Back to Multiple platform build/check report for BioC 3.20: simplified long |
|
This page was generated on 2024-06-25 11:38 -0400 (Tue, 25 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" | 4690 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.1 RC (2024-06-06 r86719) -- "Race for Your Life" | 4404 |
kjohnson3 | macOS 13.6.5 Ventura | arm64 | 4.4.1 RC (2024-06-06 r86719) -- "Race for Your Life" | 4353 |
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 554/2242 | 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 | ![]() | ||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | ![]() | ||||||||
kjohnson3 | macOS 13.6.5 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: 2.13.0 |
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: 2024-06-24 19:53:39 -0400 (Mon, 24 Jun 2024) |
EndedAt: 2024-06-24 19:56:57 -0400 (Mon, 24 Jun 2024) |
EllapsedTime: 197.4 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 12.419 12.448 8.654 * 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 0.05485702 secs Time difference of 0.2226021 secs Time difference of 0.1568561 secs Time difference of 0.02810407 secs Time difference of 0.0126729 secs Time difference of 0.1014102 secs Time difference of 1.623202 secs Time difference of 0.01960206 secs Time difference of 0.3866901 secs [1] "hroest_K120808_Strep10%PlasmaBiolRepl1_R03_SW_filt" [2] "hroest_K120809_Strep0%PlasmaBiolRepl2_R04_SW_filt" Time difference of 0.01748586 secs Time difference of 0.1783559 secs Time difference of 0.09808397 secs Time difference of 0.02012515 secs Time difference of 0.007243872 secs Time difference of 0.06779909 secs Time difference of 0.8211012 secs Time difference of 0.00675106 secs Time difference of 0.9075379 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 0.01909399 secs Time difference of 0.192683 secs Time difference of 0.09398699 secs Time difference of 0.09840083 secs Time difference of 0.01050282 secs Time difference of 0.07843208 secs Time difference of 1.233002 secs Time difference of 0.02115297 secs Time difference of 0.345289 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 0.02103615 secs Time difference of 0.01805997 secs Time difference of 0.0006201267 secs Time difference of 0.1046731 secs Time difference of 0.01658821 secs Time difference of 0.07595396 secs Time difference of 0.01648498 secs Time difference of 0.008134127 secs Time difference of 0.0897851 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 0.00836587 secs Time difference of 0.02895808 secs Time difference of 0.009614944 secs Time difference of 0.01464605 secs Time difference of 0.009639978 secs Time difference of 0.04261494 secs Time difference of 0.08685613 secs Time difference of 0.005145073 secs Time difference of 0.1868072 secs [1] "chludwig_K150309_004b_SW_1_16" "chludwig_K150309_008_SW_1_4" [3] "chludwig_K150309_013_SW_0" Time difference of 0.01062083 secs Time difference of 0.01341009 secs Time difference of 0.001485825 secs Time difference of 0.02228498 secs Time difference of 0.01366806 secs Time difference of 0.1221859 secs Time difference of 0.006753922 secs Time difference of 0.01901102 secs Time difference of 0.1999021 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 0.1047511 secs Time difference of 0.018121 secs Time difference of 0.002584219 secs Time difference of 0.01160789 secs Time difference of 0.04792213 secs Time difference of 0.01875305 secs Time difference of 0.01691699 secs Time difference of 0.09488106 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 0.0299921 secs [1] "run0 run1\nrun2 run2" Time difference of 0.203366 secs Time difference of 0.09703612 secs Time difference of 0.01021409 secs Time difference of 0.111109 secs Time difference of 1.263008 secs Time difference of 0.01336503 secs Time difference of 0.3855438 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 0.14978 secs Time difference of 0.7837281 secs Time difference of 5.983685 secs Time difference of 0.4230959 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 0.1110229 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 1.195956 secs Time difference of 0.3038812 secs [1] "Written /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/DIAlignR/extdata/temp_1_2.rds" Time difference of 0.9444671 secs [1] "Written /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/DIAlignR/extdata/temp_2_2.rds" Time difference of 0.33126 secs Time difference of 0.1799679 secs [1] "Written /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/DIAlignR/extdata/temp_all_2.rds" Time difference of 0.162461 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 0.09796095 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 1.013406 secs Time difference of 0.3004429 secs [1] "Written /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/DIAlignR/extdata/temp_1_2.rds" Time difference of 0.458303 secs [1] "Written /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/DIAlignR/extdata/temp_2_2.rds" Time difference of 0.315614 secs Time difference of 0.01571989 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 61.402 8.889 51.472
DIAlignR.Rcheck/DIAlignR-Ex.timings
name | user | system | elapsed | |
MSTperBatch | 0.001 | 0.001 | 0.003 | |
addFlankToLeft | 0.002 | 0.001 | 0.003 | |
addFlankToRight | 0.002 | 0.001 | 0.002 | |
addXIC | 0.000 | 0.001 | 0.001 | |
alignChromatogramsCpp | 0.029 | 0.007 | 0.035 | |
alignTargetedRuns | 12.419 | 12.448 | 8.654 | |
alignToMaster | 1.534 | 0.155 | 1.654 | |
alignToRef | 0.001 | 0.001 | 0.002 | |
alignToRefMST | 0.000 | 0.001 | 0.001 | |
alignedXIC | 0.099 | 0.005 | 0.105 | |
analytesFromFeatures | 0.045 | 0.005 | 0.051 | |
approxFill | 0.001 | 0.000 | 0.002 | |
areaIntegrator | 0.003 | 0.002 | 0.004 | |
blobXICs | 0.002 | 0.002 | 0.004 | |
calculateIntensity | 0.002 | 0.001 | 0.004 | |
checkOverlap | 0 | 0 | 0 | |
checkParams | 0 | 0 | 0 | |
childXIC | 0.090 | 0.004 | 0.095 | |
childXICs | 0.551 | 0.021 | 0.577 | |
constrainSimCpp | 0.000 | 0.001 | 0.000 | |
createMZML | 0.003 | 0.001 | 0.004 | |
createSqMass | 0.003 | 0.001 | 0.003 | |
dialignrLoess | 0.000 | 0.001 | 0.001 | |
doAffineAlignmentCpp | 0.001 | 0.000 | 0.001 | |
doAlignmentCpp | 0.001 | 0.000 | 0.001 | |
extractXIC_group | 0.847 | 0.028 | 0.879 | |
extractXIC_group2 | 0.001 | 0.000 | 0.002 | |
fetchAnalytesInfo | 0.009 | 0.001 | 0.010 | |
fetchFeaturesFromRun | 0.008 | 0.001 | 0.009 | |
fetchPeptidesInfo | 0.007 | 0.001 | 0.009 | |
fetchPeptidesInfo2 | 0.009 | 0.001 | 0.010 | |
fetchPrecursorsInfo | 0.001 | 0.000 | 0.002 | |
fetchTransitionsFromRun | 0.008 | 0.001 | 0.009 | |
filenamesFromMZML | 0.000 | 0.001 | 0.002 | |
filenamesFromOSW | 0.001 | 0.001 | 0.002 | |
getAlignObj | 0.021 | 0.003 | 0.023 | |
getAlignObjs | 1.178 | 0.032 | 1.217 | |
getAlignedFigs | 0.141 | 0.007 | 0.151 | |
getAlignedIndices | 0.009 | 0.002 | 0.011 | |
getAlignedTimes | 0.018 | 0.004 | 0.023 | |
getAlignedTimesCpp | 0.006 | 0.002 | 0.007 | |
getAlignedTimesFast | 0.016 | 0.006 | 0.021 | |
getBaseGapPenaltyCpp | 0 | 0 | 0 | |
getChildFeature | 0.046 | 0.005 | 0.053 | |
getChildXICpp | 0.007 | 0.001 | 0.008 | |
getChildXICs | 0.677 | 0.025 | 0.704 | |
getChromSimMatCpp | 0.003 | 0.002 | 0.005 | |
getChromatogramIndices | 0.115 | 0.004 | 0.121 | |
getFeatures | 0.046 | 0.005 | 0.051 | |
getGlobalAlignMaskCpp | 0.001 | 0.000 | 0.002 | |
getGlobalAlignment | 0.007 | 0.001 | 0.008 | |
getGlobalFits | 0.383 | 0.009 | 0.395 | |
getLOESSfit | 0.003 | 0.001 | 0.005 | |
getLinearfit | 0.002 | 0.001 | 0.004 | |
getMST | 0.001 | 0.000 | 0.000 | |
getMZMLpointers | 0.016 | 0.002 | 0.019 | |
getMappedRT | 0.009 | 0.002 | 0.010 | |
getMultipeptide | 2.041 | 0.052 | 2.102 | |
getNativeIDs | 0.025 | 0.001 | 0.027 | |
getNodeIDs | 0.000 | 0.000 | 0.001 | |
getNodeRun | 0.412 | 0.016 | 0.431 | |
getOswAnalytes | 0.009 | 0.002 | 0.010 | |
getOswFiles | 0.009 | 0.001 | 0.010 | |
getPeptideScores | 0.037 | 0.004 | 0.041 | |
getPrecursorByID | 0.016 | 0.003 | 0.019 | |
getPrecursorIndices | 0.056 | 0.005 | 0.061 | |
getPrecursors | 0.027 | 0.003 | 0.030 | |
getRSE | 0.003 | 0.001 | 0.004 | |
getRTdf | 0.006 | 0.001 | 0.007 | |
getRefExpFeatureMap | 0.302 | 0.011 | 0.315 | |
getRefRun | 0.322 | 0.009 | 0.332 | |
getRunNames | 0.011 | 0.001 | 0.013 | |
getSeqSimMatCpp | 0.000 | 0.001 | 0.000 | |
getTransitions | 0.143 | 0.007 | 0.151 | |
getTree | 0.028 | 0.002 | 0.032 | |
getXICs | 0.092 | 0.006 | 0.099 | |
getXICs4AlignObj | 0.069 | 0.004 | 0.075 | |
get_ropenms | 0 | 0 | 0 | |
imputeChromatogram | 0.017 | 0.001 | 0.018 | |
ipfReassignFDR | 0.000 | 0.001 | 0.000 | |
mapIdxToTime | 0 | 0 | 0 | |
mappedRTfromAlignObj | 0.003 | 0.001 | 0.004 | |
mergeXIC | 0.003 | 0.001 | 0.003 | |
mstAlignRuns | 1.799 | 0.053 | 1.864 | |
mstScript1 | 0.562 | 0.354 | 0.643 | |
mstScript2 | 2.374 | 0.532 | 2.645 | |
nrDesc | 0 | 0 | 0 | |
otherChildXICpp | 0.006 | 0.002 | 0.009 | |
paramsDIAlignR | 0 | 0 | 0 | |
perBatch | 0.001 | 0.001 | 0.002 | |
pickNearestFeature | 0.004 | 0.001 | 0.004 | |
plotAlignedAnalytes | 0.545 | 0.018 | 0.564 | |
plotAlignmentPath | 0.372 | 0.033 | 0.408 | |
plotAnalyteXICs | 0.414 | 0.018 | 0.433 | |
plotXICgroup | 0.313 | 0.010 | 0.324 | |
populateReferenceExperimentFeatureAlignmentMap | 0.010 | 0.002 | 0.012 | |
progAlignRuns | 0.001 | 0.001 | 0.001 | |
readMzMLHeader | 0.000 | 0.001 | 0.001 | |
readSqMassHeader | 0.001 | 0.000 | 0.001 | |
recalculateIntensity | 0.278 | 0.010 | 0.290 | |
reduceXICs | 0.082 | 0.005 | 0.087 | |
script1 | 0.933 | 0.923 | 1.170 | |
script2 | 2.757 | 1.669 | 3.533 | |
setAlignmentRank | 0.012 | 0.002 | 0.015 | |
sgolayCpp | 0.003 | 0.001 | 0.004 | |
sgolayFill | 0.000 | 0.000 | 0.001 | |
smoothSingleXIC | 0.002 | 0.001 | 0.003 | |
smoothXICs | 0.006 | 0.002 | 0.008 | |
splineFill | 0.001 | 0.000 | 0.001 | |
splineFillCpp | 0.003 | 0.000 | 0.004 | |
traverseDown | 1.528 | 0.049 | 1.598 | |
traverseMST | 0 | 0 | 0 | |
traverseUp | 1.507 | 0.031 | 1.547 | |
trfrParentFeature | 0.042 | 0.006 | 0.048 | |
trimXICs | 0.002 | 0.002 | 0.004 | |
uncompressVec | 0.005 | 0.001 | 0.006 | |
updateFileInfo | 0.009 | 0.001 | 0.010 | |
writeOutFeatureAlignmentMap | 0.004 | 0.001 | 0.006 | |
writeTables | 0.003 | 0.001 | 0.005 | |