Back to Multiple platform build/check report for BioC 3.21: simplified long |
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This page was generated on 2025-03-20 11:45 -0400 (Thu, 20 Mar 2025).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | R Under development (unstable) (2025-03-13 r87965) -- "Unsuffered Consequences" | 4777 |
palomino7 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2025-03-01 r87860 ucrt) -- "Unsuffered Consequences" | 4545 |
lconway | macOS 12.7.1 Monterey | x86_64 | R Under development (unstable) (2025-03-02 r87868) -- "Unsuffered Consequences" | 4576 |
kjohnson3 | macOS 13.7.1 Ventura | arm64 | R Under development (unstable) (2025-03-02 r87868) -- "Unsuffered Consequences" | 4528 |
kunpeng2 | Linux (openEuler 24.03 LTS) | aarch64 | R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" | 4458 |
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 568/2313 | 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 24.03 LTS) / 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: 2025-03-19 19:09:49 -0400 (Wed, 19 Mar 2025) |
EndedAt: 2025-03-19 19:10:54 -0400 (Wed, 19 Mar 2025) |
EllapsedTime: 65.8 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) (2025-03-02 r87868) * using platform: aarch64-apple-darwin20 * R was compiled by Apple clang version 14.0.0 (clang-1400.0.29.202) GNU Fortran (GCC) 14.2.0 * 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 11.5Mb sub-directories of 1Mb or more: extdata 4.0Mb metabo 4.1Mb ptms 1.5Mb * checking package directory ... OK * checking DESCRIPTION meta-information ... OK * checking top-level files ... OK * checking for left-over files ... OK * checking index information ... OK * checking package subdirectories ... OK * checking code files for non-ASCII characters ... OK * checking R files for syntax errors ... OK * checking whether the package can be loaded ... OK * checking whether the package can be loaded with stated dependencies ... OK * checking whether the package can be unloaded cleanly ... OK * checking whether the namespace can be loaded with stated dependencies ... OK * checking whether the namespace can be unloaded cleanly ... OK * checking 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 3.406 4.917 3.086 * 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 10 | WARN 3 | SKIP 8 | PASS 622 ] 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’ ... ** this is package ‘DIAlignR’ version ‘2.15.1’ ** 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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 0.02565694 secs Time difference of 0.04653215 secs Time difference of 0.05510497 secs Time difference of 0.01032782 secs Time difference of 0.002550125 secs Time difference of 0.02788401 secs Time difference of 0.3731959 secs Time difference of 0.006249905 secs Time difference of 0.1082439 secs [1] "hroest_K120808_Strep10%PlasmaBiolRepl1_R03_SW_filt" [2] "hroest_K120809_Strep0%PlasmaBiolRepl2_R04_SW_filt" Time difference of 0.006218195 secs Time difference of 0.04320621 secs Time difference of 0.03015304 secs Time difference of 0.00600481 secs Time difference of 0.001715183 secs Time difference of 0.01605606 secs Time difference of 0.195112 secs Time difference of 0.0025599 secs Time difference of 0.21243 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 0.005724192 secs Time difference of 0.04987216 secs Time difference of 0.02586913 secs Time difference of 0.03615022 secs Time difference of 0.002652884 secs Time difference of 0.01622605 secs Time difference of 0.2807848 secs Time difference of 0.005480051 secs Time difference of 0.08524919 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 0.006134987 secs Time difference of 0.004412889 secs Time difference of 9.298325e-05 secs Time difference of 0.03906012 secs Time difference of 0.003251076 secs Time difference of 0.01302004 secs Time difference of 0.003868818 secs Time difference of 0.002358913 secs Time difference of 0.02568102 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 0.002468824 secs Time difference of 0.008080006 secs Time difference of 0.002844095 secs Time difference of 0.00383687 secs Time difference of 0.002130985 secs Time difference of 0.01089001 secs Time difference of 0.01786208 secs Time difference of 0.008823872 secs Time difference of 0.06358719 secs [1] "chludwig_K150309_004b_SW_1_16" "chludwig_K150309_008_SW_1_4" [3] "chludwig_K150309_013_SW_0" Time difference of 0.003615856 secs Time difference of 0.003612995 secs Time difference of 0.0003139973 secs Time difference of 0.006086111 secs Time difference of 0.004127979 secs Time difference of 0.01446605 secs Time difference of 0.001465797 secs Time difference of 0.01182008 secs Time difference of 0.05894709 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 0.03739405 secs Time difference of 0.01031899 secs Time difference of 0.0009510517 secs Time difference of 0.004434824 secs Time difference of 0.01402307 secs Time difference of 0.00376296 secs Time difference of 0.004523993 secs Time difference of 0.02491784 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 0.008533955 secs [1] "run0 run1\nrun2 run2" Time difference of 0.2185321 secs Time difference of 0.02790499 secs Time difference of 0.003196955 secs Time difference of 0.01663899 secs Time difference of 0.4290462 secs Time difference of 0.00555706 secs Time difference of 0.09863305 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 0.07823801 secs Time difference of 0.2622292 secs Time difference of 1.833961 secs Time difference of 0.1169651 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 0.04505014 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 0.2741072 secs Time difference of 0.08373594 secs [1] "Written /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/DIAlignR/extdata/temp_1_2.rds" Time difference of 0.1727569 secs [1] "Written /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/DIAlignR/extdata/temp_2_2.rds" Time difference of 0.08825016 secs Time difference of 0.05004406 secs [1] "Written /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/DIAlignR/extdata/temp_all_2.rds" Time difference of 0.04081583 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 0.03715301 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 0.2707491 secs Time difference of 0.2611709 secs [1] "Written /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/DIAlignR/extdata/temp_1_2.rds" Time difference of 0.115335 secs [1] "Written /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/DIAlignR/extdata/temp_2_2.rds" Time difference of 0.08836508 secs Time difference of 0.003772974 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 10 | WARN 3 | SKIP 8 | PASS 622 ] ══ 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_align_dia_runs.R:122:3'): test_getAlignObjs ────────────────── outData[[2]][["4618"]][["run1_run2"]][["ref"]] not equal to lapply(...). Component 1: Attributes: < Component 2: Component 2: 2 string mismatches > Component 2: Attributes: < Component 2: Component 2: 2 string mismatches > Component 3: Attributes: < Component 2: Component 2: 2 string mismatches > Component 4: Attributes: < Component 2: Component 2: 2 string mismatches > Component 5: Attributes: < Component 2: Component 2: 2 string mismatches > Component 6: Attributes: < Component 2: Component 2: 2 string mismatches > ── Failure ('test_align_dia_runs.R:124:3'): test_getAlignObjs ────────────────── outData[[2]][["4618"]][["run1_run2"]][["eXp"]] not equal to lapply(...). Component 1: Attributes: < Component 2: Component 2: 2 string mismatches > Component 2: Attributes: < Component 2: Component 2: 2 string mismatches > Component 3: Attributes: < Component 2: Component 2: 2 string mismatches > Component 4: Attributes: < Component 2: Component 2: 2 string mismatches > Component 5: Attributes: < Component 2: Component 2: 2 string mismatches > Component 6: Attributes: < Component 2: Component 2: 2 string mismatches > ── 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_get_peaks_chromatograms.R:48:3'): test_getXICs4AlignObj ────── outData[["hroest_K120808_Strep10%PlasmaBiolRepl1_R03_SW_filt"]][["4618"]] not equal to lapply(XICs[[runs[["run0"]]]][["4618"]], as.matrix). Component 1: Attributes: < Component 2: Component 2: 2 string mismatches > Component 2: Attributes: < Component 2: Component 2: 2 string mismatches > Component 3: Attributes: < Component 2: Component 2: 2 string mismatches > Component 4: Attributes: < Component 2: Component 2: 2 string mismatches > Component 5: Attributes: < Component 2: Component 2: 2 string mismatches > Component 6: Attributes: < Component 2: Component 2: 2 string mismatches > ── Failure ('test_get_peaks_chromatograms.R:49:3'): test_getXICs4AlignObj ────── outData[["hroest_K120809_Strep0%PlasmaBiolRepl2_R04_SW_filt"]][["4618"]] not equal to lapply(XICs[[runs[["run1"]]]][["4618"]], as.matrix). Component 1: Attributes: < Component 2: Component 2: 2 string mismatches > Component 2: Attributes: < Component 2: Component 2: 2 string mismatches > Component 3: Attributes: < Component 2: Component 2: 2 string mismatches > Component 4: Attributes: < Component 2: Component 2: 2 string mismatches > Component 5: Attributes: < Component 2: Component 2: 2 string mismatches > Component 6: Attributes: < Component 2: Component 2: 2 string mismatches > ── Failure ('test_get_peaks_chromatograms.R:68:3'): test_getXICs ─────────────── outData[["hroest_K120808_Strep10%PlasmaBiolRepl1_R03_SW_filt"]][["4618"]] not equal to lapply(...). Component 1: Attributes: < Component 2: Component 2: 2 string mismatches > Component 2: Attributes: < Component 2: Component 2: 2 string mismatches > Component 3: Attributes: < Component 2: Component 2: 2 string mismatches > Component 4: Attributes: < Component 2: Component 2: 2 string mismatches > Component 5: Attributes: < Component 2: Component 2: 2 string mismatches > Component 6: Attributes: < Component 2: Component 2: 2 string mismatches > ── Failure ('test_get_peaks_chromatograms.R:70:3'): test_getXICs ─────────────── outData[["hroest_K120809_Strep10%PlasmaBiolRepl2_R04_SW_filt"]][["4618"]] not equal to lapply(...). Component 1: Attributes: < Component 2: Component 2: 2 string mismatches > Component 2: Attributes: < Component 2: Component 2: 2 string mismatches > Component 3: Attributes: < Component 2: Component 2: 2 string mismatches > Component 4: Attributes: < Component 2: Component 2: 2 string mismatches > Component 5: Attributes: < Component 2: Component 2: 2 string mismatches > Component 6: Attributes: < Component 2: Component 2: 2 string mismatches > ── 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 10 | WARN 3 | SKIP 8 | PASS 622 ] Error: Test failures Execution halted
DIAlignR.Rcheck/DIAlignR-Ex.timings
name | user | system | elapsed | |
MSTperBatch | 0 | 0 | 0 | |
addFlankToLeft | 0.000 | 0.000 | 0.001 | |
addFlankToRight | 0 | 0 | 0 | |
addXIC | 0.000 | 0.000 | 0.001 | |
alignChromatogramsCpp | 0.010 | 0.002 | 0.011 | |
alignTargetedRuns | 3.406 | 4.917 | 3.086 | |
alignToMaster | 0.539 | 0.037 | 0.396 | |
alignToRef | 0.001 | 0.001 | 0.000 | |
alignToRefMST | 0 | 0 | 0 | |
alignedXIC | 0.041 | 0.001 | 0.042 | |
analytesFromFeatures | 0.013 | 0.002 | 0.014 | |
approxFill | 0.000 | 0.000 | 0.001 | |
areaIntegrator | 0.002 | 0.001 | 0.001 | |
blobXICs | 0.000 | 0.000 | 0.001 | |
calculateIntensity | 0.000 | 0.000 | 0.001 | |
checkOverlap | 0 | 0 | 0 | |
checkParams | 0 | 0 | 0 | |
childXIC | 0.040 | 0.001 | 0.041 | |
childXICs | 0.166 | 0.008 | 0.173 | |
constrainSimCpp | 0.000 | 0.000 | 0.001 | |
createMZML | 0.001 | 0.001 | 0.002 | |
createSqMass | 0.001 | 0.001 | 0.001 | |
dialignrLoess | 0 | 0 | 0 | |
doAffineAlignmentCpp | 0.001 | 0.000 | 0.001 | |
doAlignmentCpp | 0.000 | 0.001 | 0.001 | |
extractXIC_group | 0.241 | 0.010 | 0.250 | |
extractXIC_group2 | 0 | 0 | 0 | |
fetchAnalytesInfo | 0.003 | 0.001 | 0.003 | |
fetchFeaturesFromRun | 0.002 | 0.000 | 0.003 | |
fetchPeptidesInfo | 0.002 | 0.001 | 0.002 | |
fetchPeptidesInfo2 | 0.002 | 0.000 | 0.002 | |
fetchPrecursorsInfo | 0.000 | 0.000 | 0.001 | |
fetchTransitionsFromRun | 0.002 | 0.000 | 0.002 | |
filenamesFromMZML | 0.000 | 0.001 | 0.000 | |
filenamesFromOSW | 0.000 | 0.000 | 0.001 | |
getAlignObj | 0.007 | 0.001 | 0.008 | |
getAlignObjs | 0.305 | 0.010 | 0.314 | |
getAlignedFigs | 0.034 | 0.002 | 0.036 | |
getAlignedIndices | 0.004 | 0.001 | 0.004 | |
getAlignedTimes | 0.006 | 0.001 | 0.007 | |
getAlignedTimesCpp | 0.002 | 0.001 | 0.002 | |
getAlignedTimesFast | 0.005 | 0.001 | 0.006 | |
getBaseGapPenaltyCpp | 0.000 | 0.000 | 0.001 | |
getChildFeature | 0.014 | 0.002 | 0.015 | |
getChildXICpp | 0.002 | 0.001 | 0.003 | |
getChildXICs | 0.310 | 0.026 | 0.181 | |
getChromSimMatCpp | 0.002 | 0.001 | 0.001 | |
getChromatogramIndices | 0.054 | 0.005 | 0.031 | |
getFeatures | 0.033 | 0.004 | 0.020 | |
getGlobalAlignMaskCpp | 0.001 | 0.001 | 0.000 | |
getGlobalAlignment | 0.006 | 0.001 | 0.003 | |
getGlobalFits | 0.171 | 0.009 | 0.091 | |
getLOESSfit | 0.002 | 0.001 | 0.002 | |
getLinearfit | 0.003 | 0.000 | 0.002 | |
getMST | 0 | 0 | 0 | |
getMZMLpointers | 0.010 | 0.001 | 0.006 | |
getMappedRT | 0.007 | 0.002 | 0.005 | |
getMultipeptide | 0.818 | 0.055 | 0.671 | |
getNativeIDs | 0.010 | 0.001 | 0.008 | |
getNodeIDs | 0.001 | 0.000 | 0.000 | |
getNodeRun | 0.208 | 0.016 | 0.115 | |
getOswAnalytes | 0.005 | 0.001 | 0.003 | |
getOswFiles | 0.004 | 0.000 | 0.003 | |
getPeptideScores | 0.022 | 0.002 | 0.012 | |
getPrecursorByID | 0.007 | 0.001 | 0.004 | |
getPrecursorIndices | 0.028 | 0.003 | 0.016 | |
getPrecursors | 0.016 | 0.001 | 0.009 | |
getRSE | 0.003 | 0.000 | 0.001 | |
getRTdf | 0.004 | 0.001 | 0.002 | |
getRefExpFeatureMap | 0.141 | 0.007 | 0.075 | |
getRefRun | 0.158 | 0.008 | 0.084 | |
getRunNames | 0.007 | 0.001 | 0.004 | |
getSeqSimMatCpp | 0.001 | 0.001 | 0.000 | |
getTransitions | 0.101 | 0.008 | 0.054 | |
getTree | 0.017 | 0.001 | 0.009 | |
getXICs | 0.051 | 0.004 | 0.028 | |
getXICs4AlignObj | 0.031 | 0.002 | 0.016 | |
get_ropenms | 0 | 0 | 0 | |
imputeChromatogram | 0.007 | 0.001 | 0.004 | |
ipfReassignFDR | 0 | 0 | 0 | |
mapIdxToTime | 0 | 0 | 0 | |
mappedRTfromAlignObj | 0.002 | 0.001 | 0.001 | |
mergeXIC | 0.002 | 0.000 | 0.001 | |
mstAlignRuns | 0.612 | 0.028 | 0.440 | |
mstScript1 | 0.208 | 0.118 | 0.245 | |
mstScript2 | 0.795 | 0.258 | 0.785 | |
nrDesc | 0.000 | 0.000 | 0.001 | |
otherChildXICpp | 0.002 | 0.000 | 0.003 | |
paramsDIAlignR | 0 | 0 | 0 | |
perBatch | 0 | 0 | 0 | |
pickNearestFeature | 0.001 | 0.000 | 0.002 | |
plotAlignedAnalytes | 0.155 | 0.006 | 0.160 | |
plotAlignmentPath | 0.118 | 0.014 | 0.132 | |
plotAnalyteXICs | 0.125 | 0.007 | 0.132 | |
plotXICgroup | 0.107 | 0.006 | 0.112 | |
populateReferenceExperimentFeatureAlignmentMap | 0.005 | 0.001 | 0.005 | |
progAlignRuns | 0.001 | 0.000 | 0.000 | |
readMzMLHeader | 0.000 | 0.000 | 0.001 | |
readSqMassHeader | 0.001 | 0.000 | 0.000 | |
recalculateIntensity | 0.066 | 0.003 | 0.068 | |
reduceXICs | 0.047 | 0.005 | 0.035 | |
script1 | 0.482 | 0.440 | 0.469 | |
script2 | 0.900 | 0.566 | 1.007 | |
setAlignmentRank | 0.004 | 0.001 | 0.005 | |
sgolayCpp | 0.001 | 0.001 | 0.001 | |
sgolayFill | 0 | 0 | 0 | |
smoothSingleXIC | 0.001 | 0.001 | 0.002 | |
smoothXICs | 0.002 | 0.000 | 0.003 | |
splineFill | 0.000 | 0.001 | 0.000 | |
splineFillCpp | 0.001 | 0.000 | 0.001 | |
traverseDown | 0.529 | 0.044 | 0.379 | |
traverseMST | 0 | 0 | 0 | |
traverseUp | 0.524 | 0.031 | 0.362 | |
trfrParentFeature | 0.013 | 0.002 | 0.014 | |
trimXICs | 0.001 | 0.000 | 0.001 | |
uncompressVec | 0.001 | 0.000 | 0.002 | |
updateFileInfo | 0.003 | 0.000 | 0.003 | |
writeOutFeatureAlignmentMap | 0.001 | 0.001 | 0.002 | |
writeTables | 0.001 | 0.000 | 0.001 | |