| Back to Multiple platform build/check report for BioC 3.21: simplified long |
|
This page was generated on 2025-10-16 11:40 -0400 (Thu, 16 Oct 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4833 |
| merida1 | macOS 12.7.6 Monterey | x86_64 | 4.5.1 RC (2025-06-05 r88288) -- "Great Square Root" | 4614 |
| kjohnson1 | macOS 13.7.5 Ventura | arm64 | 4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" | 4555 |
| kunpeng2 | Linux (openEuler 24.03 LTS) | aarch64 | R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" | 4586 |
| 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 576/2341 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
Shubham Gupta
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | ERROR | |||||||||
| merida1 | macOS 12.7.6 Monterey / x86_64 | OK | OK | ERROR | OK | |||||||||
| kjohnson1 | macOS 13.7.5 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: 2.16.0 |
| 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_2.16.0.tar.gz |
| StartedAt: 2025-10-14 19:38:33 -0400 (Tue, 14 Oct 2025) |
| EndedAt: 2025-10-14 19:42:04 -0400 (Tue, 14 Oct 2025) |
| EllapsedTime: 211.1 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_2.16.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/DIAlignR.Rcheck’
* using R version 4.5.1 Patched (2025-06-14 r88325)
* using platform: aarch64-apple-darwin20
* R was compiled by
Apple clang version 16.0.0 (clang-1600.0.26.6)
GNU Fortran (GCC) 14.2.0
* running under: macOS Ventura 13.7.5
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘DIAlignR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘DIAlignR’ version ‘2.16.0’
* 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 ... INFO
installed size is 11.4Mb
sub-directories of 1Mb or more:
extdata 4.0Mb
metabo 4.1Mb
ptms 1.5Mb
* checking package directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking whether startup messages can be suppressed ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
alignTargetedRuns: no visible binding for global variable ‘peptide_id’
alignTargetedRuns : <anonymous>: no visible global function definition
for ‘.’
alignTargetedRuns: no visible binding for global variable ‘intensity’
alignToRoot4: no visible binding for global variable ‘trees’
alignToRoot4: no visible binding for global variable ‘precursors’
alignToRoot4: no visible binding for global variable ‘intensity’
childXICs: possible error in cummax(v = cummax(ifelse(is.na(x), -Inf,
x))): unused argument (v = cummax(ifelse(is.na(x), -Inf, x)))
distMat.rSqrd : <anonymous> : <anonymous>: no visible binding for
global variable ‘RT.ref’
distMat.rSqrd : <anonymous> : <anonymous>: no visible binding for
global variable ‘RT.eXp’
fetchPrecursorsInfo: no visible binding for global variable
‘transition_id’
fetchPrecursorsInfo: no visible global function definition for ‘.’
fetchPrecursorsInfo: no visible binding for global variable
‘transition_group_id’
fetchTransitionsFromRun: no visible binding for global variable
‘intensity’
fetchTransitionsFromRun: no visible global function definition for ‘.’
fetchTransitionsFromRun: no visible binding for global variable
‘transition_group_id’
fetchTransitionsFromRun: no visible binding for global variable
‘peak_group_rank’
fetchTransitionsFromRun: no visible global function definition for
‘head’
getNativeIDs: no visible binding for global variable ‘peptide_id’
getPeptideScores: no visible binding for global variable ‘col2’
getPeptideScores: no visible binding for global variable ‘run’
getQuery: no visible binding for global variable
‘identifying.transitionPEPfilter’
getRTdf: no visible binding for global variable ‘peak_group_rank’
getRTdf: no visible binding for global variable ‘m_score’
getRTdf: no visible global function definition for ‘.’
getRTdf: no visible binding for global variable ‘transition_group_id’
getRTdf: no visible binding for global variable ‘RT’
getRefRun : <anonymous>: no visible binding for global variable
‘pvalue’
ipfReassignFDR: no visible binding for global variable ‘ref_run’
ipfReassignFDR: no visible binding for global variable ‘run’
ipfReassignFDR: no visible global function definition for ‘.’
ipfReassignFDR: no visible binding for global variable ‘i.to’
ipfReassignFDR: no visible binding for global variable ‘m_score_new’
ipfReassignFDR: no visible binding for global variable ‘ms2_m_score’
ipfReassignFDR: no visible binding for global variable ‘m_score’
mstAlignRuns: no visible binding for global variable ‘ropenms’
mstAlignRuns: no visible binding for global variable ‘peptide_id’
mstAlignRuns : <anonymous>: no visible global function definition for
‘.’
mstAlignRuns: no visible binding for global variable ‘intensity’
mstScript1: no visible binding for global variable ‘ropenms’
mstScript2: no visible binding for global variable ‘fileInfo’
mstScript2: no visible binding for global variable ‘peptide_id’
mstScript2: no visible binding for global variable ‘features’
mstScript2 : <anonymous>: no visible global function definition for ‘.’
mstScript2 : <anonymous>: no visible binding for global variable
‘features’
mstScript2: no visible binding for global variable ‘intensity’
populateReferenceExperimentFeatureAlignmentMap: no visible binding for
global variable ‘run’
populateReferenceExperimentFeatureAlignmentMap: no visible binding for
global variable ‘transition_group_id’
populateReferenceExperimentFeatureAlignmentMap: no visible binding for
global variable ‘feature_id’
progAlignRuns: no visible binding for global variable ‘peptide_id’
progAlignRuns : <anonymous>: no visible global function definition for
‘.’
progAlignRuns: no visible binding for global variable ‘intensity’
progComb3: no visible binding for global variable ‘precursors’
progComb3: no visible binding for global variable ‘ropenms’
progSplit2: no visible binding for global variable ‘trees’
progSplit2: no visible binding for global variable ‘scoreFile’
progSplit2: no visible binding for global variable ‘precursors’
progSplit2 : <anonymous>: no visible global function definition for ‘.’
progSplit2: no visible binding for global variable ‘ropenms’
progSplit4: no visible binding for global variable ‘precursors’
progSplit4 : <anonymous>: no visible global function definition for ‘.’
progSplit4: no visible binding for global variable ‘intensity’
progTree1: no visible binding for global variable ‘ropenms’
progTree1: no visible binding for global variable ‘peptide_id’
reIntensity: no visible binding for global variable ‘run’
reIntensity: no visible binding for global variable ‘alignment_rank’
recalculateIntensity: no visible binding for global variable
‘peptide_id’
recalculateIntensity: no visible binding for global variable
‘chromatogramIndex’
script2: no visible binding for global variable ‘fileInfo’
script2: no visible binding for global variable ‘peptide_id’
script2 : <anonymous>: no visible global function definition for ‘.’
script2: no visible binding for global variable ‘features’
script2: no visible binding for global variable ‘globalFits’
script2: no visible binding for global variable ‘RSE’
script2: no visible binding for global variable ‘intensity’
setRootRank : <anonymous>: no visible global function definition for
‘.’
writeOutFeatureAlignmentMap: no visible binding for global variable
‘reference_feature_id’
writeOutFeatureAlignmentMap: no visible binding for global variable
‘experiment_feature_id’
writeOutFeatureAlignmentMap: no visible binding for global variable
‘ALIGNMENT_GROUP_ID’
writeOutFeatureAlignmentMap: no visible binding for global variable
‘REFERENCE’
writeOutFeatureAlignmentMap: no visible global function definition for
‘.’
writeOutFeatureAlignmentMap: no visible binding for global variable
‘i.to’
writeTables: no visible binding for global variable ‘peptide_id’
writeTables: no visible binding for global variable ‘run’
writeTables: no visible binding for global variable ‘precursor’
Undefined global functions or variables:
. ALIGNMENT_GROUP_ID REFERENCE RSE RT RT.eXp RT.ref alignment_rank
chromatogramIndex col2 experiment_feature_id feature_id features
fileInfo globalFits head i.to identifying.transitionPEPfilter
intensity m_score m_score_new ms2_m_score peak_group_rank peptide_id
precursor precursors pvalue ref_run reference_feature_id ropenms run
scoreFile transition_group_id transition_id trees
Consider adding
importFrom("datasets", "trees")
importFrom("utils", "head")
to your NAMESPACE file.
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... NOTE
Documented arguments not in \usage in Rd file 'alignToRef.Rd':
‘feature_alignment_mapping’
Documented arguments not in \usage in Rd file 'blobXICs.Rd':
‘nativeId’
Documented arguments not in \usage in Rd file 'extractXIC_group2.Rd':
‘mz’
Documented arguments not in \usage in Rd file 'getOswAnalytes.Rd':
‘dataPath’ ‘filenames’
Documented arguments not in \usage in Rd file 'getOswFiles.Rd':
‘dataPath’ ‘filenames’
Documented arguments not in \usage in Rd file 'perBatch.Rd':
‘rownum’
Documented arguments not in \usage in Rd file 'readSqMassHeader.Rd':
‘mzmlName’
Documented arguments not in \usage in Rd file 'setAlignmentRank.Rd':
‘XICs.eXp’
Documented arguments not in \usage in Rd file 'traverseDown.Rd':
‘analytes’
Documented arguments not in \usage in Rd file 'writeTables.Rd':
‘filename’
Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
File ‘/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/DIAlignR/libs/DIAlignR.so’:
Found ‘__ZNSt3__14coutE’, possibly from ‘std::cout’ (C++)
Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs nor [v]sprintf. The detected symbols are linked into
the code but might come from libraries and not actually be called.
See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
alignTargetedRuns 9.852 14.233 9.666
* 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
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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/4.5-arm64/Resources/library’
* installing *source* package ‘DIAlignR’ ...
** this is package ‘DIAlignR’ version ‘2.16.0’
** 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/4.5-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
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
R version 4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root"
Copyright (C) 2025 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)
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 0.05149198 secs
Time difference of 0.1813049 secs
Time difference of 0.205549 secs
Time difference of 0.03130579 secs
Time difference of 0.009050131 secs
Time difference of 0.1063271 secs
Time difference of 1.608519 secs
Time difference of 0.02377701 secs
Time difference of 0.356405 secs
[1] "hroest_K120808_Strep10%PlasmaBiolRepl1_R03_SW_filt"
[2] "hroest_K120809_Strep0%PlasmaBiolRepl2_R04_SW_filt"
Time difference of 0.02101588 secs
Time difference of 0.1498239 secs
Time difference of 0.103816 secs
Time difference of 0.02359295 secs
Time difference of 0.01003003 secs
Time difference of 0.05286002 secs
Time difference of 0.793066 secs
Time difference of 0.009256124 secs
Time difference of 0.833601 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 0.02242804 secs
Time difference of 0.180923 secs
Time difference of 0.09198904 secs
Time difference of 0.1327319 secs
Time difference of 0.01058197 secs
Time difference of 0.06216884 secs
Time difference of 0.9651561 secs
Time difference of 0.01943994 secs
Time difference of 0.2917149 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 0.02095699 secs
Time difference of 0.03542304 secs
Time difference of 0.0003371239 secs
Time difference of 0.1252551 secs
Time difference of 0.01188898 secs
Time difference of 0.04969192 secs
Time difference of 0.01361799 secs
Time difference of 0.007261992 secs
Time difference of 0.09099889 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 0.00781703 secs
Time difference of 0.02486897 secs
Time difference of 0.008927107 secs
Time difference of 0.01356387 secs
Time difference of 0.007563114 secs
Time difference of 0.05762005 secs
Time difference of 0.05387187 secs
Time difference of 0.006657124 secs
Time difference of 0.203424 secs
[1] "chludwig_K150309_004b_SW_1_16" "chludwig_K150309_008_SW_1_4"
[3] "chludwig_K150309_013_SW_0"
Time difference of 0.009903908 secs
Time difference of 0.01209784 secs
Time difference of 0.001214981 secs
Time difference of 0.0158639 secs
Time difference of 0.0101552 secs
Time difference of 0.05042791 secs
Time difference of 0.005938053 secs
Time difference of 0.01770186 secs
Time difference of 0.2111859 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 0.1311049 secs
Time difference of 0.01662993 secs
Time difference of 0.001738071 secs
Time difference of 0.009831905 secs
Time difference of 0.04606795 secs
Time difference of 0.01149201 secs
Time difference of 0.01533294 secs
Time difference of 0.09046507 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 0.03411412 secs
[1] "run0 run1\nrun2 run2"
Time difference of 0.189539 secs
Time difference of 0.123513 secs
Time difference of 0.01300788 secs
Time difference of 0.06600809 secs
Time difference of 1.487585 secs
Time difference of 0.01593399 secs
Time difference of 0.3134339 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 0.1783369 secs
Time difference of 0.9934621 secs
Time difference of 5.369204 secs
Time difference of 0.3804159 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 0.130213 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 1.00239 secs
Time difference of 0.3260779 secs
[1] "Written /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/DIAlignR/extdata/temp_1_2.rds"
Time difference of 0.4374669 secs
[1] "Written /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/DIAlignR/extdata/temp_2_2.rds"
Time difference of 0.3177781 secs
Time difference of 0.1811969 secs
[1] "Written /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/DIAlignR/extdata/temp_all_2.rds"
Time difference of 0.1427422 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 0.1277409 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 0.820677 secs
Time difference of 0.311542 secs
[1] "Written /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/DIAlignR/extdata/temp_1_2.rds"
Time difference of 0.3709219 secs
[1] "Written /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/DIAlignR/extdata/temp_2_2.rds"
Time difference of 0.3044622 secs
Time difference of 0.01476884 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 | 0.001 | 0.001 | 0.002 | |
| addFlankToLeft | 0.002 | 0.000 | 0.003 | |
| addFlankToRight | 0.001 | 0.000 | 0.001 | |
| addXIC | 0.000 | 0.001 | 0.000 | |
| alignChromatogramsCpp | 0.031 | 0.007 | 0.037 | |
| alignTargetedRuns | 9.852 | 14.233 | 9.666 | |
| alignToMaster | 1.383 | 0.091 | 1.502 | |
| alignToRef | 0.001 | 0.001 | 0.001 | |
| alignToRefMST | 0.001 | 0.001 | 0.004 | |
| alignedXIC | 0.130 | 0.008 | 0.154 | |
| analytesFromFeatures | 0.048 | 0.007 | 0.055 | |
| approxFill | 0.001 | 0.000 | 0.001 | |
| areaIntegrator | 0.004 | 0.002 | 0.006 | |
| blobXICs | 0.003 | 0.002 | 0.004 | |
| calculateIntensity | 0.003 | 0.001 | 0.004 | |
| checkOverlap | 0.000 | 0.000 | 0.001 | |
| checkParams | 0 | 0 | 0 | |
| childXIC | 0.117 | 0.006 | 0.124 | |
| childXICs | 0.802 | 0.032 | 0.841 | |
| constrainSimCpp | 0.001 | 0.001 | 0.002 | |
| createMZML | 0.004 | 0.004 | 0.007 | |
| createSqMass | 0.002 | 0.002 | 0.005 | |
| dialignrLoess | 0.001 | 0.000 | 0.001 | |
| doAffineAlignmentCpp | 0.002 | 0.001 | 0.001 | |
| doAlignmentCpp | 0.001 | 0.001 | 0.002 | |
| extractXIC_group | 0.777 | 0.037 | 0.826 | |
| extractXIC_group2 | 0.002 | 0.000 | 0.002 | |
| fetchAnalytesInfo | 0.010 | 0.002 | 0.011 | |
| fetchFeaturesFromRun | 0.010 | 0.002 | 0.011 | |
| fetchPeptidesInfo | 0.008 | 0.001 | 0.010 | |
| fetchPeptidesInfo2 | 0.007 | 0.001 | 0.008 | |
| fetchPrecursorsInfo | 0.001 | 0.000 | 0.001 | |
| fetchTransitionsFromRun | 0.009 | 0.002 | 0.011 | |
| filenamesFromMZML | 0.001 | 0.001 | 0.001 | |
| filenamesFromOSW | 0.001 | 0.000 | 0.001 | |
| getAlignObj | 0.022 | 0.004 | 0.026 | |
| getAlignObjs | 1.680 | 0.035 | 1.735 | |
| getAlignedFigs | 0.127 | 0.010 | 0.138 | |
| getAlignedIndices | 0.011 | 0.003 | 0.014 | |
| getAlignedTimes | 0.022 | 0.008 | 0.034 | |
| getAlignedTimesCpp | 0.008 | 0.003 | 0.013 | |
| getAlignedTimesFast | 0.016 | 0.007 | 0.024 | |
| getBaseGapPenaltyCpp | 0 | 0 | 0 | |
| getChildFeature | 0.049 | 0.007 | 0.056 | |
| getChildXICpp | 0.008 | 0.005 | 0.012 | |
| getChildXICs | 0.602 | 0.028 | 0.635 | |
| getChromSimMatCpp | 0.002 | 0.002 | 0.003 | |
| getChromatogramIndices | 0.110 | 0.006 | 0.121 | |
| getFeatures | 0.045 | 0.005 | 0.052 | |
| getGlobalAlignMaskCpp | 0.001 | 0.000 | 0.002 | |
| getGlobalAlignment | 0.009 | 0.002 | 0.011 | |
| getGlobalFits | 0.326 | 0.010 | 0.343 | |
| getLOESSfit | 0.004 | 0.002 | 0.007 | |
| getLinearfit | 0.004 | 0.002 | 0.007 | |
| getMST | 0.001 | 0.000 | 0.001 | |
| getMZMLpointers | 0.016 | 0.003 | 0.018 | |
| getMappedRT | 0.015 | 0.004 | 0.018 | |
| getMultipeptide | 1.926 | 0.078 | 2.037 | |
| getNativeIDs | 0.024 | 0.002 | 0.029 | |
| getNodeIDs | 0.000 | 0.000 | 0.001 | |
| getNodeRun | 0.359 | 0.021 | 0.382 | |
| getOswAnalytes | 0.009 | 0.002 | 0.010 | |
| getOswFiles | 0.007 | 0.001 | 0.008 | |
| getPeptideScores | 0.040 | 0.003 | 0.044 | |
| getPrecursorByID | 0.015 | 0.001 | 0.017 | |
| getPrecursorIndices | 0.058 | 0.006 | 0.065 | |
| getPrecursors | 0.032 | 0.003 | 0.051 | |
| getRSE | 0.005 | 0.003 | 0.012 | |
| getRTdf | 0.008 | 0.002 | 0.011 | |
| getRefExpFeatureMap | 0.250 | 0.013 | 0.267 | |
| getRefRun | 0.288 | 0.008 | 0.300 | |
| getRunNames | 0.011 | 0.001 | 0.013 | |
| getSeqSimMatCpp | 0.000 | 0.000 | 0.001 | |
| getTransitions | 0.179 | 0.011 | 0.193 | |
| getTree | 0.030 | 0.004 | 0.037 | |
| getXICs | 0.104 | 0.007 | 0.114 | |
| getXICs4AlignObj | 0.086 | 0.006 | 0.097 | |
| get_ropenms | 0.000 | 0.001 | 0.000 | |
| imputeChromatogram | 0.010 | 0.001 | 0.012 | |
| ipfReassignFDR | 0 | 0 | 0 | |
| mapIdxToTime | 0.000 | 0.000 | 0.001 | |
| mappedRTfromAlignObj | 0.003 | 0.005 | 0.019 | |
| mergeXIC | 0.003 | 0.003 | 0.009 | |
| mstAlignRuns | 1.564 | 0.102 | 1.691 | |
| mstScript1 | 0.629 | 0.431 | 0.823 | |
| mstScript2 | 2.077 | 0.930 | 2.789 | |
| nrDesc | 0.001 | 0.000 | 0.001 | |
| otherChildXICpp | 0.007 | 0.004 | 0.012 | |
| paramsDIAlignR | 0 | 0 | 0 | |
| perBatch | 0.001 | 0.001 | 0.001 | |
| pickNearestFeature | 0.004 | 0.002 | 0.006 | |
| plotAlignedAnalytes | 0.839 | 0.030 | 0.877 | |
| plotAlignmentPath | 0.390 | 0.046 | 0.440 | |
| plotAnalyteXICs | 0.618 | 0.020 | 0.646 | |
| plotXICgroup | 0.561 | 0.013 | 0.582 | |
| populateReferenceExperimentFeatureAlignmentMap | 0.014 | 0.004 | 0.018 | |
| progAlignRuns | 0.001 | 0.000 | 0.001 | |
| readMzMLHeader | 0.001 | 0.000 | 0.001 | |
| readSqMassHeader | 0.001 | 0.001 | 0.001 | |
| recalculateIntensity | 0.316 | 0.030 | 0.350 | |
| reduceXICs | 0.076 | 0.006 | 0.082 | |
| script1 | 0.930 | 1.247 | 1.425 | |
| script2 | 2.401 | 1.645 | 3.326 | |
| setAlignmentRank | 0.014 | 0.005 | 0.019 | |
| sgolayCpp | 0.004 | 0.003 | 0.008 | |
| sgolayFill | 0.001 | 0.000 | 0.001 | |
| smoothSingleXIC | 0.002 | 0.003 | 0.005 | |
| smoothXICs | 0.008 | 0.004 | 0.016 | |
| splineFill | 0.001 | 0.000 | 0.001 | |
| splineFillCpp | 0.002 | 0.000 | 0.003 | |
| traverseDown | 1.180 | 0.051 | 1.238 | |
| traverseMST | 0 | 0 | 0 | |
| traverseUp | 1.232 | 0.044 | 1.288 | |
| trfrParentFeature | 0.047 | 0.007 | 0.055 | |
| trimXICs | 0.003 | 0.003 | 0.006 | |
| uncompressVec | 0.006 | 0.001 | 0.008 | |
| updateFileInfo | 0.008 | 0.001 | 0.009 | |
| writeOutFeatureAlignmentMap | 0.005 | 0.003 | 0.008 | |
| writeTables | 0.005 | 0.002 | 0.005 | |