difference of 0.001899004 secs Time difference of 0.009907961 secs Time difference of 0.05464387 secs Time difference of 0.014148 secs Time difference of 0.01658297 secs Time difference of 0.08760095 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 0.03331995 secs [1] "run0 run1\nrun2 run2" Time difference of 0.226341 secs Time difference of 0.09668398 secs Time difference of 0.00909996 secs Time difference of 0.06806016 secs Time difference of 1.298254 secs Time difference of 0.01458502 secs Time difference of 0.3255959 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 0.1710849 secs Time difference of 0.8801041 secs Time difference of 5.89178 secs Time difference of 0.442045 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 0.1090798 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 1.129563 secs Time difference of 0.3266859 secs [1] "Written /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/DIAlignR/extdata/temp_1_2.rds" Time difference of 0.5426321 secs [1] "Written /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/DIAlignR/extdata/temp_2_2.rds" Time difference of 0.333112 secs Time difference of 0.199975 secs [1] "Written /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/DIAlignR/extdata/temp_all_2.rds" Time difference of 0.2321351 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 0.1092741 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 1.11306 secs Time difference of 0.307919 secs [1] "Written /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/DIAlignR/extdata/temp_1_2.rds" Time difference of 0.563405 secs [1] "Written /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/DIAlignR/extdata/temp_2_2.rds" Time difference of 0.3298571 secs Time difference of 0.01590204 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 61.584 9.142 52.270
DIAlignR.Rcheck/DIAlignR-Ex.timings
name | user | system | elapsed | |
MSTperBatch | 0.001 | 0.001 | 0.002 | |
addFlankToLeft | 0.001 | 0.000 | 0.002 | |
addFlankToRight | 0.001 | 0.000 | 0.002 | |
addXIC | 0.000 | 0.001 | 0.000 | |
alignChromatogramsCpp | 0.026 | 0.006 | 0.032 | |
alignTargetedRuns | 12.646 | 12.045 | 8.593 | |
alignToMaster | 1.541 | 0.073 | 1.621 | |
alignToRef | 0.001 | 0.001 | 0.002 | |
alignToRefMST | 0.002 | 0.001 | 0.002 | |
alignedXIC | 0.091 | 0.004 | 0.096 | |
analytesFromFeatures | 0.039 | 0.007 | 0.047 | |
approxFill | 0.001 | 0.000 | 0.001 | |
areaIntegrator | 0.003 | 0.001 | 0.004 | |
blobXICs | 0.002 | 0.001 | 0.003 | |
calculateIntensity | 0.002 | 0.001 | 0.003 | |
checkOverlap | 0 | 0 | 0 | |
checkParams | 0.000 | 0.000 | 0.001 | |
childXIC | 0.091 | 0.003 | 0.094 | |
childXICs | 0.509 | 0.018 | 0.529 | |
constrainSimCpp | 0.000 | 0.000 | 0.001 | |
createMZML | 0.003 | 0.002 | 0.005 | |
createSqMass | 0.002 | 0.001 | 0.003 | |
dialignrLoess | 0.001 | 0.000 | 0.000 | |
doAffineAlignmentCpp | 0.001 | 0.000 | 0.002 | |
doAlignmentCpp | 0.000 | 0.001 | 0.002 | |
extractXIC_group | 0.760 | 0.028 | 0.791 | |
extractXIC_group2 | 0.001 | 0.000 | 0.001 | |
fetchAnalytesInfo | 0.008 | 0.001 | 0.011 | |
fetchFeaturesFromRun | 0.009 | 0.002 | 0.010 | |
fetchPeptidesInfo | 0.008 | 0.002 | 0.010 | |
fetchPeptidesInfo2 | 0.009 | 0.002 | 0.010 | |
fetchPrecursorsInfo | 0.001 | 0.001 | 0.002 | |
fetchTransitionsFromRun | 0.009 | 0.002 | 0.010 | |
filenamesFromMZML | 0.001 | 0.001 | 0.001 | |
filenamesFromOSW | 0.001 | 0.001 | 0.001 | |
getAlignObj | 0.019 | 0.002 | 0.022 | |
getAlignObjs | 1.095 | 0.030 | 1.130 | |
getAlignedFigs | 0.137 | 0.007 | 0.145 | |
getAlignedIndices | 0.008 | 0.002 | 0.011 | |
getAlignedTimes | 0.019 | 0.004 | 0.023 | |
getAlignedTimesCpp | 0.006 | 0.001 | 0.008 | |
getAlignedTimesFast | 0.013 | 0.005 | 0.018 | |
getBaseGapPenaltyCpp | 0.000 | 0.000 | 0.001 | |
getChildFeature | 0.038 | 0.005 | 0.044 | |
getChildXICpp | 0.005 | 0.001 | 0.006 | |
getChildXICs | 0.594 | 0.019 | 0.614 | |
getChromSimMatCpp | 0.002 | 0.002 | 0.003 | |
getChromatogramIndices | 0.105 | 0.004 | 0.110 | |
getFeatures | 0.041 | 0.005 | 0.046 | |
getGlobalAlignMaskCpp | 0.001 | 0.001 | 0.002 | |
getGlobalAlignment | 0.008 | 0.001 | 0.009 | |
getGlobalFits | 0.356 | 0.007 | 0.364 | |
getLOESSfit | 0.003 | 0.001 | 0.004 | |
getLinearfit | 0.003 | 0.001 | 0.004 | |
getMST | 0.000 | 0.001 | 0.001 | |
getMZMLpointers | 0.018 | 0.002 | 0.020 | |
getMappedRT | 0.020 | 0.002 | 0.023 | |
getMultipeptide | 1.950 | 0.064 | 2.026 | |
getNativeIDs | 0.021 | 0.002 | 0.023 | |
getNodeIDs | 0.000 | 0.000 | 0.001 | |
getNodeRun | 0.387 | 0.015 | 0.403 | |
getOswAnalytes | 0.009 | 0.002 | 0.011 | |
getOswFiles | 0.009 | 0.002 | 0.011 | |
getPeptideScores | 0.042 | 0.003 | 0.046 | |
getPrecursorByID | 0.019 | 0.002 | 0.022 | |
getPrecursorIndices | 0.056 | 0.004 | 0.062 | |
getPrecursors | 0.025 | 0.003 | 0.029 | |
getRSE | 0.004 | 0.001 | 0.005 | |
getRTdf | 0.007 | 0.001 | 0.008 | |
getRefExpFeatureMap | 0.308 | 0.009 | 0.318 | |
getRefRun | 0.327 | 0.010 | 0.341 | |
getRunNames | 0.011 | 0.001 | 0.013 | |
getSeqSimMatCpp | 0.001 | 0.000 | 0.001 | |
getTransitions | 0.159 | 0.010 | 0.171 | |
getTree | 0.024 | 0.003 | 0.029 | |
getXICs | 0.086 | 0.005 | 0.091 | |
getXICs4AlignObj | 0.063 | 0.004 | 0.067 | |
get_ropenms | 0 | 0 | 0 | |
imputeChromatogram | 0.013 | 0.001 | 0.013 | |
ipfReassignFDR | 0.000 | 0.001 | 0.001 | |
mapIdxToTime | 0 | 0 | 0 | |
mappedRTfromAlignObj | 0.002 | 0.001 | 0.003 | |
mergeXIC | 0.003 | 0.001 | 0.005 | |
mstAlignRuns | 1.704 | 0.051 | 1.763 | |
mstScript1 | 0.574 | 0.394 | 0.682 | |
mstScript2 | 2.392 | 0.646 | 2.730 | |
nrDesc | 0.001 | 0.000 | 0.001 | |
otherChildXICpp | 0.005 | 0.001 | 0.006 | |
paramsDIAlignR | 0 | 0 | 0 | |
perBatch | 0.001 | 0.001 | 0.002 | |
pickNearestFeature | 0.004 | 0.001 | 0.004 | |
plotAlignedAnalytes | 0.576 | 0.021 | 0.600 | |
plotAlignmentPath | 0.402 | 0.037 | 0.441 | |
plotAnalyteXICs | 0.434 | 0.019 | 0.457 | |
plotXICgroup | 0.373 | 0.011 | 0.387 | |
populateReferenceExperimentFeatureAlignmentMap | 0.015 | 0.003 | 0.017 | |
progAlignRuns | 0.002 | 0.001 | 0.002 | |
readMzMLHeader | 0.000 | 0.001 | 0.002 | |
readSqMassHeader | 0.001 | 0.001 | 0.002 | |
recalculateIntensity | 0.279 | 0.010 | 0.290 | |
reduceXICs | 0.079 | 0.004 | 0.085 | |
script1 | 0.941 | 1.127 | 1.269 | |
script2 | 2.773 | 1.334 | 3.389 | |
setAlignmentRank | 0.012 | 0.003 | 0.014 | |
sgolayCpp | 0.003 | 0.001 | 0.004 | |
sgolayFill | 0.001 | 0.000 | 0.001 | |
smoothSingleXIC | 0.001 | 0.001 | 0.004 | |
smoothXICs | 0.007 | 0.002 | 0.008 | |
splineFill | 0.001 | 0.000 | 0.001 | |
splineFillCpp | 0.004 | 0.000 | 0.005 | |
traverseDown | 1.474 | 0.037 | 1.518 | |
traverseMST | 0.001 | 0.000 | 0.001 | |
traverseUp | 1.501 | 0.032 | 1.538 | |
trfrParentFeature | 0.047 | 0.006 | 0.056 | |
trimXICs | 0.002 | 0.001 | 0.002 | |
uncompressVec | 0.006 | 0.002 | 0.007 | |
updateFileInfo | 0.010 | 0.002 | 0.012 | |
writeOutFeatureAlignmentMap | 0.005 | 0.001 | 0.007 | |
writeTables | 0.003 | 0.001 | 0.005 | |