Back to Multiple platform build/check report for BioC 3.19: simplified long |
|
This page was generated on 2024-06-25 17:43 -0400 (Tue, 25 Jun 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4760 |
palomino3 | Windows Server 2022 Datacenter | x64 | 4.4.0 (2024-04-24 ucrt) -- "Puppy Cup" | 4494 |
merida1 | macOS 12.7.4 Monterey | x86_64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4508 |
kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4466 |
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 | |||||||||
palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | |||||||||
merida1 | macOS 12.7.4 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: 2024-06-24 17:48:29 -0400 (Mon, 24 Jun 2024) |
EndedAt: 2024-06-24 17:51:47 -0400 (Mon, 24 Jun 2024) |
EllapsedTime: 198.1 seconds |
RetCode: 1 |
Status: ERROR |
CheckDir: DIAlignR.Rcheck |
Warnings: NA |
############################################################################## ############################################################################## ### ### 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 4.4.0 (2024-04-24) * using platform: aarch64-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 Ventura 13.6.6 * 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 15.0.0 (clang-1500.0.40.1)’ * 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 11.4Mb 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-arm64/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 9.704 11.41 8.589 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘testthat.R’ ERROR Running the tests in ‘tests/testthat.R’ failed. Last 13 lines of output: ── Failure ('test_get_global_fit.R:21:3'): test_dialignrLoess ────────────────── outData$pars$span not equal to 0.8. 1/1 mismatches [1] 0.4 - 0.8 == -0.4 ── Failure ('test_get_global_fit.R:22:3'): test_dialignrLoess ────────────────── predict(outData, newdata = data.frame(RT.ref = 13.5))[[1]] not equal to 5.5. 1/1 mismatches [1] 2.75 - 5.5 == -2.75 ── Failure ('test_utils.R:276:3'): test_ipfReassignFDR ───────────────────────── `finalTbl` not equal to `expData`. Column 'RT': 'is.NA' value mismatch: 2 in current 0 in target [ FAIL 3 | WARN 3 | SKIP 8 | PASS 629 ] Error: Test failures Execution halted * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking running R code from vignettes ... SKIPPED * checking re-building of vignette outputs ... SKIPPED * checking PDF version of manual ... OK * DONE Status: 1 ERROR, 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-arm64/Resources/library’ * installing *source* package ‘DIAlignR’ ... ** using staged installation ** libs using C++ compiler: ‘Apple clang version 15.0.0 (clang-1500.0.40.1)’ using C++14 using SDK: ‘MacOSX11.3.sdk’ clang++ -arch arm64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c ChromatogramPeak.cpp -o ChromatogramPeak.o clang++ -arch arm64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c DPosition.cpp -o DPosition.o clang++ -arch arm64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c MSChromatogram.cpp -o MSChromatogram.o clang++ -arch arm64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c PeakIntegrator.cpp -o PeakIntegrator.o clang++ -arch arm64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c RcppExports.cpp -o RcppExports.o In file included from RcppExports.cpp:4: In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/RcppEigen.h:25: In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/RcppEigenForward.h:29: In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/Eigen/Sparse:26: In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/Eigen/SparseCore:61: /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/Eigen/src/SparseCore/TriangularSolver.h:273:13: warning: variable 'count' set but not used [-Wunused-but-set-variable] Index count = 0; ^ In file included from RcppExports.cpp:4: In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/RcppEigen.h:25: In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/RcppEigenForward.h:29: In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/Eigen/Sparse:29: In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/Eigen/SparseLU:35: /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/Eigen/src/SparseLU/SparseLU_heap_relax_snode.h:78:9: warning: variable 'nsuper_et_post' set but not used [-Wunused-but-set-variable] Index nsuper_et_post = 0; // Number of relaxed snodes in postordered etree ^ /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/Eigen/src/SparseLU/SparseLU_heap_relax_snode.h:79:9: warning: variable 'nsuper_et' set but not used [-Wunused-but-set-variable] Index nsuper_et = 0; // Number of relaxed snodes in the original etree ^ In file included from RcppExports.cpp:4: In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/RcppEigen.h:25: In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/RcppEigenForward.h:31: In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/unsupported/Eigen/IterativeSolvers:46: /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/unsupported/Eigen/src/IterativeSolvers/IDRS.h:72:10: warning: variable 'replacements' set but not used [-Wunused-but-set-variable] Index replacements = 0; ^ In file included from RcppExports.cpp:4: In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/RcppEigen.h:25: In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/RcppEigenForward.h:37: In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/unsupported/Eigen/SparseExtra:45: /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/unsupported/Eigen/src/SparseExtra/MarketIO.h:246:7: warning: variable 'count' set but not used [-Wunused-but-set-variable] int count = 0; ^ 5 warnings generated. clang++ -arch arm64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include' -I/opt/R/arm64/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 arm64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c SavitzkyGolayFilter.cpp -o SavitzkyGolayFilter.o In file included from SavitzkyGolayFilter.cpp:1: In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/RcppEigen.h:25: In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/RcppEigenForward.h:29: In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/Eigen/Sparse:26: In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/Eigen/SparseCore:61: /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/Eigen/src/SparseCore/TriangularSolver.h:273:13: warning: variable 'count' set but not used [-Wunused-but-set-variable] Index count = 0; ^ In file included from SavitzkyGolayFilter.cpp:1: In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/RcppEigen.h:25: In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/RcppEigenForward.h:29: In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/Eigen/Sparse:29: In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/Eigen/SparseLU:35: /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/Eigen/src/SparseLU/SparseLU_heap_relax_snode.h:78:9: warning: variable 'nsuper_et_post' set but not used [-Wunused-but-set-variable] Index nsuper_et_post = 0; // Number of relaxed snodes in postordered etree ^ /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/Eigen/src/SparseLU/SparseLU_heap_relax_snode.h:79:9: warning: variable 'nsuper_et' set but not used [-Wunused-but-set-variable] Index nsuper_et = 0; // Number of relaxed snodes in the original etree ^ In file included from SavitzkyGolayFilter.cpp:1: In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/RcppEigen.h:25: In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/RcppEigenForward.h:31: In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/unsupported/Eigen/IterativeSolvers:46: /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/unsupported/Eigen/src/IterativeSolvers/IDRS.h:72:10: warning: variable 'replacements' set but not used [-Wunused-but-set-variable] Index replacements = 0; ^ In file included from SavitzkyGolayFilter.cpp:1: In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/RcppEigen.h:25: In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/RcppEigenForward.h:37: In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/unsupported/Eigen/SparseExtra:45: /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/unsupported/Eigen/src/SparseExtra/MarketIO.h:246:7: warning: variable 'count' set but not used [-Wunused-but-set-variable] int count = 0; ^ 5 warnings generated. clang++ -arch arm64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c affinealignment.cpp -o affinealignment.o clang++ -arch arm64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c affinealignobj.cpp -o affinealignobj.o clang++ -arch arm64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c alignment.cpp -o alignment.o clang++ -arch arm64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c chromSimMatrix.cpp -o chromSimMatrix.o clang++ -arch arm64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include' -I/opt/R/arm64/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 arm64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c gapPenalty.cpp -o gapPenalty.o clang++ -arch arm64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c integrateArea.cpp -o integrateArea.o clang++ -arch arm64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c interface.cpp -o interface.o clang++ -arch arm64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include' -I/opt/R/arm64/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 arm64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c run_alignment.cpp -o run_alignment.o clang++ -arch arm64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c simpleFcn.cpp -o simpleFcn.o clang++ -arch arm64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c spline.cpp -o spline.o clang++ -arch arm64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include' -I/opt/R/arm64/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 arm64 -std=gnu++14 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/arm64/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-arm64/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.fail
R version 4.4.0 (2024-04-24) -- "Puppy Cup" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: aarch64-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 0.05033612 secs Time difference of 0.192354 secs Time difference of 0.161031 secs Time difference of 0.03698802 secs Time difference of 0.01252294 secs Time difference of 0.1141388 secs Time difference of 1.706896 secs Time difference of 0.02349901 secs Time difference of 0.351335 secs [1] "hroest_K120808_Strep10%PlasmaBiolRepl1_R03_SW_filt" [2] "hroest_K120809_Strep0%PlasmaBiolRepl2_R04_SW_filt" Time difference of 0.01963401 secs Time difference of 0.1575172 secs Time difference of 0.07930017 secs Time difference of 0.02264786 secs Time difference of 0.008131027 secs Time difference of 0.06273484 secs Time difference of 0.7536569 secs Time difference of 0.006932974 secs Time difference of 0.8553081 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 0.0224092 secs Time difference of 0.1753509 secs Time difference of 0.07577586 secs Time difference of 0.118571 secs Time difference of 0.01110911 secs Time difference of 0.077209 secs Time difference of 1.040202 secs Time difference of 0.02009702 secs Time difference of 0.302892 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 0.02018213 secs Time difference of 0.01497793 secs Time difference of 0.0003938675 secs Time difference of 0.12076 secs Time difference of 0.01110196 secs Time difference of 0.04896402 secs Time difference of 0.01566195 secs Time difference of 0.007137775 secs Time difference of 0.1022999 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 0.007916927 secs Time difference of 0.02414298 secs Time difference of 0.007463932 secs Time difference of 0.01529598 secs Time difference of 0.009690046 secs Time difference of 0.0384419 secs Time difference of 0.09277201 secs Time difference of 0.006927013 secs Time difference of 0.201565 secs [1] "chludwig_K150309_004b_SW_1_16" "chludwig_K150309_008_SW_1_4" [3] "chludwig_K150309_013_SW_0" Time difference of 0.010566 secs Time difference of 0.01069117 secs Time difference of 0.0008471012 secs Time difference of 0.01759911 secs Time difference of 0.01245904 secs Time difference of 0.07207704 secs Time difference of 0.008727074 secs Time difference of 0.01649499 secs Time difference of 0.208519 secs <simpleWarning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, drop.square = drop.square, normalize = normalize, statistics = control$statistics, surface = control$surface, cell = control$cell, iterations = iterations, iterTrace = control$iterTrace, trace.hat = control$trace.hat): span too small. fewer data values than degrees of freedom.> <simpleWarning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, drop.square = drop.square, normalize = normalize, statistics = control$statistics, surface = control$surface, cell = control$cell, iterations = iterations, iterTrace = control$iterTrace, trace.hat = control$trace.hat): span too small. fewer data values than degrees of freedom.> <simpleError in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, drop.square = drop.square, normalize = normalize, statistics = control$statistics, surface = control$surface, cell = control$cell, iterations = iterations, iterTrace = control$iterTrace, trace.hat = control$trace.hat): span is too small> runName run0 hroest_K120808_Strep10%PlasmaBiolRepl1_R03_SW_filt run1 hroest_K120809_Strep0%PlasmaBiolRepl2_R04_SW_filt run2 hroest_K120809_Strep10%PlasmaBiolRepl2_R04_SW_filt Time difference of 0.120688 secs Time difference of 0.01646996 secs Time difference of 0.001694918 secs Time difference of 0.01361585 secs Time difference of 0.0528152 secs Time difference of 0.01523495 secs Time difference of 0.01332498 secs Time difference of 0.09609389 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 0.02843308 secs [1] "run0 run1\nrun2 run2" Time difference of 0.1870928 secs Time difference of 0.07419086 secs Time difference of 0.01079917 secs Time difference of 0.08400202 secs Time difference of 1.213223 secs Time difference of 0.01572013 secs Time difference of 0.373873 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 0.1632259 secs Time difference of 0.885947 secs Time difference of 6.251382 secs Time difference of 0.3992581 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 0.1232641 secs [1] "Written /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/DIAlignR/extdata/temp_prog1.RData" [1] "Written /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/DIAlignR/extdata/temp_0_2.rds" [1] "progTree1 is done." Time difference of 1.485421 secs Time difference of 0.334291 secs [1] "Written /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/DIAlignR/extdata/temp_1_2.rds" Time difference of 0.534955 secs [1] "Written /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/DIAlignR/extdata/temp_2_2.rds" Time difference of 0.344918 secs Time difference of 0.156379 secs [1] "Written /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/DIAlignR/extdata/temp_all_2.rds" Time difference of 0.1740389 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 0.143446 secs [1] "Written /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/DIAlignR/extdata/temp_prog1.RData" [1] "Written /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/DIAlignR/extdata/temp_0_2.rds" [1] "progTree1 is done." Time difference of 0.9724441 secs Time difference of 0.3338881 secs [1] "Written /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/DIAlignR/extdata/temp_1_2.rds" Time difference of 0.8722999 secs [1] "Written /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/DIAlignR/extdata/temp_2_2.rds" Time difference of 0.301569 secs Time difference of 0.01222706 secs [1] "Written /Library/Frameworks/R.framework/Versions/4.4-arm64/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 3 | WARN 3 | SKIP 8 | PASS 629 ] ══ 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' ══ Failed tests ════════════════════════════════════════════════════════════════ ── Failure ('test_get_global_fit.R:21:3'): test_dialignrLoess ────────────────── outData$pars$span not equal to 0.8. 1/1 mismatches [1] 0.4 - 0.8 == -0.4 ── Failure ('test_get_global_fit.R:22:3'): test_dialignrLoess ────────────────── predict(outData, newdata = data.frame(RT.ref = 13.5))[[1]] not equal to 5.5. 1/1 mismatches [1] 2.75 - 5.5 == -2.75 ── Failure ('test_utils.R:276:3'): test_ipfReassignFDR ───────────────────────── `finalTbl` not equal to `expData`. Column 'RT': 'is.NA' value mismatch: 2 in current 0 in target [ FAIL 3 | WARN 3 | SKIP 8 | PASS 629 ] Error: Test failures Execution halted
DIAlignR.Rcheck/DIAlignR-Ex.timings
name | user | system | elapsed | |
MSTperBatch | 0.001 | 0.002 | 0.014 | |
addFlankToLeft | 0.002 | 0.001 | 0.002 | |
addFlankToRight | 0.001 | 0.001 | 0.001 | |
addXIC | 0 | 0 | 0 | |
alignChromatogramsCpp | 0.029 | 0.006 | 0.035 | |
alignTargetedRuns | 9.704 | 11.410 | 8.589 | |
alignToMaster | 1.308 | 0.052 | 1.387 | |
alignToRef | 0.002 | 0.001 | 0.002 | |
alignToRefMST | 0.001 | 0.001 | 0.001 | |
alignedXIC | 0.128 | 0.004 | 0.136 | |
analytesFromFeatures | 0.047 | 0.007 | 0.062 | |
approxFill | 0.001 | 0.000 | 0.001 | |
areaIntegrator | 0.004 | 0.001 | 0.005 | |
blobXICs | 0.002 | 0.001 | 0.003 | |
calculateIntensity | 0.003 | 0.000 | 0.004 | |
checkOverlap | 0 | 0 | 0 | |
checkParams | 0.001 | 0.000 | 0.000 | |
childXIC | 0.135 | 0.004 | 0.140 | |
childXICs | 0.430 | 0.015 | 0.460 | |
constrainSimCpp | 0 | 0 | 0 | |
createMZML | 0.002 | 0.000 | 0.003 | |
createSqMass | 0.001 | 0.000 | 0.001 | |
dialignrLoess | 0 | 0 | 0 | |
doAffineAlignmentCpp | 0.001 | 0.001 | 0.001 | |
doAlignmentCpp | 0 | 0 | 0 | |
extractXIC_group | 0.499 | 0.022 | 0.533 | |
extractXIC_group2 | 0.001 | 0.001 | 0.001 | |
fetchAnalytesInfo | 0.009 | 0.001 | 0.011 | |
fetchFeaturesFromRun | 0.008 | 0.001 | 0.010 | |
fetchPeptidesInfo | 0.008 | 0.001 | 0.009 | |
fetchPeptidesInfo2 | 0.011 | 0.002 | 0.012 | |
fetchPrecursorsInfo | 0.002 | 0.001 | 0.002 | |
fetchTransitionsFromRun | 0.011 | 0.001 | 0.012 | |
filenamesFromMZML | 0.001 | 0.000 | 0.002 | |
filenamesFromOSW | 0.001 | 0.000 | 0.002 | |
getAlignObj | 0.026 | 0.003 | 0.028 | |
getAlignObjs | 1.063 | 0.029 | 1.123 | |
getAlignedFigs | 0.143 | 0.009 | 0.155 | |
getAlignedIndices | 0.012 | 0.003 | 0.015 | |
getAlignedTimes | 0.023 | 0.004 | 0.029 | |
getAlignedTimesCpp | 0.007 | 0.001 | 0.008 | |
getAlignedTimesFast | 0.016 | 0.004 | 0.033 | |
getBaseGapPenaltyCpp | 0.000 | 0.000 | 0.001 | |
getChildFeature | 0.051 | 0.006 | 0.059 | |
getChildXICpp | 0.007 | 0.001 | 0.008 | |
getChildXICs | 0.610 | 0.025 | 0.655 | |
getChromSimMatCpp | 0.002 | 0.003 | 0.004 | |
getChromatogramIndices | 0.106 | 0.005 | 0.116 | |
getFeatures | 0.044 | 0.005 | 0.051 | |
getGlobalAlignMaskCpp | 0.000 | 0.001 | 0.002 | |
getGlobalAlignment | 0.008 | 0.001 | 0.009 | |
getGlobalFits | 0.301 | 0.007 | 0.309 | |
getLOESSfit | 0.004 | 0.001 | 0.004 | |
getLinearfit | 0.004 | 0.001 | 0.005 | |
getMST | 0.001 | 0.000 | 0.001 | |
getMZMLpointers | 0.017 | 0.002 | 0.019 | |
getMappedRT | 0.014 | 0.001 | 0.018 | |
getMultipeptide | 2.102 | 0.059 | 2.179 | |
getNativeIDs | 0.024 | 0.001 | 0.026 | |
getNodeIDs | 0.000 | 0.000 | 0.001 | |
getNodeRun | 0.357 | 0.018 | 0.376 | |
getOswAnalytes | 0.009 | 0.002 | 0.010 | |
getOswFiles | 0.010 | 0.002 | 0.011 | |
getPeptideScores | 0.045 | 0.005 | 0.051 | |
getPrecursorByID | 0.017 | 0.003 | 0.021 | |
getPrecursorIndices | 0.053 | 0.005 | 0.058 | |
getPrecursors | 0.030 | 0.002 | 0.032 | |
getRSE | 0.004 | 0.001 | 0.006 | |
getRTdf | 0.008 | 0.002 | 0.009 | |
getRefExpFeatureMap | 0.267 | 0.011 | 0.278 | |
getRefRun | 0.261 | 0.011 | 0.276 | |
getRunNames | 0.012 | 0.002 | 0.016 | |
getSeqSimMatCpp | 0.000 | 0.000 | 0.002 | |
getTransitions | 0.172 | 0.010 | 0.183 | |
getTree | 0.033 | 0.004 | 0.037 | |
getXICs | 0.096 | 0.007 | 0.103 | |
getXICs4AlignObj | 0.064 | 0.005 | 0.069 | |
get_ropenms | 0.000 | 0.001 | 0.000 | |
imputeChromatogram | 0.012 | 0.001 | 0.012 | |
ipfReassignFDR | 0 | 0 | 0 | |
mapIdxToTime | 0.001 | 0.000 | 0.000 | |
mappedRTfromAlignObj | 0.004 | 0.001 | 0.004 | |
mergeXIC | 0.003 | 0.001 | 0.004 | |
mstAlignRuns | 1.564 | 0.052 | 1.618 | |
mstScript1 | 0.632 | 0.291 | 0.717 | |
mstScript2 | 2.161 | 0.567 | 2.535 | |
nrDesc | 0.000 | 0.000 | 0.001 | |
otherChildXICpp | 0.007 | 0.001 | 0.010 | |
paramsDIAlignR | 0 | 0 | 0 | |
perBatch | 0.001 | 0.000 | 0.001 | |
pickNearestFeature | 0.005 | 0.000 | 0.005 | |
plotAlignedAnalytes | 0.529 | 0.022 | 0.552 | |
plotAlignmentPath | 0.393 | 0.039 | 0.433 | |
plotAnalyteXICs | 0.444 | 0.021 | 0.466 | |
plotXICgroup | 0.328 | 0.012 | 0.342 | |
populateReferenceExperimentFeatureAlignmentMap | 0.014 | 0.002 | 0.017 | |
progAlignRuns | 0.001 | 0.001 | 0.002 | |
readMzMLHeader | 0.001 | 0.000 | 0.002 | |
readSqMassHeader | 0.001 | 0.000 | 0.002 | |
recalculateIntensity | 0.264 | 0.011 | 0.275 | |
reduceXICs | 0.083 | 0.005 | 0.089 | |
script1 | 0.934 | 0.911 | 1.241 | |
script2 | 2.409 | 1.488 | 3.178 | |
setAlignmentRank | 0.014 | 0.002 | 0.015 | |
sgolayCpp | 0.003 | 0.001 | 0.004 | |
sgolayFill | 0.001 | 0.000 | 0.001 | |
smoothSingleXIC | 0.003 | 0.001 | 0.004 | |
smoothXICs | 0.007 | 0.001 | 0.009 | |
splineFill | 0.000 | 0.000 | 0.001 | |
splineFillCpp | 0.003 | 0.001 | 0.004 | |
traverseDown | 1.341 | 0.050 | 1.395 | |
traverseMST | 0 | 0 | 0 | |
traverseUp | 1.353 | 0.042 | 1.397 | |
trfrParentFeature | 0.052 | 0.006 | 0.059 | |
trimXICs | 0.002 | 0.001 | 0.004 | |
uncompressVec | 0.006 | 0.001 | 0.007 | |
updateFileInfo | 0.011 | 0.002 | 0.013 | |
writeOutFeatureAlignmentMap | 0.006 | 0.001 | 0.006 | |
writeTables | 0.005 | 0.000 | 0.005 | |