Shubham Gupta
| Snapshot Date: 2024-03-27 14:05:05 -0400 (Wed, 27 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 -0400 (Tue, 24 Oct 2023) |
| Back to Multiple platform build/check report for BioC 3.18: simplified long |
|
This page was generated on 2024-03-29 11:37:40 -0400 (Fri, 29 Mar 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.3.3 (2024-02-29) -- "Angel Food Cake" | 4669 |
| palomino4 | Windows Server 2022 Datacenter | x64 | 4.3.3 (2024-02-29 ucrt) -- "Angel Food Cake" | 4404 |
| merida1 | macOS 12.7.1 Monterey | x86_64 | 4.3.3 (2024-02-29) -- "Angel Food Cake" | 4427 |
| 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 | | ||||||||
| merida1 | 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: 2024-03-28 01:53:53 -0400 (Thu, 28 Mar 2024) |
| EndedAt: 2024-03-28 02:00:01 -0400 (Thu, 28 Mar 2024) |
| EllapsedTime: 367.7 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 4.3.3 (2024-02-29)
* using platform: x86_64-apple-darwin20 (64-bit)
* R was compiled by
Apple clang version 14.0.0 (clang-1400.0.29.202)
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 18.373 21.384 13.586
script2 5.287 1.844 6.223
mstScript2 4.332 0.868 5.080
* 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 4.3.3 (2024-02-29) -- "Angel Food Cake"
Copyright (C) 2024 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 0.09608912 secs
Time difference of 0.432019 secs
Time difference of 0.2641909 secs
Time difference of 0.04666305 secs
Time difference of 0.01503491 secs
Time difference of 0.1909699 secs
Time difference of 2.75894 secs
Time difference of 0.04910493 secs
Time difference of 0.7648408 secs
[1] "hroest_K120808_Strep10%PlasmaBiolRepl1_R03_SW_filt"
[2] "hroest_K120809_Strep0%PlasmaBiolRepl2_R04_SW_filt"
Time difference of 0.03046393 secs
Time difference of 0.3744481 secs
Time difference of 0.206255 secs
Time difference of 0.03180385 secs
Time difference of 0.01214099 secs
Time difference of 0.112252 secs
Time difference of 1.781879 secs
Time difference of 0.01535702 secs
Time difference of 1.745647 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 0.03072095 secs
Time difference of 0.482393 secs
Time difference of 0.1934822 secs
Time difference of 0.191011 secs
Time difference of 0.01545501 secs
Time difference of 0.1276188 secs
Time difference of 2.509604 secs
Time difference of 0.04026699 secs
Time difference of 0.600337 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 0.048985 secs
Time difference of 0.03188396 secs
Time difference of 0.000797987 secs
Time difference of 0.194293 secs
Time difference of 0.01462102 secs
Time difference of 0.1001718 secs
Time difference of 0.031528 secs
Time difference of 0.01515198 secs
Time difference of 0.1523321 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 0.01278996 secs
Time difference of 0.05617404 secs
Time difference of 0.01726484 secs
Time difference of 0.02118397 secs
Time difference of 0.01025295 secs
Time difference of 0.06924105 secs
Time difference of 0.1622009 secs
Time difference of 0.01313806 secs
Time difference of 0.3647189 secs
[1] "chludwig_K150309_004b_SW_1_16" "chludwig_K150309_008_SW_1_4"
[3] "chludwig_K150309_013_SW_0"
Time difference of 0.01834106 secs
Time difference of 0.01962304 secs
Time difference of 0.002119064 secs
Time difference of 0.03036904 secs
Time difference of 0.01810694 secs
Time difference of 0.0918169 secs
Time difference of 0.01161599 secs
Time difference of 0.0401051 secs
Time difference of 0.4962282 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 0.2024491 secs
Time difference of 0.03582811 secs
Time difference of 0.00391221 secs
Time difference of 0.01814699 secs
Time difference of 0.09164405 secs
Time difference of 0.03480005 secs
Time difference of 0.02900505 secs
Time difference of 0.19521 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 0.05310702 secs
[1] "run0 run1\nrun2 run2"
Time difference of 0.4576459 secs
Time difference of 0.2064691 secs
Time difference of 0.01954103 secs
Time difference of 0.1624379 secs
Time difference of 2.702935 secs
Time difference of 0.02995181 secs
Time difference of 0.6309121 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 0.2535381 secs
Time difference of 1.955575 secs
Time difference of 12.20012 secs
Time difference of 0.907079 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 0.2045941 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 2.907384 secs
Time difference of 0.646353 secs
[1] "Written /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/DIAlignR/extdata/temp_1_2.rds"
Time difference of 1.141219 secs
[1] "Written /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/DIAlignR/extdata/temp_2_2.rds"
Time difference of 0.731719 secs
Time difference of 0.3563299 secs
[1] "Written /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/DIAlignR/extdata/temp_all_2.rds"
Time difference of 0.3544879 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 0.1968708 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 2.13605 secs
Time difference of 0.596195 secs
[1] "Written /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/DIAlignR/extdata/temp_1_2.rds"
Time difference of 1.098121 secs
[1] "Written /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/DIAlignR/extdata/temp_2_2.rds"
Time difference of 0.6439459 secs
Time difference of 0.02752495 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
117.279 15.986 107.839
DIAlignR.Rcheck/DIAlignR-Ex.timings
| name | user | system | elapsed | |
| MSTperBatch | 0.001 | 0.001 | 0.002 | |
| addFlankToLeft | 0.003 | 0.001 | 0.005 | |
| addFlankToRight | 0.002 | 0.001 | 0.003 | |
| addXIC | 0.000 | 0.001 | 0.000 | |
| alignChromatogramsCpp | 0.040 | 0.011 | 0.055 | |
| alignTargetedRuns | 18.373 | 21.384 | 13.586 | |
| alignToMaster | 3.421 | 0.122 | 3.733 | |
| alignToRef | 0.015 | 0.001 | 0.017 | |
| alignToRefMST | 0.002 | 0.001 | 0.003 | |
| alignedXIC | 0.159 | 0.008 | 0.175 | |
| analytesFromFeatures | 0.066 | 0.008 | 0.078 | |
| approxFill | 0.002 | 0.001 | 0.002 | |
| areaIntegrator | 0.005 | 0.002 | 0.007 | |
| blobXICs | 0.003 | 0.003 | 0.006 | |
| calculateIntensity | 0.004 | 0.002 | 0.006 | |
| checkOverlap | 0.001 | 0.000 | 0.001 | |
| checkParams | 0 | 0 | 0 | |
| childXIC | 0.162 | 0.004 | 0.176 | |
| childXICs | 1.426 | 0.027 | 1.543 | |
| constrainSimCpp | 0.001 | 0.001 | 0.003 | |
| createMZML | 0.005 | 0.003 | 0.008 | |
| createSqMass | 0.003 | 0.003 | 0.006 | |
| dialignrLoess | 0.001 | 0.001 | 0.001 | |
| doAffineAlignmentCpp | 0.002 | 0.001 | 0.004 | |
| doAlignmentCpp | 0.003 | 0.003 | 0.006 | |
| extractXIC_group | 1.530 | 0.034 | 1.645 | |
| extractXIC_group2 | 0.002 | 0.001 | 0.004 | |
| fetchAnalytesInfo | 0.014 | 0.003 | 0.017 | |
| fetchFeaturesFromRun | 0.012 | 0.002 | 0.015 | |
| fetchPeptidesInfo | 0.013 | 0.002 | 0.015 | |
| fetchPeptidesInfo2 | 0.012 | 0.002 | 0.013 | |
| fetchPrecursorsInfo | 0.002 | 0.001 | 0.003 | |
| fetchTransitionsFromRun | 0.012 | 0.002 | 0.016 | |
| filenamesFromMZML | 0.002 | 0.001 | 0.002 | |
| filenamesFromOSW | 0.001 | 0.001 | 0.003 | |
| getAlignObj | 0.036 | 0.004 | 0.041 | |
| getAlignObjs | 2.820 | 0.043 | 3.019 | |
| getAlignedFigs | 0.212 | 0.011 | 0.234 | |
| getAlignedIndices | 0.017 | 0.003 | 0.022 | |
| getAlignedTimes | 0.032 | 0.009 | 0.042 | |
| getAlignedTimesCpp | 0.009 | 0.002 | 0.011 | |
| getAlignedTimesFast | 0.024 | 0.010 | 0.036 | |
| getBaseGapPenaltyCpp | 0.001 | 0.001 | 0.001 | |
| getChildFeature | 0.074 | 0.014 | 0.105 | |
| getChildXICpp | 0.010 | 0.002 | 0.012 | |
| getChildXICs | 1.276 | 0.039 | 1.379 | |
| getChromSimMatCpp | 0.005 | 0.007 | 0.012 | |
| getChromatogramIndices | 0.190 | 0.006 | 0.204 | |
| getFeatures | 0.066 | 0.008 | 0.076 | |
| getGlobalAlignMaskCpp | 0.001 | 0.002 | 0.004 | |
| getGlobalAlignment | 0.011 | 0.002 | 0.014 | |
| getGlobalFits | 0.760 | 0.012 | 0.809 | |
| getLOESSfit | 0.005 | 0.002 | 0.007 | |
| getLinearfit | 0.006 | 0.001 | 0.007 | |
| getMST | 0.000 | 0.000 | 0.001 | |
| getMZMLpointers | 0.026 | 0.003 | 0.031 | |
| getMappedRT | 0.018 | 0.003 | 0.022 | |
| getMultipeptide | 2.829 | 0.038 | 3.016 | |
| getNativeIDs | 0.033 | 0.002 | 0.038 | |
| getNodeIDs | 0.001 | 0.000 | 0.001 | |
| getNodeRun | 0.788 | 0.029 | 0.863 | |
| getOswAnalytes | 0.014 | 0.003 | 0.017 | |
| getOswFiles | 0.013 | 0.002 | 0.017 | |
| getPeptideScores | 0.062 | 0.005 | 0.072 | |
| getPrecursorByID | 0.025 | 0.003 | 0.028 | |
| getPrecursorIndices | 0.079 | 0.005 | 0.086 | |
| getPrecursors | 0.043 | 0.004 | 0.053 | |
| getRSE | 0.006 | 0.002 | 0.006 | |
| getRTdf | 0.010 | 0.002 | 0.013 | |
| getRefExpFeatureMap | 0.571 | 0.027 | 0.629 | |
| getRefRun | 0.590 | 0.022 | 0.642 | |
| getRunNames | 0.016 | 0.003 | 0.020 | |
| getSeqSimMatCpp | 0.001 | 0.002 | 0.003 | |
| getTransitions | 0.282 | 0.017 | 0.315 | |
| getTree | 0.050 | 0.005 | 0.057 | |
| getXICs | 0.151 | 0.008 | 0.166 | |
| getXICs4AlignObj | 0.105 | 0.005 | 0.119 | |
| get_ropenms | 0.000 | 0.001 | 0.002 | |
| imputeChromatogram | 0.026 | 0.003 | 0.031 | |
| ipfReassignFDR | 0 | 0 | 0 | |
| mapIdxToTime | 0.000 | 0.000 | 0.001 | |
| mappedRTfromAlignObj | 0.005 | 0.002 | 0.006 | |
| mergeXIC | 0.004 | 0.002 | 0.006 | |
| mstAlignRuns | 3.562 | 0.075 | 3.818 | |
| mstScript1 | 0.674 | 0.413 | 0.734 | |
| mstScript2 | 4.332 | 0.868 | 5.080 | |
| nrDesc | 0.001 | 0.000 | 0.001 | |
| otherChildXICpp | 0.011 | 0.003 | 0.015 | |
| paramsDIAlignR | 0.000 | 0.000 | 0.001 | |
| perBatch | 0.002 | 0.000 | 0.002 | |
| pickNearestFeature | 0.005 | 0.002 | 0.007 | |
| plotAlignedAnalytes | 1.406 | 0.033 | 1.516 | |
| plotAlignmentPath | 0.685 | 0.053 | 0.780 | |
| plotAnalyteXICs | 1.043 | 0.028 | 1.122 | |
| plotXICgroup | 0.959 | 0.018 | 1.027 | |
| populateReferenceExperimentFeatureAlignmentMap | 0.022 | 0.003 | 0.025 | |
| progAlignRuns | 0.002 | 0.001 | 0.003 | |
| readMzMLHeader | 0.002 | 0.001 | 0.003 | |
| readSqMassHeader | 0.002 | 0.001 | 0.002 | |
| recalculateIntensity | 0.433 | 0.013 | 0.469 | |
| reduceXICs | 0.137 | 0.007 | 0.148 | |
| script1 | 1.353 | 1.552 | 1.771 | |
| script2 | 5.287 | 1.844 | 6.223 | |
| setAlignmentRank | 0.022 | 0.004 | 0.027 | |
| sgolayCpp | 0.005 | 0.001 | 0.005 | |
| sgolayFill | 0.001 | 0.001 | 0.002 | |
| smoothSingleXIC | 0.003 | 0.003 | 0.006 | |
| smoothXICs | 0.014 | 0.002 | 0.017 | |
| splineFill | 0.002 | 0.001 | 0.003 | |
| splineFillCpp | 0.007 | 0.001 | 0.008 | |
| traverseDown | 3.207 | 0.052 | 3.434 | |
| traverseMST | 0.000 | 0.001 | 0.001 | |
| traverseUp | 2.913 | 0.038 | 3.110 | |
| trfrParentFeature | 0.074 | 0.009 | 0.086 | |
| trimXICs | 0.004 | 0.002 | 0.007 | |
| uncompressVec | 0.008 | 0.002 | 0.009 | |
| updateFileInfo | 0.016 | 0.003 | 0.021 | |
| writeOutFeatureAlignmentMap | 0.007 | 0.002 | 0.010 | |
| writeTables | 0.006 | 0.002 | 0.009 | |