Shubham Gupta
| Snapshot Date: 2024-06-09 14:00 -0400 (Sun, 09 Jun 2024) |
| git_url: https://git.bioconductor.org/packages/DIAlignR |
| git_branch: devel |
| git_last_commit: 782a3f0 |
| git_last_commit_date: 2024-04-30 11:20:26 -0400 (Tue, 30 Apr 2024) |
| Back to Multiple platform build/check report for BioC 3.20: simplified long |
|
This page was generated on 2024-06-11 15:43 -0400 (Tue, 11 Jun 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.0 RC (2024-04-16 r86468) -- "Puppy Cup" | 4679 |
| palomino4 | Windows Server 2022 Datacenter | x64 | 4.4.0 RC (2024-04-16 r86468 ucrt) -- "Puppy Cup" | 4414 |
| merida1 | macOS 12.7.4 Monterey | x86_64 | 4.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup" | 4441 |
| kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup" | 4394 |
| 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 553/2239 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| DIAlignR 2.13.0 (landing page) Shubham Gupta
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino4 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| merida1 | macOS 12.7.4 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | OK | ERROR | OK | |||||||||
|
To the developers/maintainers of the DIAlignR package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/DIAlignR.git to reflect on this report. See Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
| Package: DIAlignR |
| Version: 2.13.0 |
| Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:DIAlignR.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings DIAlignR_2.13.0.tar.gz |
| StartedAt: 2024-06-10 17:47:15 -0400 (Mon, 10 Jun 2024) |
| EndedAt: 2024-06-10 17:50:33 -0400 (Mon, 10 Jun 2024) |
| EllapsedTime: 198.2 seconds |
| RetCode: 1 |
| Status: ERROR |
| CheckDir: DIAlignR.Rcheck |
| Warnings: NA |
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###
### Running command:
###
### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:DIAlignR.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings DIAlignR_2.13.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/DIAlignR.Rcheck’
* using R version 4.4.0 Patched (2024-04-24 r86482)
* using platform: aarch64-apple-darwin20
* R was compiled by
Apple clang version 14.0.0 (clang-1400.0.29.202)
GNU Fortran (GCC) 12.2.0
* running under: macOS Ventura 13.6.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘DIAlignR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘DIAlignR’ version ‘2.13.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘DIAlignR’ can be installed ... OK
* used C++ compiler: ‘Apple clang version 15.0.0 (clang-1500.0.40.1)’
* used SDK: ‘MacOSX11.3.sdk’
* checking C++ specification ... NOTE
Specified C++14: please drop specification unless essential
* checking installed package size ... NOTE
installed size is 11.4Mb
sub-directories of 1Mb or more:
extdata 4.0Mb
metabo 4.1Mb
ptms 1.5Mb
* checking package directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
alignTargetedRuns: no visible binding for global variable ‘peptide_id’
alignTargetedRuns : <anonymous>: no visible global function definition
for ‘.’
alignTargetedRuns: no visible binding for global variable ‘intensity’
alignToRoot4: no visible binding for global variable ‘trees’
alignToRoot4: no visible binding for global variable ‘precursors’
alignToRoot4: no visible binding for global variable ‘intensity’
childXICs: possible error in cummax(v = cummax(ifelse(is.na(x), -Inf,
x))): unused argument (v = cummax(ifelse(is.na(x), -Inf, x)))
distMat.rSqrd : <anonymous> : <anonymous>: no visible binding for
global variable ‘RT.ref’
distMat.rSqrd : <anonymous> : <anonymous>: no visible binding for
global variable ‘RT.eXp’
fetchPrecursorsInfo: no visible binding for global variable
‘transition_id’
fetchPrecursorsInfo: no visible global function definition for ‘.’
fetchPrecursorsInfo: no visible binding for global variable
‘transition_group_id’
fetchTransitionsFromRun: no visible binding for global variable
‘intensity’
fetchTransitionsFromRun: no visible global function definition for ‘.’
fetchTransitionsFromRun: no visible binding for global variable
‘transition_group_id’
fetchTransitionsFromRun: no visible binding for global variable
‘peak_group_rank’
fetchTransitionsFromRun: no visible global function definition for
‘head’
getNativeIDs: no visible binding for global variable ‘peptide_id’
getPeptideScores: no visible binding for global variable ‘col2’
getPeptideScores: no visible binding for global variable ‘run’
getQuery: no visible binding for global variable
‘identifying.transitionPEPfilter’
getRTdf: no visible binding for global variable ‘peak_group_rank’
getRTdf: no visible binding for global variable ‘m_score’
getRTdf: no visible global function definition for ‘.’
getRTdf: no visible binding for global variable ‘transition_group_id’
getRTdf: no visible binding for global variable ‘RT’
getRefRun : <anonymous>: no visible binding for global variable
‘pvalue’
ipfReassignFDR: no visible binding for global variable ‘ref_run’
ipfReassignFDR: no visible binding for global variable ‘run’
ipfReassignFDR: no visible global function definition for ‘.’
ipfReassignFDR: no visible binding for global variable ‘i.to’
ipfReassignFDR: no visible binding for global variable ‘m_score_new’
ipfReassignFDR: no visible binding for global variable ‘ms2_m_score’
ipfReassignFDR: no visible binding for global variable ‘m_score’
mstAlignRuns: no visible binding for global variable ‘ropenms’
mstAlignRuns: no visible binding for global variable ‘peptide_id’
mstAlignRuns : <anonymous>: no visible global function definition for
‘.’
mstAlignRuns: no visible binding for global variable ‘intensity’
mstScript1: no visible binding for global variable ‘ropenms’
mstScript2: no visible binding for global variable ‘fileInfo’
mstScript2: no visible binding for global variable ‘peptide_id’
mstScript2: no visible binding for global variable ‘features’
mstScript2 : <anonymous>: no visible global function definition for ‘.’
mstScript2 : <anonymous>: no visible binding for global variable
‘features’
mstScript2: no visible binding for global variable ‘intensity’
populateReferenceExperimentFeatureAlignmentMap: no visible binding for
global variable ‘run’
populateReferenceExperimentFeatureAlignmentMap: no visible binding for
global variable ‘transition_group_id’
populateReferenceExperimentFeatureAlignmentMap: no visible binding for
global variable ‘feature_id’
progAlignRuns: no visible binding for global variable ‘peptide_id’
progAlignRuns : <anonymous>: no visible global function definition for
‘.’
progAlignRuns: no visible binding for global variable ‘intensity’
progComb3: no visible binding for global variable ‘precursors’
progComb3: no visible binding for global variable ‘ropenms’
progSplit2: no visible binding for global variable ‘trees’
progSplit2: no visible binding for global variable ‘scoreFile’
progSplit2: no visible binding for global variable ‘precursors’
progSplit2 : <anonymous>: no visible global function definition for ‘.’
progSplit2: no visible binding for global variable ‘ropenms’
progSplit4: no visible binding for global variable ‘precursors’
progSplit4 : <anonymous>: no visible global function definition for ‘.’
progSplit4: no visible binding for global variable ‘intensity’
progTree1: no visible binding for global variable ‘ropenms’
progTree1: no visible binding for global variable ‘peptide_id’
reIntensity: no visible binding for global variable ‘run’
reIntensity: no visible binding for global variable ‘alignment_rank’
recalculateIntensity: no visible binding for global variable
‘peptide_id’
recalculateIntensity: no visible binding for global variable
‘chromatogramIndex’
script2: no visible binding for global variable ‘fileInfo’
script2: no visible binding for global variable ‘peptide_id’
script2 : <anonymous>: no visible global function definition for ‘.’
script2: no visible binding for global variable ‘features’
script2: no visible binding for global variable ‘globalFits’
script2: no visible binding for global variable ‘RSE’
script2: no visible binding for global variable ‘intensity’
setRootRank : <anonymous>: no visible global function definition for
‘.’
writeOutFeatureAlignmentMap: no visible binding for global variable
‘reference_feature_id’
writeOutFeatureAlignmentMap: no visible binding for global variable
‘experiment_feature_id’
writeOutFeatureAlignmentMap: no visible binding for global variable
‘ALIGNMENT_GROUP_ID’
writeOutFeatureAlignmentMap: no visible binding for global variable
‘REFERENCE’
writeOutFeatureAlignmentMap: no visible global function definition for
‘.’
writeOutFeatureAlignmentMap: no visible binding for global variable
‘i.to’
writeTables: no visible binding for global variable ‘peptide_id’
writeTables: no visible binding for global variable ‘run’
writeTables: no visible binding for global variable ‘precursor’
Undefined global functions or variables:
. ALIGNMENT_GROUP_ID REFERENCE RSE RT RT.eXp RT.ref alignment_rank
chromatogramIndex col2 experiment_feature_id feature_id features
fileInfo globalFits head i.to identifying.transitionPEPfilter
intensity m_score m_score_new ms2_m_score peak_group_rank peptide_id
precursor precursors pvalue ref_run reference_feature_id ropenms run
scoreFile transition_group_id transition_id trees
Consider adding
importFrom("datasets", "trees")
importFrom("utils", "head")
to your NAMESPACE file.
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... NOTE
Documented arguments not in \usage in Rd file 'alignToRef.Rd':
‘feature_alignment_mapping’
Documented arguments not in \usage in Rd file 'blobXICs.Rd':
‘nativeId’
Documented arguments not in \usage in Rd file 'extractXIC_group2.Rd':
‘mz’
Documented arguments not in \usage in Rd file 'getOswAnalytes.Rd':
‘dataPath’ ‘filenames’
Documented arguments not in \usage in Rd file 'getOswFiles.Rd':
‘dataPath’ ‘filenames’
Documented arguments not in \usage in Rd file 'perBatch.Rd':
‘rownum’
Documented arguments not in \usage in Rd file 'readSqMassHeader.Rd':
‘mzmlName’
Documented arguments not in \usage in Rd file 'setAlignmentRank.Rd':
‘XICs.eXp’
Documented arguments not in \usage in Rd file 'traverseDown.Rd':
‘analytes’
Documented arguments not in \usage in Rd file 'writeTables.Rd':
‘filename’
Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
File ‘/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/DIAlignR/libs/DIAlignR.so’:
Found ‘__ZNSt3__14coutE’, possibly from ‘std::cout’ (C++)
Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs nor [v]sprintf. The detected symbols are linked into
the code but might come from libraries and not actually be called.
See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
alignTargetedRuns 9.751 11.421 8.604
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’
ERROR
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
── Failure ('test_get_global_fit.R:21:3'): test_dialignrLoess ──────────────────
outData$pars$span not equal to 0.8.
1/1 mismatches
[1] 0.4 - 0.8 == -0.4
── Failure ('test_get_global_fit.R:22:3'): test_dialignrLoess ──────────────────
predict(outData, newdata = data.frame(RT.ref = 13.5))[[1]] not equal to 5.5.
1/1 mismatches
[1] 2.75 - 5.5 == -2.75
── Failure ('test_utils.R:276:3'): test_ipfReassignFDR ─────────────────────────
`finalTbl` not equal to `expData`.
Column 'RT': 'is.NA' value mismatch: 2 in current 0 in target
[ FAIL 3 | WARN 3 | SKIP 8 | PASS 629 ]
Error: Test failures
Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: 1 ERROR, 5 NOTEs
See
‘/Users/biocbuild/bbs-3.20-bioc/meat/DIAlignR.Rcheck/00check.log’
for details.
DIAlignR.Rcheck/00install.out
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###
### Running command:
###
### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL DIAlignR
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library’
* installing *source* package ‘DIAlignR’ ...
** using staged installation
** libs
using C++ compiler: ‘Apple clang version 15.0.0 (clang-1500.0.40.1)’
using C++14
using SDK: ‘MacOSX11.3.sdk’
clang++ -arch arm64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c ChromatogramPeak.cpp -o ChromatogramPeak.o
clang++ -arch arm64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c DPosition.cpp -o DPosition.o
clang++ -arch arm64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c MSChromatogram.cpp -o MSChromatogram.o
clang++ -arch arm64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c PeakIntegrator.cpp -o PeakIntegrator.o
clang++ -arch arm64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c RcppExports.cpp -o RcppExports.o
In file included from RcppExports.cpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/RcppEigen.h:25:
In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/RcppEigenForward.h:29:
In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/Eigen/Sparse:26:
In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/Eigen/SparseCore:61:
/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/Eigen/src/SparseCore/TriangularSolver.h:273:13: warning: variable 'count' set but not used [-Wunused-but-set-variable]
Index count = 0;
^
In file included from RcppExports.cpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/RcppEigen.h:25:
In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/RcppEigenForward.h:29:
In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/Eigen/Sparse:29:
In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/Eigen/SparseLU:35:
/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/Eigen/src/SparseLU/SparseLU_heap_relax_snode.h:78:9: warning: variable 'nsuper_et_post' set but not used [-Wunused-but-set-variable]
Index nsuper_et_post = 0; // Number of relaxed snodes in postordered etree
^
/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/Eigen/src/SparseLU/SparseLU_heap_relax_snode.h:79:9: warning: variable 'nsuper_et' set but not used [-Wunused-but-set-variable]
Index nsuper_et = 0; // Number of relaxed snodes in the original etree
^
In file included from RcppExports.cpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/RcppEigen.h:25:
In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/RcppEigenForward.h:31:
In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/unsupported/Eigen/IterativeSolvers:46:
/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/unsupported/Eigen/src/IterativeSolvers/IDRS.h:72:10: warning: variable 'replacements' set but not used [-Wunused-but-set-variable]
Index replacements = 0;
^
In file included from RcppExports.cpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/RcppEigen.h:25:
In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/RcppEigenForward.h:37:
In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/unsupported/Eigen/SparseExtra:45:
/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/unsupported/Eigen/src/SparseExtra/MarketIO.h:246:7: warning: variable 'count' set but not used [-Wunused-but-set-variable]
int count = 0;
^
5 warnings generated.
clang++ -arch arm64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c Rmain.cpp -o Rmain.o
In file included from Rmain.cpp:19:
./miscell.h:14:19: warning: unused function 'detect_end_na' [-Wunused-function]
static bool const detect_end_na(double a, double b);
^
./miscell.h:16:19: warning: unused function 'detect_start_na' [-Wunused-function]
static bool const detect_start_na(double a, double b);
^
./miscell.h:18:19: warning: unused function 'lessZero' [-Wunused-function]
static bool const lessZero(double a);
^
3 warnings generated.
clang++ -arch arm64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c SavitzkyGolayFilter.cpp -o SavitzkyGolayFilter.o
In file included from SavitzkyGolayFilter.cpp:1:
In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/RcppEigen.h:25:
In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/RcppEigenForward.h:29:
In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/Eigen/Sparse:26:
In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/Eigen/SparseCore:61:
/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/Eigen/src/SparseCore/TriangularSolver.h:273:13: warning: variable 'count' set but not used [-Wunused-but-set-variable]
Index count = 0;
^
In file included from SavitzkyGolayFilter.cpp:1:
In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/RcppEigen.h:25:
In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/RcppEigenForward.h:29:
In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/Eigen/Sparse:29:
In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/Eigen/SparseLU:35:
/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/Eigen/src/SparseLU/SparseLU_heap_relax_snode.h:78:9: warning: variable 'nsuper_et_post' set but not used [-Wunused-but-set-variable]
Index nsuper_et_post = 0; // Number of relaxed snodes in postordered etree
^
/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/Eigen/src/SparseLU/SparseLU_heap_relax_snode.h:79:9: warning: variable 'nsuper_et' set but not used [-Wunused-but-set-variable]
Index nsuper_et = 0; // Number of relaxed snodes in the original etree
^
In file included from SavitzkyGolayFilter.cpp:1:
In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/RcppEigen.h:25:
In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/RcppEigenForward.h:31:
In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/unsupported/Eigen/IterativeSolvers:46:
/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/unsupported/Eigen/src/IterativeSolvers/IDRS.h:72:10: warning: variable 'replacements' set but not used [-Wunused-but-set-variable]
Index replacements = 0;
^
In file included from SavitzkyGolayFilter.cpp:1:
In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/RcppEigen.h:25:
In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/RcppEigenForward.h:37:
In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/unsupported/Eigen/SparseExtra:45:
/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/unsupported/Eigen/src/SparseExtra/MarketIO.h:246:7: warning: variable 'count' set but not used [-Wunused-but-set-variable]
int count = 0;
^
5 warnings generated.
clang++ -arch arm64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c affinealignment.cpp -o affinealignment.o
clang++ -arch arm64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c affinealignobj.cpp -o affinealignobj.o
clang++ -arch arm64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c alignment.cpp -o alignment.o
clang++ -arch arm64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c chromSimMatrix.cpp -o chromSimMatrix.o
clang++ -arch arm64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c constrainMat.cpp -o constrainMat.o
constrainMat.cpp:78:10: warning: unused variable 'mapped' [-Wunused-variable]
double mapped = 0.0;
^
1 warning generated.
clang++ -arch arm64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c gapPenalty.cpp -o gapPenalty.o
clang++ -arch arm64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c integrateArea.cpp -o integrateArea.o
clang++ -arch arm64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c interface.cpp -o interface.o
clang++ -arch arm64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c miscell.cpp -o miscell.o
miscell.cpp:53:19: warning: unused function 'lessZero' [-Wunused-function]
static bool const lessZero(double a){
^
1 warning generated.
clang++ -arch arm64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c run_alignment.cpp -o run_alignment.o
clang++ -arch arm64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c simpleFcn.cpp -o simpleFcn.o
clang++ -arch arm64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c spline.cpp -o spline.o
clang++ -arch arm64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c utils.cpp -o utils.o
utils.cpp:48:9: warning: unused variable 'idx' [-Wunused-variable]
int idx = n*(1-p);
^
1 warning generated.
clang++ -arch arm64 -std=gnu++14 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/arm64/lib -o DIAlignR.so ChromatogramPeak.o DPosition.o MSChromatogram.o PeakIntegrator.o RcppExports.o Rmain.o SavitzkyGolayFilter.o affinealignment.o affinealignobj.o alignment.o chromSimMatrix.o constrainMat.o gapPenalty.o integrateArea.o interface.o miscell.o run_alignment.o simpleFcn.o spline.o utils.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/00LOCK-DIAlignR/00new/DIAlignR/libs
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (DIAlignR)
DIAlignR.Rcheck/tests/testthat.Rout.fail
R version 4.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin20
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> library(testthat)
> library(DIAlignR)
>
> test_check("DIAlignR")
[1] "hroest_K120808_Strep10%PlasmaBiolRepl1_R03_SW_filt"
[2] "hroest_K120809_Strep0%PlasmaBiolRepl2_R04_SW_filt"
[3] "hroest_K120809_Strep10%PlasmaBiolRepl2_R04_SW_filt"
Time difference of 0.04725289 secs
Time difference of 0.2051609 secs
Time difference of 0.1509621 secs
Time difference of 0.03273201 secs
Time difference of 0.01224113 secs
Time difference of 0.1072409 secs
Time difference of 1.714204 secs
Time difference of 0.023664 secs
Time difference of 0.3629389 secs
[1] "hroest_K120808_Strep10%PlasmaBiolRepl1_R03_SW_filt"
[2] "hroest_K120809_Strep0%PlasmaBiolRepl2_R04_SW_filt"
Time difference of 0.01960087 secs
Time difference of 0.1589301 secs
Time difference of 0.07708192 secs
Time difference of 0.02341199 secs
Time difference of 0.008531094 secs
Time difference of 0.06141901 secs
Time difference of 0.744729 secs
Time difference of 0.007616997 secs
Time difference of 0.8481829 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 0.02122188 secs
Time difference of 0.17836 secs
Time difference of 0.07760191 secs
Time difference of 0.118773 secs
Time difference of 0.009345055 secs
Time difference of 0.08561707 secs
Time difference of 1.02518 secs
Time difference of 0.01867104 secs
Time difference of 0.3123529 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 0.02063584 secs
Time difference of 0.01705313 secs
Time difference of 0.0003919601 secs
Time difference of 0.1159649 secs
Time difference of 0.01071692 secs
Time difference of 0.04413891 secs
Time difference of 0.01308393 secs
Time difference of 0.007545948 secs
Time difference of 0.1023421 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 0.009603024 secs
Time difference of 0.02715421 secs
Time difference of 0.009346962 secs
Time difference of 0.01536894 secs
Time difference of 0.008177042 secs
Time difference of 0.04138803 secs
Time difference of 0.09499907 secs
Time difference of 0.006279945 secs
Time difference of 0.2034879 secs
[1] "chludwig_K150309_004b_SW_1_16" "chludwig_K150309_008_SW_1_4"
[3] "chludwig_K150309_013_SW_0"
Time difference of 0.01152706 secs
Time difference of 0.01264191 secs
Time difference of 0.0008921623 secs
Time difference of 0.01740003 secs
Time difference of 0.01192188 secs
Time difference of 0.07082796 secs
Time difference of 0.009178877 secs
Time difference of 0.01725721 secs
Time difference of 0.2119579 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 0.119323 secs
Time difference of 0.01590586 secs
Time difference of 0.002370119 secs
Time difference of 0.01267505 secs
Time difference of 0.04810596 secs
Time difference of 0.01399994 secs
Time difference of 0.01343489 secs
Time difference of 0.09362316 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 0.03446198 secs
[1] "run0 run1\nrun2 run2"
Time difference of 0.1940799 secs
Time difference of 0.07730007 secs
Time difference of 0.01506996 secs
Time difference of 0.08919191 secs
Time difference of 1.226514 secs
Time difference of 0.01421213 secs
Time difference of 0.362278 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 0.142791 secs
Time difference of 0.8313198 secs
Time difference of 6.10861 secs
Time difference of 0.4237418 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 0.1285162 secs
[1] "Written /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/DIAlignR/extdata/temp_prog1.RData"
[1] "Written /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/DIAlignR/extdata/temp_0_2.rds"
[1] "progTree1 is done."
Time difference of 1.480529 secs
Time difference of 0.328141 secs
[1] "Written /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/DIAlignR/extdata/temp_1_2.rds"
Time difference of 0.5238211 secs
[1] "Written /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/DIAlignR/extdata/temp_2_2.rds"
Time difference of 0.3416588 secs
Time difference of 0.150223 secs
[1] "Written /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/DIAlignR/extdata/temp_all_2.rds"
Time difference of 0.163048 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 0.1180551 secs
[1] "Written /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/DIAlignR/extdata/temp_prog1.RData"
[1] "Written /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/DIAlignR/extdata/temp_0_2.rds"
[1] "progTree1 is done."
Time difference of 0.9777081 secs
Time difference of 0.3406248 secs
[1] "Written /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/DIAlignR/extdata/temp_1_2.rds"
Time difference of 0.9181678 secs
[1] "Written /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/DIAlignR/extdata/temp_2_2.rds"
Time difference of 0.348449 secs
Time difference of 0.01304388 secs
[1] "Written /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/DIAlignR/extdata/temp_all_2.rds"
Error in reticulate::use_condaenv(condaEnv, required = TRUE) :
Unable to locate conda environment 'TricEnvr'.
Error in reticulate::use_condaenv(condaEnv, required = TRUE) :
Unable to locate conda environment 'TricEnvr'.
Error in reticulate::use_condaenv(condaEnv, required = TRUE) :
Unable to locate conda environment 'TricEnvr'.
[ FAIL 3 | WARN 3 | SKIP 8 | PASS 629 ]
══ Skipped tests (8) ═══════════════════════════════════════════════════════════
• empty test (5): 'test_get_filenames.R:77:1', 'test_get_filenames.R:82:1',
'test_utils.R:200:1', 'test_utils.R:203:1', 'test_utils.R:206:1'
• ropenms not available for testing. A conda environment with name TricEnvr is
MUST for testing. (3): 'test_pyopenms.R:4:3', 'test_pyopenms.R:8:3',
'test_pyopenms.R:27:3'
══ Failed tests ════════════════════════════════════════════════════════════════
── Failure ('test_get_global_fit.R:21:3'): test_dialignrLoess ──────────────────
outData$pars$span not equal to 0.8.
1/1 mismatches
[1] 0.4 - 0.8 == -0.4
── Failure ('test_get_global_fit.R:22:3'): test_dialignrLoess ──────────────────
predict(outData, newdata = data.frame(RT.ref = 13.5))[[1]] not equal to 5.5.
1/1 mismatches
[1] 2.75 - 5.5 == -2.75
── Failure ('test_utils.R:276:3'): test_ipfReassignFDR ─────────────────────────
`finalTbl` not equal to `expData`.
Column 'RT': 'is.NA' value mismatch: 2 in current 0 in target
[ FAIL 3 | WARN 3 | SKIP 8 | PASS 629 ]
Error: Test failures
Execution halted
DIAlignR.Rcheck/DIAlignR-Ex.timings
| name | user | system | elapsed | |
| MSTperBatch | 0.001 | 0.001 | 0.001 | |
| addFlankToLeft | 0.002 | 0.001 | 0.002 | |
| addFlankToRight | 0.001 | 0.000 | 0.001 | |
| addXIC | 0.000 | 0.001 | 0.000 | |
| alignChromatogramsCpp | 0.030 | 0.005 | 0.035 | |
| alignTargetedRuns | 9.751 | 11.421 | 8.604 | |
| alignToMaster | 1.396 | 0.056 | 1.539 | |
| alignToRef | 0.001 | 0.000 | 0.002 | |
| alignToRefMST | 0.001 | 0.001 | 0.001 | |
| alignedXIC | 0.127 | 0.003 | 0.133 | |
| analytesFromFeatures | 0.046 | 0.007 | 0.054 | |
| approxFill | 0.001 | 0.000 | 0.001 | |
| areaIntegrator | 0.003 | 0.001 | 0.005 | |
| blobXICs | 0.002 | 0.002 | 0.003 | |
| calculateIntensity | 0.003 | 0.001 | 0.004 | |
| checkOverlap | 0 | 0 | 0 | |
| checkParams | 0.000 | 0.001 | 0.000 | |
| childXIC | 0.129 | 0.003 | 0.134 | |
| childXICs | 0.577 | 0.018 | 0.598 | |
| constrainSimCpp | 0.001 | 0.001 | 0.001 | |
| createMZML | 0.004 | 0.002 | 0.006 | |
| createSqMass | 0.002 | 0.002 | 0.003 | |
| dialignrLoess | 0.000 | 0.000 | 0.001 | |
| doAffineAlignmentCpp | 0.001 | 0.001 | 0.001 | |
| doAlignmentCpp | 0.001 | 0.001 | 0.002 | |
| extractXIC_group | 0.810 | 0.027 | 0.842 | |
| extractXIC_group2 | 0.001 | 0.001 | 0.002 | |
| fetchAnalytesInfo | 0.009 | 0.002 | 0.011 | |
| fetchFeaturesFromRun | 0.008 | 0.001 | 0.010 | |
| fetchPeptidesInfo | 0.008 | 0.002 | 0.009 | |
| fetchPeptidesInfo2 | 0.010 | 0.001 | 0.011 | |
| fetchPrecursorsInfo | 0.002 | 0.000 | 0.002 | |
| fetchTransitionsFromRun | 0.009 | 0.001 | 0.010 | |
| filenamesFromMZML | 0.001 | 0.001 | 0.002 | |
| filenamesFromOSW | 0.001 | 0.000 | 0.001 | |
| getAlignObj | 0.026 | 0.002 | 0.027 | |
| getAlignObjs | 1.071 | 0.029 | 1.104 | |
| getAlignedFigs | 0.147 | 0.009 | 0.157 | |
| getAlignedIndices | 0.011 | 0.002 | 0.013 | |
| getAlignedTimes | 0.021 | 0.005 | 0.025 | |
| getAlignedTimesCpp | 0.007 | 0.002 | 0.009 | |
| getAlignedTimesFast | 0.015 | 0.004 | 0.020 | |
| getBaseGapPenaltyCpp | 0 | 0 | 0 | |
| getChildFeature | 0.048 | 0.006 | 0.054 | |
| getChildXICpp | 0.008 | 0.002 | 0.010 | |
| getChildXICs | 0.621 | 0.023 | 0.646 | |
| getChromSimMatCpp | 0.001 | 0.001 | 0.003 | |
| getChromatogramIndices | 0.105 | 0.004 | 0.110 | |
| getFeatures | 0.049 | 0.005 | 0.054 | |
| getGlobalAlignMaskCpp | 0.001 | 0.001 | 0.001 | |
| getGlobalAlignment | 0.008 | 0.001 | 0.009 | |
| getGlobalFits | 0.332 | 0.009 | 0.343 | |
| getLOESSfit | 0.005 | 0.001 | 0.006 | |
| getLinearfit | 0.004 | 0.001 | 0.005 | |
| getMST | 0.001 | 0.001 | 0.001 | |
| getMZMLpointers | 0.017 | 0.002 | 0.018 | |
| getMappedRT | 0.014 | 0.002 | 0.015 | |
| getMultipeptide | 2.100 | 0.068 | 2.190 | |
| getNativeIDs | 0.023 | 0.002 | 0.025 | |
| getNodeIDs | 0.001 | 0.000 | 0.001 | |
| getNodeRun | 0.358 | 0.015 | 0.373 | |
| getOswAnalytes | 0.012 | 0.002 | 0.013 | |
| getOswFiles | 0.012 | 0.001 | 0.013 | |
| getPeptideScores | 0.044 | 0.003 | 0.048 | |
| getPrecursorByID | 0.020 | 0.003 | 0.023 | |
| getPrecursorIndices | 0.057 | 0.005 | 0.063 | |
| getPrecursors | 0.029 | 0.002 | 0.032 | |
| getRSE | 0.004 | 0.000 | 0.005 | |
| getRTdf | 0.007 | 0.001 | 0.009 | |
| getRefExpFeatureMap | 0.26 | 0.01 | 0.27 | |
| getRefRun | 0.271 | 0.009 | 0.281 | |
| getRunNames | 0.011 | 0.001 | 0.013 | |
| getSeqSimMatCpp | 0 | 0 | 0 | |
| getTransitions | 0.175 | 0.009 | 0.186 | |
| getTree | 0.030 | 0.003 | 0.033 | |
| getXICs | 0.093 | 0.007 | 0.101 | |
| getXICs4AlignObj | 0.062 | 0.003 | 0.066 | |
| get_ropenms | 0 | 0 | 0 | |
| imputeChromatogram | 0.012 | 0.001 | 0.014 | |
| ipfReassignFDR | 0 | 0 | 0 | |
| mapIdxToTime | 0.001 | 0.000 | 0.000 | |
| mappedRTfromAlignObj | 0.003 | 0.000 | 0.004 | |
| mergeXIC | 0.003 | 0.000 | 0.003 | |
| mstAlignRuns | 1.569 | 0.053 | 1.626 | |
| mstScript1 | 0.634 | 0.286 | 0.726 | |
| mstScript2 | 2.144 | 0.736 | 2.689 | |
| nrDesc | 0.001 | 0.001 | 0.000 | |
| otherChildXICpp | 0.008 | 0.001 | 0.010 | |
| paramsDIAlignR | 0 | 0 | 0 | |
| perBatch | 0.001 | 0.001 | 0.001 | |
| pickNearestFeature | 0.004 | 0.001 | 0.005 | |
| plotAlignedAnalytes | 0.534 | 0.023 | 0.561 | |
| plotAlignmentPath | 0.405 | 0.038 | 0.445 | |
| plotAnalyteXICs | 0.426 | 0.018 | 0.448 | |
| plotXICgroup | 0.337 | 0.011 | 0.355 | |
| populateReferenceExperimentFeatureAlignmentMap | 0.014 | 0.002 | 0.017 | |
| progAlignRuns | 0.001 | 0.001 | 0.002 | |
| readMzMLHeader | 0.001 | 0.001 | 0.002 | |
| readSqMassHeader | 0.001 | 0.001 | 0.003 | |
| recalculateIntensity | 0.242 | 0.011 | 0.258 | |
| reduceXICs | 0.077 | 0.005 | 0.083 | |
| script1 | 0.895 | 1.069 | 1.262 | |
| script2 | 2.427 | 1.125 | 2.985 | |
| setAlignmentRank | 0.014 | 0.002 | 0.016 | |
| sgolayCpp | 0.003 | 0.001 | 0.005 | |
| sgolayFill | 0.001 | 0.001 | 0.001 | |
| smoothSingleXIC | 0.002 | 0.001 | 0.003 | |
| smoothXICs | 0.007 | 0.002 | 0.009 | |
| splineFill | 0.001 | 0.000 | 0.001 | |
| splineFillCpp | 0.004 | 0.001 | 0.004 | |
| traverseDown | 1.367 | 0.056 | 1.440 | |
| traverseMST | 0.001 | 0.000 | 0.001 | |
| traverseUp | 1.289 | 0.036 | 1.337 | |
| trfrParentFeature | 0.052 | 0.007 | 0.060 | |
| trimXICs | 0.003 | 0.002 | 0.004 | |
| uncompressVec | 0.006 | 0.001 | 0.007 | |
| updateFileInfo | 0.010 | 0.002 | 0.012 | |
| writeOutFeatureAlignmentMap | 0.006 | 0.002 | 0.007 | |
| writeTables | 0.005 | 0.001 | 0.006 | |