Shubham Gupta
| Snapshot Date: 2024-03-03 14:05:05 -0500 (Sun, 03 Mar 2024) |
| git_url: https://git.bioconductor.org/packages/DIAlignR |
| git_branch: RELEASE_3_18 |
| git_last_commit: d616e54 |
| git_last_commit_date: 2023-10-24 11:19:06 -0500 (Tue, 24 Oct 2023) |
| Back to Multiple platform build/check report for BioC 3.18: simplified long |
|
This page was generated on 2024-03-04 11:37:17 -0500 (Mon, 04 Mar 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.3.2 Patched (2023-11-13 r85521) -- "Eye Holes" | 4692 |
| palomino4 | Windows Server 2022 Datacenter | x64 | 4.3.2 (2023-10-31 ucrt) -- "Eye Holes" | 4445 |
| lconway | macOS 12.7.1 Monterey | x86_64 | 4.3.2 Patched (2023-11-01 r85457) -- "Eye Holes" | 4466 |
| Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X | ||||
| Package 557/2266 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| DIAlignR 2.10.0 (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 | | ||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson1 | macOS 13.6.1 Ventura / arm64 | see weekly results here | ||||||||||||
|
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: 2.10.0 |
| 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_2.10.0.tar.gz |
| StartedAt: 2024-03-03 20:11:38 -0500 (Sun, 03 Mar 2024) |
| EndedAt: 2024-03-03 20:15:00 -0500 (Sun, 03 Mar 2024) |
| EllapsedTime: 202.3 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: DIAlignR.Rcheck |
| Warnings: 0 |
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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_2.10.0.tar.gz
###
##############################################################################
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* using log directory ‘/Users/biocbuild/bbs-3.18-bioc/meat/DIAlignR.Rcheck’
* using R version 4.3.2 Patched (2023-11-01 r85457)
* using platform: x86_64-apple-darwin20 (64-bit)
* R was compiled by
Apple clang version 14.0.3 (clang-1403.0.22.14.1)
GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘DIAlignR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘DIAlignR’ version ‘2.10.0’
* 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 14.0.0 (clang-1400.0.29.202)’
* 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 11.5Mb
sub-directories of 1Mb or more:
extdata 4.0Mb
metabo 4.1Mb
ptms 1.5Mb
* checking package directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R 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 ... OK
* 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/4.3-x86_64/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 11.392 12.255 8.088
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’
OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: 4 NOTEs
See
‘/Users/biocbuild/bbs-3.18-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
###
##############################################################################
##############################################################################
* installing to library ‘/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library’
* installing *source* package ‘DIAlignR’ ...
** using staged installation
** libs
using C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
using C++14
using SDK: ‘MacOSX11.3.sdk’
clang++ -arch x86_64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppEigen/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c ChromatogramPeak.cpp -o ChromatogramPeak.o
clang++ -arch x86_64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppEigen/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c DPosition.cpp -o DPosition.o
clang++ -arch x86_64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppEigen/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c MSChromatogram.cpp -o MSChromatogram.o
clang++ -arch x86_64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppEigen/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c PeakIntegrator.cpp -o PeakIntegrator.o
clang++ -arch x86_64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppEigen/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c RcppExports.cpp -o RcppExports.o
clang++ -arch x86_64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppEigen/include' -I/opt/R/x86_64/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 x86_64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppEigen/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c SavitzkyGolayFilter.cpp -o SavitzkyGolayFilter.o
clang++ -arch x86_64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppEigen/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c affinealignment.cpp -o affinealignment.o
clang++ -arch x86_64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppEigen/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c affinealignobj.cpp -o affinealignobj.o
clang++ -arch x86_64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppEigen/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c alignment.cpp -o alignment.o
clang++ -arch x86_64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppEigen/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c chromSimMatrix.cpp -o chromSimMatrix.o
clang++ -arch x86_64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppEigen/include' -I/opt/R/x86_64/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 x86_64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppEigen/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c gapPenalty.cpp -o gapPenalty.o
clang++ -arch x86_64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppEigen/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c integrateArea.cpp -o integrateArea.o
clang++ -arch x86_64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppEigen/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c interface.cpp -o interface.o
clang++ -arch x86_64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppEigen/include' -I/opt/R/x86_64/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 x86_64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppEigen/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c run_alignment.cpp -o run_alignment.o
clang++ -arch x86_64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppEigen/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c simpleFcn.cpp -o simpleFcn.o
clang++ -arch x86_64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppEigen/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c spline.cpp -o spline.o
clang++ -arch x86_64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppEigen/include' -I/opt/R/x86_64/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 x86_64 -std=gnu++14 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/x86_64/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/4.3-x86_64/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
R version 4.3.2 Patched (2023-11-01 r85457) -- "Eye Holes"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20 (64-bit)
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 0.04421782 secs
Time difference of 0.1931658 secs
Time difference of 0.159662 secs
Time difference of 0.02928305 secs
Time difference of 0.01092601 secs
Time difference of 0.09383702 secs
Time difference of 1.494687 secs
Time difference of 0.02488399 secs
Time difference of 0.407068 secs
[1] "hroest_K120808_Strep10%PlasmaBiolRepl1_R03_SW_filt"
[2] "hroest_K120809_Strep0%PlasmaBiolRepl2_R04_SW_filt"
Time difference of 0.01457596 secs
Time difference of 0.177454 secs
Time difference of 0.09268999 secs
Time difference of 0.02085209 secs
Time difference of 0.007863045 secs
Time difference of 0.0695951 secs
Time difference of 0.846004 secs
Time difference of 0.007574081 secs
Time difference of 0.90082 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 0.01671886 secs
Time difference of 0.21259 secs
Time difference of 0.09135509 secs
Time difference of 0.1156979 secs
Time difference of 0.01090407 secs
Time difference of 0.07036901 secs
Time difference of 1.156671 secs
Time difference of 0.01673508 secs
Time difference of 0.3326011 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 0.01685405 secs
Time difference of 0.01747894 secs
Time difference of 0.0005428791 secs
Time difference of 0.109931 secs
Time difference of 0.01158714 secs
Time difference of 0.07094312 secs
Time difference of 0.01651502 secs
Time difference of 0.008417845 secs
Time difference of 0.08218193 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 0.009097099 secs
Time difference of 0.03252888 secs
Time difference of 0.01052189 secs
Time difference of 0.01543212 secs
Time difference of 0.007585049 secs
Time difference of 0.04348898 secs
Time difference of 0.09342408 secs
Time difference of 0.007583857 secs
Time difference of 0.2049091 secs
[1] "chludwig_K150309_004b_SW_1_16" "chludwig_K150309_008_SW_1_4"
[3] "chludwig_K150309_013_SW_0"
Time difference of 0.01128101 secs
Time difference of 0.01109505 secs
Time difference of 0.001640081 secs
Time difference of 0.02105093 secs
Time difference of 0.01262403 secs
Time difference of 0.05906892 secs
Time difference of 0.00517416 secs
Time difference of 0.02753901 secs
Time difference of 0.1997201 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.>
<simpleWarning in sqrt(sum.squares/one.delta): NaNs produced>
<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 0.1144781 secs
Time difference of 0.01750493 secs
Time difference of 0.001414061 secs
Time difference of 0.011127 secs
Time difference of 0.06542706 secs
Time difference of 0.0159409 secs
Time difference of 0.01657796 secs
Time difference of 0.09595895 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 0.03470302 secs
[1] "run0 run1\nrun2 run2"
Time difference of 0.203042 secs
Time difference of 0.1111529 secs
Time difference of 0.01071191 secs
Time difference of 0.06727004 secs
Time difference of 1.271232 secs
Time difference of 0.01385212 secs
Time difference of 0.332617 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 0.1622169 secs
Time difference of 1.005555 secs
Time difference of 6.174238 secs
Time difference of 0.425374 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 0.1180389 secs
[1] "Written /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/DIAlignR/extdata/temp_prog1.RData"
[1] "Written /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/DIAlignR/extdata/temp_0_2.rds"
[1] "progTree1 is done."
Time difference of 1.21284 secs
Time difference of 0.3211029 secs
[1] "Written /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/DIAlignR/extdata/temp_1_2.rds"
Time difference of 0.8872929 secs
[1] "Written /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/DIAlignR/extdata/temp_2_2.rds"
Time difference of 0.662514 secs
Time difference of 0.177335 secs
[1] "Written /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/DIAlignR/extdata/temp_all_2.rds"
Time difference of 0.1712642 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 0.1181328 secs
[1] "Written /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/DIAlignR/extdata/temp_prog1.RData"
[1] "Written /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/DIAlignR/extdata/temp_0_2.rds"
[1] "progTree1 is done."
Time difference of 1.03793 secs
Time difference of 0.3007052 secs
[1] "Written /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/DIAlignR/extdata/temp_1_2.rds"
Time difference of 0.4635201 secs
[1] "Written /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/DIAlignR/extdata/temp_2_2.rds"
Time difference of 0.3302519 secs
Time difference of 0.01655698 secs
[1] "Written /Library/Frameworks/R.framework/Versions/4.3-x86_64/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 0 | WARN 0 | SKIP 8 | PASS 632 ]
══ 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'
[ FAIL 0 | WARN 0 | SKIP 8 | PASS 632 ]
>
> proc.time()
user system elapsed
61.927 9.955 52.747
DIAlignR.Rcheck/DIAlignR-Ex.timings
| name | user | system | elapsed | |
| MSTperBatch | 0.001 | 0.000 | 0.002 | |
| addFlankToLeft | 0.001 | 0.000 | 0.002 | |
| addFlankToRight | 0.002 | 0.001 | 0.002 | |
| addXIC | 0 | 0 | 0 | |
| alignChromatogramsCpp | 0.026 | 0.008 | 0.035 | |
| alignTargetedRuns | 11.392 | 12.255 | 8.088 | |
| alignToMaster | 1.865 | 0.087 | 1.968 | |
| alignToRef | 0.001 | 0.000 | 0.001 | |
| alignToRefMST | 0.001 | 0.001 | 0.002 | |
| alignedXIC | 0.105 | 0.005 | 0.111 | |
| analytesFromFeatures | 0.039 | 0.005 | 0.044 | |
| approxFill | 0.001 | 0.000 | 0.001 | |
| areaIntegrator | 0.002 | 0.001 | 0.003 | |
| blobXICs | 0.001 | 0.001 | 0.002 | |
| calculateIntensity | 0.003 | 0.001 | 0.004 | |
| checkOverlap | 0 | 0 | 0 | |
| checkParams | 0 | 0 | 0 | |
| childXIC | 0.090 | 0.004 | 0.096 | |
| childXICs | 0.786 | 0.035 | 0.833 | |
| constrainSimCpp | 0.000 | 0.000 | 0.001 | |
| createMZML | 0.003 | 0.001 | 0.005 | |
| createSqMass | 0.002 | 0.001 | 0.002 | |
| dialignrLoess | 0.001 | 0.000 | 0.001 | |
| doAffineAlignmentCpp | 0.001 | 0.000 | 0.001 | |
| doAlignmentCpp | 0.001 | 0.002 | 0.003 | |
| extractXIC_group | 0.788 | 0.023 | 0.819 | |
| extractXIC_group2 | 0.001 | 0.001 | 0.002 | |
| fetchAnalytesInfo | 0.009 | 0.002 | 0.011 | |
| fetchFeaturesFromRun | 0.006 | 0.001 | 0.008 | |
| fetchPeptidesInfo | 0.006 | 0.001 | 0.008 | |
| fetchPeptidesInfo2 | 0.009 | 0.001 | 0.011 | |
| fetchPrecursorsInfo | 0.001 | 0.000 | 0.001 | |
| fetchTransitionsFromRun | 0.008 | 0.001 | 0.010 | |
| filenamesFromMZML | 0.001 | 0.001 | 0.001 | |
| filenamesFromOSW | 0.002 | 0.001 | 0.002 | |
| getAlignObj | 0.022 | 0.003 | 0.025 | |
| getAlignObjs | 1.469 | 0.037 | 1.518 | |
| getAlignedFigs | 0.145 | 0.009 | 0.156 | |
| getAlignedIndices | 0.010 | 0.003 | 0.012 | |
| getAlignedTimes | 0.031 | 0.005 | 0.036 | |
| getAlignedTimesCpp | 0.006 | 0.002 | 0.008 | |
| getAlignedTimesFast | 0.013 | 0.004 | 0.017 | |
| getBaseGapPenaltyCpp | 0 | 0 | 0 | |
| getChildFeature | 0.041 | 0.006 | 0.046 | |
| getChildXICpp | 0.005 | 0.001 | 0.006 | |
| getChildXICs | 0.653 | 0.026 | 0.684 | |
| getChromSimMatCpp | 0.001 | 0.002 | 0.003 | |
| getChromatogramIndices | 0.124 | 0.006 | 0.131 | |
| getFeatures | 0.041 | 0.005 | 0.047 | |
| getGlobalAlignMaskCpp | 0.001 | 0.000 | 0.001 | |
| getGlobalAlignment | 0.006 | 0.000 | 0.007 | |
| getGlobalFits | 0.396 | 0.009 | 0.407 | |
| getLOESSfit | 0.003 | 0.001 | 0.004 | |
| getLinearfit | 0.004 | 0.001 | 0.005 | |
| getMST | 0.001 | 0.000 | 0.001 | |
| getMZMLpointers | 0.014 | 0.002 | 0.016 | |
| getMappedRT | 0.011 | 0.003 | 0.022 | |
| getMultipeptide | 1.550 | 0.037 | 1.596 | |
| getNativeIDs | 0.023 | 0.002 | 0.025 | |
| getNodeIDs | 0.001 | 0.001 | 0.000 | |
| getNodeRun | 0.413 | 0.019 | 0.435 | |
| getOswAnalytes | 0.008 | 0.001 | 0.009 | |
| getOswFiles | 0.008 | 0.001 | 0.010 | |
| getPeptideScores | 0.039 | 0.004 | 0.044 | |
| getPrecursorByID | 0.018 | 0.002 | 0.020 | |
| getPrecursorIndices | 0.056 | 0.006 | 0.064 | |
| getPrecursors | 0.027 | 0.003 | 0.030 | |
| getRSE | 0.003 | 0.001 | 0.004 | |
| getRTdf | 0.005 | 0.001 | 0.006 | |
| getRefExpFeatureMap | 0.282 | 0.019 | 0.305 | |
| getRefRun | 0.290 | 0.012 | 0.302 | |
| getRunNames | 0.009 | 0.002 | 0.011 | |
| getSeqSimMatCpp | 0.000 | 0.001 | 0.001 | |
| getTransitions | 0.176 | 0.014 | 0.198 | |
| getTree | 0.026 | 0.003 | 0.030 | |
| getXICs | 0.091 | 0.006 | 0.099 | |
| getXICs4AlignObj | 0.062 | 0.003 | 0.066 | |
| get_ropenms | 0 | 0 | 0 | |
| imputeChromatogram | 0.011 | 0.000 | 0.012 | |
| ipfReassignFDR | 0 | 0 | 0 | |
| mapIdxToTime | 0.000 | 0.000 | 0.001 | |
| mappedRTfromAlignObj | 0.002 | 0.001 | 0.003 | |
| mergeXIC | 0.002 | 0.001 | 0.004 | |
| mstAlignRuns | 1.829 | 0.055 | 1.894 | |
| mstScript1 | 0.520 | 0.344 | 0.612 | |
| mstScript2 | 2.341 | 0.538 | 2.643 | |
| nrDesc | 0 | 0 | 0 | |
| otherChildXICpp | 0.006 | 0.002 | 0.008 | |
| paramsDIAlignR | 0 | 0 | 0 | |
| perBatch | 0.001 | 0.001 | 0.002 | |
| pickNearestFeature | 0.004 | 0.001 | 0.005 | |
| plotAlignedAnalytes | 0.749 | 0.022 | 0.777 | |
| plotAlignmentPath | 0.394 | 0.035 | 0.432 | |
| plotAnalyteXICs | 0.555 | 0.022 | 0.582 | |
| plotXICgroup | 0.532 | 0.014 | 0.552 | |
| populateReferenceExperimentFeatureAlignmentMap | 0.015 | 0.003 | 0.017 | |
| progAlignRuns | 0.001 | 0.001 | 0.002 | |
| readMzMLHeader | 0.001 | 0.000 | 0.001 | |
| readSqMassHeader | 0.001 | 0.001 | 0.002 | |
| recalculateIntensity | 0.265 | 0.012 | 0.279 | |
| reduceXICs | 0.078 | 0.005 | 0.085 | |
| script1 | 0.925 | 1.111 | 1.255 | |
| script2 | 3.024 | 1.348 | 3.614 | |
| setAlignmentRank | 0.013 | 0.002 | 0.016 | |
| sgolayCpp | 0.002 | 0.001 | 0.004 | |
| sgolayFill | 0.001 | 0.000 | 0.001 | |
| smoothSingleXIC | 0.003 | 0.002 | 0.004 | |
| smoothXICs | 0.008 | 0.002 | 0.009 | |
| splineFill | 0.001 | 0.000 | 0.001 | |
| splineFillCpp | 0.004 | 0.000 | 0.004 | |
| traverseDown | 1.728 | 0.048 | 1.788 | |
| traverseMST | 0 | 0 | 0 | |
| traverseUp | 1.404 | 0.037 | 1.458 | |
| trfrParentFeature | 0.043 | 0.005 | 0.048 | |
| trimXICs | 0.002 | 0.002 | 0.003 | |
| uncompressVec | 0.006 | 0.001 | 0.007 | |
| updateFileInfo | 0.009 | 0.001 | 0.011 | |
| writeOutFeatureAlignmentMap | 0.005 | 0.001 | 0.006 | |
| writeTables | 0.004 | 0.001 | 0.004 | |