Package: Cardinal

Version: 2.2.6

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:Cardinal.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings Cardinal_2.2.6.tar.gz

StartedAt: 2019-10-16 01:09:53 -0400 (Wed, 16 Oct 2019)

EndedAt: 2019-10-16 01:18:42 -0400 (Wed, 16 Oct 2019)

EllapsedTime: 528.4 seconds

RetCode: 0

Status:  OK

CheckDir: Cardinal.Rcheck

Warnings: 0

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:Cardinal.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings Cardinal_2.2.6.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/Cardinal.Rcheck’
* using R version 3.6.1 (2019-07-05)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘Cardinal/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘Cardinal’ version ‘2.2.6’
* 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 ‘Cardinal’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ 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
group_by: no visible global function definition for
  ‘group_by_drop_default’
Undefined global functions or variables:
  group_by_drop_default
* 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 line endings in C/C++/Fortran sources/headers ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                      user system elapsed
spatialDGMM-methods 10.373  0.203  10.665
meansTest-methods    5.266  0.333   5.611
* 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: 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.9-bioc/meat/Cardinal.Rcheck/00check.log’
for details.

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL Cardinal
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library’
* installing *source* package ‘Cardinal’ ...
** using staged installation
** libs
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include  -fPIC  -Wall -g -O2  -c DIP.cpp -o DIP.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include  -fPIC  -Wall -g -O2  -c dynAlign.cpp -o dynAlign.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include  -fPIC  -Wall -g -O2  -c imzML.cpp -o imzML.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include  -fPIC  -Wall -g -O2  -c init.cpp -o init.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include  -fPIC  -Wall -g -O2  -c localMaxima.cpp -o localMaxima.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include  -fPIC  -Wall -g -O2  -c pugixml.cpp -o pugixml.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include  -fPIC  -Wall -g -O2  -c spatial.cpp -o spatial.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include  -fPIC  -Wall -g -O2  -c utils.cpp -o utils.o
clang++ -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 Cardinal.so DIP.o dynAlign.o imzML.o init.o localMaxima.o pugixml.o spatial.o utils.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Library/Frameworks/R.framework/Versions/3.6/Resources/library/00LOCK-Cardinal/00new/Cardinal/libs
** R
** inst
** byte-compile and prepare package for lazy loading
Creating a new generic function for ‘filter’ in package ‘Cardinal’
Creating a new generic function for ‘group_by’ in package ‘Cardinal’
Creating a new generic function for ‘slice’ in package ‘Cardinal’
** 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 (Cardinal)

R version 3.6.1 (2019-07-05) -- "Action of the Toes"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin15.6.0 (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(Cardinal)
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, basename, cbind, colnames, dirname, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
    pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
    tapply, union, unique, unsplit, which, which.max, which.min

Loading required package: BiocParallel
Loading required package: EBImage
Loading required package: S4Vectors
Loading required package: stats4

Attaching package: 'S4Vectors'

The following object is masked from 'package:base':

    expand.grid

Loading required package: ProtGenerics

Welcome to Cardinal (version 2.2.6)

    This is a big update with lots of changes!  See what's new by
    viewing 'vignette("Cardinal-2-guide")'.


Attaching package: 'Cardinal'

The following object is masked from 'package:stats':

    filter

> 
> test_check("Cardinal")
══ testthat results  ═══════════════════════════════════════════════════════════
[ OK: 462 | SKIPPED: 0 | WARNINGS: 3 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
219.820   5.973 226.081 

name	user	system	elapsed
Hashmat-class	0.294	0.029	0.322
IAnnotatedDataFrame-class	0.194	0.005	0.198
ImageData-class	0.041	0.002	0.042
ImageList-class	0.570	0.003	0.573
ImagingExperiment-class	0.053	0.003	0.056
MIAPE-Imaging-class	0.004	0.002	0.006
MSImageData-class	0.208	0.010	0.218
MSImageProcess-class	0.002	0.001	0.003
MSImageSet-class	0.431	0.051	0.482
MSImagingExperiment-class	0.174	0.031	0.204
MSImagingInfo-class	0.456	0.084	0.540
MassDataFrame-class	0.018	0.003	0.021
PCA-methods	2.180	0.142	2.325
PLS-methods	1.330	0.108	1.438
PositionDataFrame-class	0.020	0.001	0.021
SImageData-class	0.080	0.004	0.084
SImageSet-class	0.118	0.003	0.121
SparseImagingExperiment-class	0.042	0.001	0.044
XDataFrame-class	0.010	0.001	0.010
batchProcess-methods	1.445	0.057	1.502
colocalized-methods	1.627	0.142	1.769
colors-functions	1.596	0.033	1.628
dplyr-methods	2.177	0.101	2.280
findNeighbors-methods	0.109	0.051	0.160
generateSpectrum	1.460	0.048	1.511
iSet-class	0.034	0.001	0.035
image-methods	1.196	0.037	1.239
meansTest-methods	5.266	0.333	5.611
mz-methods	0.002	0.002	0.004
mzAlign-methods	0.763	0.038	0.802
mzBin-methods	0.556	0.013	0.570
normalize-methods	0.516	0.004	0.520
peakAlign-methods	1.514	0.037	1.557
peakBin-methods	0.550	0.014	0.575
peakFilter-methods	1.546	0.011	1.556
peakPick-methods	0.524	0.008	0.532
pixelApply-methods	2.072	0.064	2.136
plot-methods	1.461	0.055	1.521
process-methods	1.457	0.146	1.604
reduceBaseline-methods	0.562	0.007	0.570
reduceDimension-methods	0.248	0.009	0.256
simulateSpectrum	0.748	0.038	0.790
slice-methods	0.688	0.018	0.705
smoothSignal-methods.R	0.578	0.004	0.583
spatialDGMM-methods	10.373	0.203	10.665
spatialFastmap-methods	0.874	0.022	0.909
spatialKMeans-methods	1.967	0.037	2.023
spatialShrunkenCentroids-methods	3.431	0.056	3.488
standardizeRuns-methods	0.607	0.003	0.610
topFeatures-methods	1.694	0.015	1.709