Shubham Gupta
| Snapshot Date: 2020-10-16 14:40:19 -0400 (Fri, 16 Oct 2020) |
| URL: https://git.bioconductor.org/packages/DIAlignR |
| Branch: RELEASE_3_11 |
| Last Commit: 4f8a0db |
| Last Changed Date: 2020-05-07 15:09:23 -0400 (Thu, 07 May 2020) |
| Back to Multiple platform build/check report for BioC 3.11 |
|
This page was generated on 2020-10-17 11:58:22 -0400 (Sat, 17 Oct 2020).
| TO THE DEVELOPERS/MAINTAINERS OF THE DIAlignR PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 468/1905 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| DIAlignR 1.0.5 Shubham Gupta
| malbec2 | Linux (Ubuntu 18.04.4 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | | ||||||
| machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | [ OK ] | OK | |
| Package: DIAlignR |
| Version: 1.0.5 |
| Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:DIAlignR.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings DIAlignR_1.0.5.tar.gz |
| StartedAt: 2020-10-17 00:30:05 -0400 (Sat, 17 Oct 2020) |
| EndedAt: 2020-10-17 00:31:37 -0400 (Sat, 17 Oct 2020) |
| EllapsedTime: 91.4 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: DIAlignR.Rcheck |
| Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:DIAlignR.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings DIAlignR_1.0.5.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.11-bioc/meat/DIAlignR.Rcheck’ * using R version 4.0.3 (2020-10-10) * using platform: x86_64-apple-darwin17.0 (64-bit) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘DIAlignR/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘DIAlignR’ version ‘1.0.5’ * 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 * checking installed package size ... OK * 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 ... OK * 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/4.0/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. 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 * 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: 1 NOTE See ‘/Users/biocbuild/bbs-3.11-bioc/meat/DIAlignR.Rcheck/00check.log’ for details.
DIAlignR.Rcheck/00install.out
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###
### Running command:
###
### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL DIAlignR
###
##############################################################################
##############################################################################
* installing to library ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/library’
* installing *source* package ‘DIAlignR’ ...
** using staged installation
** libs
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -I/usr/local/include -fPIC -Wall -g -O2 -c ChromatogramPeak.cpp -o ChromatogramPeak.o
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -I/usr/local/include -fPIC -Wall -g -O2 -c DPosition.cpp -o DPosition.o
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -I/usr/local/include -fPIC -Wall -g -O2 -c MSChromatogram.cpp -o MSChromatogram.o
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -I/usr/local/include -fPIC -Wall -g -O2 -c PeakIntegrator.cpp -o PeakIntegrator.o
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -I/usr/local/include -fPIC -Wall -g -O2 -c RcppExports.cpp -o RcppExports.o
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -I/usr/local/include -fPIC -Wall -g -O2 -c Rmain.cpp -o Rmain.o
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -I/usr/local/include -fPIC -Wall -g -O2 -c affinealignment.cpp -o affinealignment.o
affinealignment.cpp:260:12: warning: enumeration value 'SS' not handled in switch [-Wswitch]
switch(TracebackPointer){
^
affinealignment.cpp:260:12: note: add missing switch cases
switch(TracebackPointer){
^
1 warning generated.
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -I/usr/local/include -fPIC -Wall -g -O2 -c affinealignobj.cpp -o affinealignobj.o
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -I/usr/local/include -fPIC -Wall -g -O2 -c alignment.cpp -o alignment.o
alignment.cpp:194:12: warning: 7 enumeration values not handled in switch: 'SS', 'DA', 'DB'... [-Wswitch]
switch(TracebackPointer){
^
alignment.cpp:194:12: note: add missing switch cases
switch(TracebackPointer){
^
1 warning generated.
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -I/usr/local/include -fPIC -Wall -g -O2 -c chromSimMatrix.cpp -o chromSimMatrix.o
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -I/usr/local/include -fPIC -Wall -g -O2 -c constrainMat.cpp -o constrainMat.o
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -I/usr/local/include -fPIC -Wall -g -O2 -c gapPenalty.cpp -o gapPenalty.o
gapPenalty.cpp:20:11: warning: variable 'gapPenalty' is used uninitialized whenever 'if' condition is false [-Wsometimes-uninitialized]
else if(SimType == "correlation")
^~~~~~~~~~~~~~~~~~~~~~~~
gapPenalty.cpp:26:10: note: uninitialized use occurs here
return gapPenalty;
^~~~~~~~~~
gapPenalty.cpp:20:8: note: remove the 'if' if its condition is always true
else if(SimType == "correlation")
^~~~~~~~~~~~~~~~~~~~~~~~~~~~
gapPenalty.cpp:6:20: note: initialize the variable 'gapPenalty' to silence this warning
double gapPenalty;
^
= 0.0
1 warning generated.
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -I/usr/local/include -fPIC -Wall -g -O2 -c integrateArea.cpp -o integrateArea.o
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -I/usr/local/include -fPIC -Wall -g -O2 -c interface.cpp -o interface.o
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -I/usr/local/include -fPIC -Wall -g -O2 -c run_alignment.cpp -o run_alignment.o
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -I/usr/local/include -fPIC -Wall -g -O2 -c simpleFcn.cpp -o simpleFcn.o
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -I/usr/local/include -fPIC -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++ -mmacosx-version-min=10.13 -std=gnu++11 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o DIAlignR.so ChromatogramPeak.o DPosition.o MSChromatogram.o PeakIntegrator.o RcppExports.o Rmain.o affinealignment.o affinealignobj.o alignment.o chromSimMatrix.o constrainMat.o gapPenalty.o integrateArea.o interface.o run_alignment.o simpleFcn.o utils.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Library/Frameworks/R.framework/Versions/4.0/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 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out"
Copyright (C) 2020 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin17.0 (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 1.111665 secs
[1] "hroest_K120808_Strep10%PlasmaBiolRepl1_R03_SW_filt"
[2] "hroest_K120809_Strep0%PlasmaBiolRepl2_R04_SW_filt"
Time difference of 0.699645 secs
[1] "hroest_K120809_Strep0%PlasmaBiolRepl2_R04_SW_filt"
[2] "hroest_K120809_Strep10%PlasmaBiolRepl2_R04_SW_filt"
══ testthat results ═══════════════════════════════════════════════════════════
[ OK: 182 | SKIPPED: 1 | WARNINGS: 0 | FAILED: 0 ]
>
> proc.time()
user system elapsed
14.567 0.416 14.975
DIAlignR.Rcheck/DIAlignR-Ex.timings
| name | user | system | elapsed | |
| alignChromatogramsCpp | 0.030 | 0.009 | 0.040 | |
| alignTargetedRuns | 4.192 | 0.139 | 4.367 | |
| analytesFromFeatures | 0.054 | 0.004 | 0.059 | |
| areaIntegrator | 0.003 | 0.001 | 0.003 | |
| calculateIntensity | 0.002 | 0.001 | 0.004 | |
| constrainSimCpp | 0.002 | 0.001 | 0.002 | |
| doAffineAlignmentCpp | 0.001 | 0.001 | 0.003 | |
| doAlignmentCpp | 0.002 | 0.002 | 0.004 | |
| extractXIC_group | 0.015 | 0.001 | 0.017 | |
| fetchAnalytesInfo | 0.010 | 0.001 | 0.011 | |
| fetchFeaturesFromRun | 0.010 | 0.001 | 0.011 | |
| fetchPrecursorsInfo | 0.001 | 0.001 | 0.001 | |
| filenamesFromMZML | 0.001 | 0.000 | 0.001 | |
| filenamesFromOSW | 0.001 | 0.000 | 0.001 | |
| getAlignObj | 0.037 | 0.002 | 0.039 | |
| getAlignObjs | 1.657 | 0.025 | 1.686 | |
| getAlignedFigs | 0.256 | 0.006 | 0.262 | |
| getAlignedIndices | 0.044 | 0.004 | 0.049 | |
| getBaseGapPenaltyCpp | 0.001 | 0.000 | 0.001 | |
| getChromSimMatCpp | 0.003 | 0.003 | 0.007 | |
| getChromatogramIndices | 0.293 | 0.004 | 0.297 | |
| getFeatures | 0.006 | 0.001 | 0.007 | |
| getGlobalAlignMaskCpp | 0.001 | 0.001 | 0.001 | |
| getGlobalAlignment | 0.024 | 0.001 | 0.025 | |
| getGlobalFits | 0.044 | 0.004 | 0.048 | |
| getLOESSfit | 0.002 | 0.000 | 0.002 | |
| getLinearfit | 0.002 | 0.001 | 0.003 | |
| getMZMLpointers | 0.036 | 0.002 | 0.038 | |
| getMappedRT | 0.023 | 0.001 | 0.025 | |
| getMultipeptide | 1.426 | 0.005 | 1.431 | |
| getOswAnalytes | 0.010 | 0.001 | 0.011 | |
| getOswFiles | 0.008 | 0.001 | 0.009 | |
| getPrecursorByID | 0.033 | 0.001 | 0.035 | |
| getPrecursors | 0.009 | 0.001 | 0.010 | |
| getRSE | 0.002 | 0.001 | 0.003 | |
| getRefRun | 0.001 | 0.000 | 0.001 | |
| getRunNames | 0.010 | 0.001 | 0.011 | |
| getSeqSimMatCpp | 0.001 | 0.001 | 0.002 | |
| getXICs | 0.170 | 0.005 | 0.176 | |
| getXICs4AlignObj | 0.124 | 0.003 | 0.126 | |
| mapIdxToTime | 0 | 0 | 0 | |
| mappedRTfromAlignObj | 0.003 | 0.001 | 0.004 | |
| pickNearestFeature | 0.002 | 0.001 | 0.003 | |
| plotAlignedAnalytes | 0.671 | 0.011 | 0.682 | |
| plotAlignmentPath | 0.496 | 0.025 | 0.559 | |
| plotAnalyteXICs | 0.611 | 0.012 | 0.625 | |
| plotXICgroup | 0.452 | 0.012 | 0.464 | |
| readChromatogramHeader | 0.000 | 0.000 | 0.001 | |
| setAlignmentRank | 0.006 | 0.001 | 0.007 | |
| smoothSingleXIC | 0.001 | 0.001 | 0.002 | |
| smoothXICs | 0.009 | 0.001 | 0.011 | |
| trimXICs | 0.001 | 0.001 | 0.002 | |
| updateFileInfo | 0.008 | 0.001 | 0.009 | |
| writeTables | 0.001 | 0.000 | 0.002 | |