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CHECK report for DIAlignR on merida1

This page was generated on 2021-05-06 12:34:47 -0400 (Thu, 06 May 2021).

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 473/1974HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
DIAlignR 1.2.0  (landing page)
Shubham Gupta
Snapshot Date: 2021-05-05 14:51:38 -0400 (Wed, 05 May 2021)
URL: https://git.bioconductor.org/packages/DIAlignR
Branch: RELEASE_3_12
Last Commit: 25b9e1a
Last Changed Date: 2020-10-27 11:52:59 -0400 (Tue, 27 Oct 2020)
malbec1Linux (Ubuntu 18.04.5 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version exists in internal repository
tokay1Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version exists in internal repository
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version exists in internal repository

Summary

Package: DIAlignR
Version: 1.2.0
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_1.2.0.tar.gz
StartedAt: 2021-05-06 01:07:01 -0400 (Thu, 06 May 2021)
EndedAt: 2021-05-06 01:08:23 -0400 (Thu, 06 May 2021)
EllapsedTime: 81.9 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: DIAlignR.Rcheck
Warnings: 1

Command output

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###
### 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_1.2.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.12-bioc/meat/DIAlignR.Rcheck’
* using R version 4.0.5 (2021-03-31)
* 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 ‘1.2.0’
* 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 ... WARNING
Found the following significant warnings:
  chromSimMatrix.cpp:288:69: warning: 'ptr_fun<double, double>' is deprecated [-Wdeprecated-declarations]
See ‘/Users/biocbuild/bbs-3.12-bioc/meat/DIAlignR.Rcheck/00install.out’ for details.
* 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 WARNING, 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.12-bioc/meat/DIAlignR.Rcheck/00check.log’
for details.



Installation output

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
In file included from RcppExports.cpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include/Rcpp.h:57:
/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include/Rcpp/DataFrame.h:136:18: warning: unused variable 'data' [-Wunused-variable]
            SEXP data = Parent::get__();
                 ^
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 Rmain.cpp -o Rmain.o
In file included from Rmain.cpp:1:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include/Rcpp.h:57:
/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include/Rcpp/DataFrame.h:136:18: warning: unused variable 'data' [-Wunused-variable]
            SEXP data = Parent::get__();
                 ^
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 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
chromSimMatrix.cpp:288:69: warning: 'ptr_fun<double, double>' is deprecated [-Wdeprecated-declarations]
  std::transform(s.data.begin(), s.data.end(), s.data.begin(), std::ptr_fun<double, double>(sqrt));
                                                                    ^
/Library/Developer/CommandLineTools/usr/bin/../include/c++/v1/functional:1097:1: note: 'ptr_fun<double, double>' has been explicitly marked deprecated here
_LIBCPP_DEPRECATED_IN_CXX11 inline _LIBCPP_INLINE_VISIBILITY
^
/Library/Developer/CommandLineTools/usr/bin/../include/c++/v1/__config:1101:39: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11'
#  define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED
                                      ^
/Library/Developer/CommandLineTools/usr/bin/../include/c++/v1/__config:1090:48: note: expanded from macro '_LIBCPP_DEPRECATED'
#    define _LIBCPP_DEPRECATED __attribute__ ((deprecated))
                                               ^
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 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
In file included from interface.cpp:1:
In file included from ./interface.h:4:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include/Rcpp.h:57:
/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include/Rcpp/DataFrame.h:136:18: warning: unused variable 'data' [-Wunused-variable]
            SEXP data = Parent::get__();
                 ^
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 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
In file included from simpleFcn.cpp:1:
In file included from ./simpleFcn.h:10:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include/Rcpp.h:57:
/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include/Rcpp/DataFrame.h:136:18: warning: unused variable 'data' [-Wunused-variable]
            SEXP data = Parent::get__();
                 ^
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 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)

Tests output

DIAlignR.Rcheck/tests/testthat.Rout


R version 4.0.5 (2021-03-31) -- "Shake and Throw"
Copyright (C) 2021 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 0.896107 secs
[1] "hroest_K120808_Strep10%PlasmaBiolRepl1_R03_SW_filt"
[2] "hroest_K120809_Strep0%PlasmaBiolRepl2_R04_SW_filt" 
Time difference of 0.6303711 secs
[1] "hroest_K120809_Strep0%PlasmaBiolRepl2_R04_SW_filt" 
[2] "hroest_K120809_Strep10%PlasmaBiolRepl2_R04_SW_filt"
══ Skipped tests ═══════════════════════════════════════════════════════════════
• empty test (1)

[ FAIL 0 | WARN 0 | SKIP 1 | PASS 182 ]
> 
> proc.time()
   user  system elapsed 
 12.046   0.340  12.379 

Example timings

DIAlignR.Rcheck/DIAlignR-Ex.timings

nameusersystemelapsed
alignChromatogramsCpp0.0220.0060.029
alignTargetedRuns3.5970.1293.813
analytesFromFeatures0.0360.0040.079
areaIntegrator0.0030.0000.004
calculateIntensity0.0020.0000.002
constrainSimCpp0.0000.0000.002
doAffineAlignmentCpp0.0010.0000.002
doAlignmentCpp0.0010.0010.002
extractXIC_group0.0140.0010.015
fetchAnalytesInfo0.0060.0000.008
fetchFeaturesFromRun0.0090.0010.010
fetchPrecursorsInfo0.0010.0010.001
filenamesFromMZML0.0000.0010.001
filenamesFromOSW0.0010.0010.002
getAlignObj0.0360.0020.038
getAlignObjs1.3680.0251.396
getAlignedFigs0.1920.0040.196
getAlignedIndices0.0360.0050.042
getBaseGapPenaltyCpp0.0010.0000.001
getChromSimMatCpp0.0020.0020.004
getChromatogramIndices0.2180.0030.222
getFeatures0.0070.0010.008
getGlobalAlignMaskCpp0.0000.0000.002
getGlobalAlignment0.0270.0010.028
getGlobalFits0.0360.0040.040
getLOESSfit0.0030.0010.003
getLinearfit0.0020.0010.003
getMZMLpointers0.0400.0020.043
getMappedRT0.0200.0010.021
getMultipeptide1.1350.0101.147
getOswAnalytes0.0100.0010.011
getOswFiles0.0060.0010.008
getPrecursorByID0.0270.0020.029
getPrecursors0.0070.0010.007
getRSE0.0020.0010.002
getRefRun0.0000.0000.001
getRunNames0.0120.0010.014
getSeqSimMatCpp0.0010.0000.002
getXICs0.1670.0050.174
getXICs4AlignObj0.1190.0020.121
mapIdxToTime0.0010.0000.001
mappedRTfromAlignObj0.0020.0010.002
pickNearestFeature0.0010.0010.002
plotAlignedAnalytes0.5700.0090.579
plotAlignmentPath0.5000.0270.528
plotAnalyteXICs0.5230.0130.537
plotXICgroup0.4680.0120.483
readChromatogramHeader0.0010.0000.002
setAlignmentRank0.0100.0010.011
smoothSingleXIC0.0020.0010.003
smoothXICs0.0010.0010.002
trimXICs0.0010.0010.002
updateFileInfo0.0080.0010.010
writeTables0.0020.0000.002