Back to Multiple platform build/check report for BioC 3.21: simplified long |
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This page was generated on 2024-12-24 11:44 -0500 (Tue, 24 Dec 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | R Under development (unstable) (2024-10-21 r87258) -- "Unsuffered Consequences" | 4754 |
palomino7 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2024-10-26 r87273 ucrt) -- "Unsuffered Consequences" | 4472 |
lconway | macOS 12.7.1 Monterey | x86_64 | R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" | 4426 |
kjohnson3 | macOS 13.7.1 Ventura | arm64 | R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" | 4381 |
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | R Under development (unstable) (2024-11-24 r87369) -- "Unsuffered Consequences" | 4373 |
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 557/2274 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
Shubham Gupta
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | ERROR | |||||||||
palomino7 | Windows Server 2022 Datacenter / x64 | OK | OK | ERROR | OK | |||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | ERROR | OK | |||||||||
kjohnson3 | macOS 13.7.1 Ventura / arm64 | OK | OK | ERROR | OK | |||||||||
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | ERROR | ||||||||||
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: 2.15.1 |
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_2.15.1.tar.gz |
StartedAt: 2024-12-23 19:02:05 -0500 (Mon, 23 Dec 2024) |
EndedAt: 2024-12-23 19:03:10 -0500 (Mon, 23 Dec 2024) |
EllapsedTime: 64.8 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_2.15.1.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/DIAlignR.Rcheck’ * using R Under development (unstable) (2024-11-20 r87352) * 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 13.7.1 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘DIAlignR/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘DIAlignR’ version ‘2.15.1’ * 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-1500.1.0.2.5)’ * used SDK: ‘MacOSX11.3.sdk’ * checking C++ specification ... NOTE Specified C++14: please drop specification unless essential * checking installed package size ... INFO 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 whether startup messages can be suppressed ... 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/4.5-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 3.307 5.436 3.368 * 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: 2. ├─testthat::compare(act$val, exp$val, ..., tolerance = tolerance) 3. └─testthat:::compare.default(act$val, exp$val, ..., tolerance = tolerance) 4. ├─base::all.equal(x, y, ...) 5. └─data.table:::all.equal.data.table(x, y, ...) 6. ├─base::all.equal(x, y, tolerance = tolerance, ..., check.attributes = check.attributes) 7. └─bit64::all.equal.integer64(...) 8. ├─base::is.na(current) 9. └─bit64::is.na.integer64(current) ── 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 4 | WARN 3 | SKIP 8 | PASS 628 ] 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, 4 NOTEs See ‘/Users/biocbuild/bbs-3.21-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/4.5-arm64/Resources/library’ * installing *source* package ‘DIAlignR’ ... ** using staged installation ** libs using C++ compiler: ‘Apple clang version 15.0.0 (clang-1500.1.0.2.5)’ 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/4.5-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/RcppEigen/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -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/4.5-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/RcppEigen/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -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/4.5-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/RcppEigen/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -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/4.5-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/RcppEigen/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -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/4.5-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/RcppEigen/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -c RcppExports.cpp -o RcppExports.o In file included from RcppExports.cpp:4: In file included from /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/RcppEigen/include/RcppEigen.h:25: In file included from /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/RcppEigen/include/RcppEigenForward.h:29: In file included from /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/RcppEigen/include/Eigen/Sparse:26: In file included from /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/RcppEigen/include/Eigen/SparseCore:61: /Library/Frameworks/R.framework/Versions/4.5-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/4.5-arm64/Resources/library/RcppEigen/include/RcppEigen.h:25: In file included from /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/RcppEigen/include/RcppEigenForward.h:29: In file included from /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/RcppEigen/include/Eigen/Sparse:29: In file included from /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/RcppEigen/include/Eigen/SparseLU:35: /Library/Frameworks/R.framework/Versions/4.5-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/4.5-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/4.5-arm64/Resources/library/RcppEigen/include/RcppEigen.h:25: In file included from /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/RcppEigen/include/RcppEigenForward.h:31: In file included from /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/RcppEigen/include/unsupported/Eigen/IterativeSolvers:46: /Library/Frameworks/R.framework/Versions/4.5-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/4.5-arm64/Resources/library/RcppEigen/include/RcppEigen.h:25: In file included from /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/RcppEigen/include/RcppEigenForward.h:37: In file included from /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/RcppEigen/include/unsupported/Eigen/SparseExtra:45: /Library/Frameworks/R.framework/Versions/4.5-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/4.5-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/RcppEigen/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -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/4.5-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/RcppEigen/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -c SavitzkyGolayFilter.cpp -o SavitzkyGolayFilter.o In file included from SavitzkyGolayFilter.cpp:1: In file included from /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/RcppEigen/include/RcppEigen.h:25: In file included from /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/RcppEigen/include/RcppEigenForward.h:29: In file included from /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/RcppEigen/include/Eigen/Sparse:26: In file included from /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/RcppEigen/include/Eigen/SparseCore:61: /Library/Frameworks/R.framework/Versions/4.5-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/4.5-arm64/Resources/library/RcppEigen/include/RcppEigen.h:25: In file included from /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/RcppEigen/include/RcppEigenForward.h:29: In file included from /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/RcppEigen/include/Eigen/Sparse:29: In file included from /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/RcppEigen/include/Eigen/SparseLU:35: /Library/Frameworks/R.framework/Versions/4.5-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/4.5-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/4.5-arm64/Resources/library/RcppEigen/include/RcppEigen.h:25: In file included from /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/RcppEigen/include/RcppEigenForward.h:31: In file included from /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/RcppEigen/include/unsupported/Eigen/IterativeSolvers:46: /Library/Frameworks/R.framework/Versions/4.5-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/4.5-arm64/Resources/library/RcppEigen/include/RcppEigen.h:25: In file included from /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/RcppEigen/include/RcppEigenForward.h:37: In file included from /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/RcppEigen/include/unsupported/Eigen/SparseExtra:45: /Library/Frameworks/R.framework/Versions/4.5-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/4.5-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/RcppEigen/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -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/4.5-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/RcppEigen/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -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/4.5-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/RcppEigen/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -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/4.5-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/RcppEigen/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -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/4.5-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/RcppEigen/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -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/4.5-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/RcppEigen/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -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/4.5-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/RcppEigen/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -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/4.5-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/RcppEigen/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -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/4.5-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/RcppEigen/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -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/4.5-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/RcppEigen/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -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/4.5-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/RcppEigen/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -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/4.5-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/RcppEigen/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -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/4.5-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/RcppEigen/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -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/4.5-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 Warning in fun(libname, pkgname) : Package 'DIAlignR' is deprecated and will be removed from Bioconductor version 3.22 ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location Warning in fun(libname, pkgname) : Package 'DIAlignR' is deprecated and will be removed from Bioconductor version 3.22 ** testing if installed package keeps a record of temporary installation path * DONE (DIAlignR)
DIAlignR.Rcheck/tests/testthat.Rout.fail
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Type 'q()' to quit R. > library(testthat) > library(DIAlignR) Warning message: In fun(libname, pkgname) : Package 'DIAlignR' is deprecated and will be removed from Bioconductor version 3.22 > > 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 0.01431012 secs Time difference of 0.05364013 secs Time difference of 0.04905701 secs Time difference of 0.008705854 secs Time difference of 0.002490044 secs Time difference of 0.02914715 secs Time difference of 0.374305 secs Time difference of 0.006205797 secs Time difference of 0.1077318 secs [1] "hroest_K120808_Strep10%PlasmaBiolRepl1_R03_SW_filt" [2] "hroest_K120809_Strep0%PlasmaBiolRepl2_R04_SW_filt" Time difference of 0.00583601 secs Time difference of 0.04519105 secs Time difference of 0.028193 secs Time difference of 0.006865978 secs Time difference of 0.00230813 secs Time difference of 0.01809788 secs Time difference of 0.2048969 secs Time difference of 0.0023911 secs Time difference of 0.224463 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 0.005647898 secs Time difference of 0.04985499 secs Time difference of 0.02495408 secs Time difference of 0.03769994 secs Time difference of 0.004050016 secs Time difference of 0.01627088 secs Time difference of 0.292155 secs Time difference of 0.005394936 secs Time difference of 0.08107805 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 0.006285906 secs Time difference of 0.004335165 secs Time difference of 8.98838e-05 secs Time difference of 0.03609204 secs Time difference of 0.002774954 secs Time difference of 0.01192307 secs Time difference of 0.003725052 secs Time difference of 0.002319098 secs Time difference of 0.02458096 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 0.002326012 secs Time difference of 0.008187056 secs Time difference of 0.003522873 secs Time difference of 0.004038095 secs Time difference of 0.002091885 secs Time difference of 0.009774923 secs Time difference of 0.01637292 secs Time difference of 0.001966 secs Time difference of 0.065979 secs [1] "chludwig_K150309_004b_SW_1_16" "chludwig_K150309_008_SW_1_4" [3] "chludwig_K150309_013_SW_0" Time difference of 0.002771139 secs Time difference of 0.002851009 secs Time difference of 0.0002539158 secs Time difference of 0.00443387 secs Time difference of 0.003143072 secs Time difference of 0.01375604 secs Time difference of 0.001449108 secs Time difference of 0.00484395 secs Time difference of 0.06871009 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 0.03696704 secs Time difference of 0.004801989 secs Time difference of 0.0005290508 secs Time difference of 0.002696991 secs Time difference of 0.01218295 secs Time difference of 0.003582001 secs Time difference of 0.0041821 secs Time difference of 0.03315783 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 0.007431984 secs [1] "run0 run1\nrun2 run2" Time difference of 0.1926091 secs Time difference of 0.025383 secs Time difference of 0.00316596 secs Time difference of 0.01645303 secs Time difference of 0.2747061 secs Time difference of 0.004381895 secs Time difference of 0.0902679 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 0.05502987 secs Time difference of 0.227073 secs Time difference of 1.746408 secs Time difference of 0.1269541 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 0.03815794 secs [1] "Written /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/DIAlignR/extdata/temp_prog1.RData" [1] "Written /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/DIAlignR/extdata/temp_0_2.rds" [1] "progTree1 is done." Time difference of 0.4533992 secs Time difference of 0.09287691 secs [1] "Written /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/DIAlignR/extdata/temp_1_2.rds" Time difference of 0.147368 secs [1] "Written /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/DIAlignR/extdata/temp_2_2.rds" Time difference of 0.1032619 secs Time difference of 0.04402995 secs [1] "Written /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/DIAlignR/extdata/temp_all_2.rds" Time difference of 0.03874588 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 0.03660512 secs [1] "Written /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/DIAlignR/extdata/temp_prog1.RData" [1] "Written /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/DIAlignR/extdata/temp_0_2.rds" [1] "progTree1 is done." Time difference of 0.2338681 secs Time difference of 0.08543682 secs [1] "Written /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/DIAlignR/extdata/temp_1_2.rds" Time difference of 0.1097291 secs [1] "Written /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/DIAlignR/extdata/temp_2_2.rds" Time difference of 0.09004688 secs Time difference of 0.00417304 secs [1] "Written /Library/Frameworks/R.framework/Versions/4.5-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 4 | WARN 3 | SKIP 8 | PASS 628 ] ══ 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$span not equal to 0.8. 1/1 mismatches [1] 0.4 - 0.8 == -0.4 ── Failure ('test_get_global_fit.R:22:3'): test_dialignrLoess ────────────────── predict(outData, newdata = data.frame(RT.ref = 13.5))[[1]] not equal to 5.5. 1/1 mismatches [1] 2.75 - 5.5 == -2.75 ── Error ('test_utils.R:76:13'): test_getRefExpFeatureMap ────────────────────── Error in `is.na.integer64(current)`: REAL() can only be applied to a 'numeric', not a 'integer' Backtrace: ▆ 1. └─testthat::expect_equal(outData[[1]], expData, tolerance = 1e-04) at test_utils.R:76:13 2. ├─testthat::compare(act$val, exp$val, ..., tolerance = tolerance) 3. └─testthat:::compare.default(act$val, exp$val, ..., tolerance = tolerance) 4. ├─base::all.equal(x, y, ...) 5. └─data.table:::all.equal.data.table(x, y, ...) 6. ├─base::all.equal(x, y, tolerance = tolerance, ..., check.attributes = check.attributes) 7. └─bit64::all.equal.integer64(...) 8. ├─base::is.na(current) 9. └─bit64::is.na.integer64(current) ── 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 4 | WARN 3 | SKIP 8 | PASS 628 ] Error: Test failures Execution halted
DIAlignR.Rcheck/DIAlignR-Ex.timings
name | user | system | elapsed | |
MSTperBatch | 0.001 | 0.000 | 0.000 | |
addFlankToLeft | 0 | 0 | 0 | |
addFlankToRight | 0.000 | 0.000 | 0.001 | |
addXIC | 0 | 0 | 0 | |
alignChromatogramsCpp | 0.010 | 0.002 | 0.012 | |
alignTargetedRuns | 3.307 | 5.436 | 3.368 | |
alignToMaster | 0.362 | 0.026 | 0.410 | |
alignToRef | 0.001 | 0.000 | 0.001 | |
alignToRefMST | 0 | 0 | 0 | |
alignedXIC | 0.042 | 0.002 | 0.044 | |
analytesFromFeatures | 0.013 | 0.001 | 0.015 | |
approxFill | 0.000 | 0.001 | 0.000 | |
areaIntegrator | 0.002 | 0.000 | 0.001 | |
blobXICs | 0.000 | 0.000 | 0.001 | |
calculateIntensity | 0.001 | 0.001 | 0.001 | |
checkOverlap | 0 | 0 | 0 | |
checkParams | 0 | 0 | 0 | |
childXIC | 0.042 | 0.001 | 0.044 | |
childXICs | 0.173 | 0.006 | 0.179 | |
constrainSimCpp | 0 | 0 | 0 | |
createMZML | 0.001 | 0.001 | 0.002 | |
createSqMass | 0.001 | 0.000 | 0.001 | |
dialignrLoess | 0.000 | 0.001 | 0.000 | |
doAffineAlignmentCpp | 0.000 | 0.000 | 0.001 | |
doAlignmentCpp | 0.001 | 0.000 | 0.001 | |
extractXIC_group | 0.248 | 0.012 | 0.261 | |
extractXIC_group2 | 0.001 | 0.000 | 0.001 | |
fetchAnalytesInfo | 0.003 | 0.000 | 0.003 | |
fetchFeaturesFromRun | 0.002 | 0.000 | 0.002 | |
fetchPeptidesInfo | 0.003 | 0.001 | 0.003 | |
fetchPeptidesInfo2 | 0.002 | 0.000 | 0.003 | |
fetchPrecursorsInfo | 0.000 | 0.000 | 0.001 | |
fetchTransitionsFromRun | 0.002 | 0.000 | 0.002 | |
filenamesFromMZML | 0.001 | 0.000 | 0.000 | |
filenamesFromOSW | 0.000 | 0.000 | 0.001 | |
getAlignObj | 0.008 | 0.001 | 0.010 | |
getAlignObjs | 0.304 | 0.010 | 0.315 | |
getAlignedFigs | 0.037 | 0.003 | 0.040 | |
getAlignedIndices | 0.004 | 0.001 | 0.004 | |
getAlignedTimes | 0.006 | 0.001 | 0.008 | |
getAlignedTimesCpp | 0.002 | 0.001 | 0.002 | |
getAlignedTimesFast | 0.004 | 0.001 | 0.006 | |
getBaseGapPenaltyCpp | 0 | 0 | 0 | |
getChildFeature | 0.014 | 0.002 | 0.015 | |
getChildXICpp | 0.002 | 0.001 | 0.003 | |
getChildXICs | 0.167 | 0.009 | 0.178 | |
getChromSimMatCpp | 0.000 | 0.001 | 0.001 | |
getChromatogramIndices | 0.031 | 0.001 | 0.033 | |
getFeatures | 0.013 | 0.002 | 0.017 | |
getGlobalAlignMaskCpp | 0.001 | 0.001 | 0.001 | |
getGlobalAlignment | 0.002 | 0.000 | 0.003 | |
getGlobalFits | 0.094 | 0.003 | 0.097 | |
getLOESSfit | 0.001 | 0.000 | 0.002 | |
getLinearfit | 0.002 | 0.001 | 0.002 | |
getMST | 0.000 | 0.000 | 0.001 | |
getMZMLpointers | 0.006 | 0.001 | 0.006 | |
getMappedRT | 0.004 | 0.001 | 0.005 | |
getMultipeptide | 0.621 | 0.046 | 0.694 | |
getNativeIDs | 0.007 | 0.001 | 0.007 | |
getNodeIDs | 0 | 0 | 0 | |
getNodeRun | 0.097 | 0.007 | 0.105 | |
getOswAnalytes | 0.002 | 0.000 | 0.003 | |
getOswFiles | 0.003 | 0.001 | 0.003 | |
getPeptideScores | 0.012 | 0.001 | 0.014 | |
getPrecursorByID | 0.005 | 0.001 | 0.006 | |
getPrecursorIndices | 0.014 | 0.002 | 0.015 | |
getPrecursors | 0.007 | 0.001 | 0.008 | |
getRSE | 0.001 | 0.000 | 0.002 | |
getRTdf | 0.002 | 0.001 | 0.003 | |
getRefExpFeatureMap | 0.080 | 0.004 | 0.088 | |
getRefRun | 0.083 | 0.004 | 0.088 | |
getRunNames | 0.003 | 0.000 | 0.004 | |
getSeqSimMatCpp | 0.000 | 0.001 | 0.000 | |
getTransitions | 0.052 | 0.002 | 0.057 | |
getTree | 0.010 | 0.001 | 0.011 | |
getXICs | 0.027 | 0.003 | 0.031 | |
getXICs4AlignObj | 0.019 | 0.002 | 0.020 | |
get_ropenms | 0 | 0 | 0 | |
imputeChromatogram | 0.004 | 0.000 | 0.005 | |
ipfReassignFDR | 0 | 0 | 0 | |
mapIdxToTime | 0 | 0 | 0 | |
mappedRTfromAlignObj | 0.001 | 0.000 | 0.001 | |
mergeXIC | 0.001 | 0.001 | 0.001 | |
mstAlignRuns | 0.444 | 0.030 | 0.485 | |
mstScript1 | 0.204 | 0.109 | 0.242 | |
mstScript2 | 0.631 | 0.245 | 0.817 | |
nrDesc | 0 | 0 | 0 | |
otherChildXICpp | 0.002 | 0.001 | 0.003 | |
paramsDIAlignR | 0 | 0 | 0 | |
perBatch | 0 | 0 | 0 | |
pickNearestFeature | 0.001 | 0.001 | 0.001 | |
plotAlignedAnalytes | 0.148 | 0.006 | 0.166 | |
plotAlignmentPath | 0.116 | 0.011 | 0.128 | |
plotAnalyteXICs | 0.119 | 0.006 | 0.126 | |
plotXICgroup | 0.096 | 0.005 | 0.102 | |
populateReferenceExperimentFeatureAlignmentMap | 0.004 | 0.001 | 0.005 | |
progAlignRuns | 0.001 | 0.000 | 0.001 | |
readMzMLHeader | 0.000 | 0.000 | 0.001 | |
readSqMassHeader | 0 | 0 | 0 | |
recalculateIntensity | 0.066 | 0.003 | 0.071 | |
reduceXICs | 0.020 | 0.002 | 0.022 | |
script1 | 0.314 | 0.316 | 0.433 | |
script2 | 0.708 | 0.473 | 0.954 | |
setAlignmentRank | 0.004 | 0.001 | 0.005 | |
sgolayCpp | 0.001 | 0.000 | 0.002 | |
sgolayFill | 0.000 | 0.001 | 0.000 | |
smoothSingleXIC | 0.001 | 0.000 | 0.002 | |
smoothXICs | 0.002 | 0.001 | 0.003 | |
splineFill | 0 | 0 | 0 | |
splineFillCpp | 0.001 | 0.001 | 0.001 | |
traverseDown | 0.483 | 0.054 | 0.544 | |
traverseMST | 0 | 0 | 0 | |
traverseUp | 0.357 | 0.023 | 0.380 | |
trfrParentFeature | 0.013 | 0.002 | 0.015 | |
trimXICs | 0.001 | 0.000 | 0.002 | |
uncompressVec | 0.001 | 0.000 | 0.002 | |
updateFileInfo | 0.003 | 0.000 | 0.003 | |
writeOutFeatureAlignmentMap | 0.002 | 0.000 | 0.002 | |
writeTables | 0.001 | 0.000 | 0.002 | |