Package: Cardinal

Version: 2.1.6

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_2.1.6.tar.gz

StartedAt: 2019-03-21 00:18:00 -0400 (Thu, 21 Mar 2019)

EndedAt: 2019-03-21 00:28:20 -0400 (Thu, 21 Mar 2019)

EllapsedTime: 620.1 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: Cardinal.Rcheck

Warnings: 2

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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_2.1.6.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/Cardinal.Rcheck’
* using R Under development (unstable) (2019-03-18 r76245)
* 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 ‘2.1.6’
* 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
predict,SpatialShrunkenCentroids2: no visible binding for global
  variable ‘x’
predict,SpatialShrunkenCentroids2 : <anonymous>: no visible binding for
  global variable ‘i’
predict,SpatialShrunkenCentroids2 : <anonymous>: no visible binding for
  global variable ‘x’
predict,SpatialShrunkenCentroids2 : <anonymous>: no visible binding for
  global variable ‘fit’
spatialShrunkenCentroids,SparseImagingExperiment-ANY : <anonymous>: no
  visible binding for global variable ‘r.weights’
Undefined global functions or variables:
  fit i r.weights x
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... WARNING
Undocumented S4 methods:
  generic 'predict' and siglist 'SpatialShrunkenCentroids2'
  generic 'spatialKMeans' and siglist 'SparseImagingExperiment'
  generic 'spatialShrunkenCentroids' and siglist
    'SparseImagingExperiment,ANY'
  generic 'spatialShrunkenCentroids' and siglist
    'SparseImagingExperiment,missing'
All user-level objects in a package (including S4 classes and methods)
should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* checking for code/documentation mismatches ... WARNING
Codoc mismatches from documentation object 'findNeighbors-methods':
\S4method{spatialWeights}{ImagingExperiment}
  Code: function(x, r = 1, method = c("gaussian", "adaptive"), dist =
                 "chebyshev", matrix = FALSE, BPPARAM = bpparam(), ...)
  Docs: function(x, r, method = c("gaussian", "adaptive"), matrix =
                 FALSE, BPPARAM = bpparam(), ...)
  Argument names in code not in docs:
    dist
  Mismatches in argument names:
    Position: 4 Code: dist Docs: matrix
    Position: 5 Code: matrix Docs: BPPARAM
    Position: 6 Code: BPPARAM Docs: ...
  Mismatches in argument default values:
    Name: 'r' Code: 1 Docs: 

Codoc mismatches from documentation object 'image-methods':
\S4method{image}{SpatialShrunkenCentroids2}
  Code: function(x, formula, values = c("probability", "class",
                 "scores"), ...)
  Docs: function(x, formula, values = c("probabilities", "classes",
                 "scores"), ...)
  Mismatches in argument default values:
    Name: 'values' Code: c("probability", "class", "scores") Docs: c("probabilities", "classes", "scores")

Codoc mismatches from documentation object 'plot-methods':
\S4method{plot}{SpatialKMeans2,missing}
  Code: function(x, formula, values = c("centers", "correlation"), ...)
  Docs: function(x, formula, values = c("centers", "betweenss",
                 "withinss"), ...)
  Mismatches in argument default values:
    Name: 'values' Code: c("centers", "correlation") Docs: c("centers", "betweenss", "withinss")
\S4method{plot}{SpatialShrunkenCentroids2,missing}
  Code: function(x, formula, values = c("centers", "statistic"), ...)
  Docs: function(x, formula, values = c("centers", "tstatistics"), ...)
  Mismatches in argument default values:
    Name: 'values' Code: c("centers", "statistic") Docs: c("centers", "tstatistics")

* 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
* 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 WARNINGs, 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   -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   -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   -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   -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   -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   -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   -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 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’
** 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 Under development (unstable) (2019-03-18 r76245) -- "Unsuffered Consequences"
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, colMeans, colSums, 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, rowMeans, rowSums,
    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 2.1.6)

    To get started, view the introductory vignettes with
    'browseVignettes("Cardinal")'.


Attaching package: 'Cardinal'

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

    filter

> 
> test_check("Cardinal")
══ testthat results  ═══════════════════════════════════════════════════════════
OK: 416 SKIPPED: 0 FAILED: 0
> 
> proc.time()
   user  system elapsed 
 74.321   2.181 139.878 

name	user	system	elapsed
Binmat-class	0.001	0.001	0.001
Hashmat-class	0.241	0.037	0.527
IAnnotatedDataFrame-class	0.249	0.004	0.443
ImageData-class	0.042	0.001	0.064
ImageList-class	0.124	0.003	0.221
ImagingExperiment-class	0.052	0.002	0.098
MIAPE-Imaging-class	0.005	0.002	0.017
MSImageData-class	0.222	0.006	0.416
MSImageProcess-class	0.002	0.002	0.003
MSImageSet-class	0.362	0.009	0.670
MSImagingExperiment-class	0.160	0.002	0.293
MSImagingInfo-class	0.335	0.004	0.592
MassDataFrame-class	0.012	0.001	0.028
OPLS-methods	0.186	0.002	0.337
PCA-methods	0.077	0.001	0.132
PLS-methods	0.597	0.002	1.095
PositionDataFrame-class	0.023	0.001	0.035
SImageData-class	0.078	0.004	0.144
SImageSet-class	0.106	0.004	0.200
SparseImagingExperiment-class	0.052	0.001	0.086
XDataFrame-class	0.016	0.001	0.033
batchProcess-methods	1.386	0.037	2.583
colors-functions	1.942	0.191	3.892
filter-methods	2.410	0.141	4.618
findNeighbors-methods	0.097	0.028	0.255
generateSpectrum	1.613	0.043	3.093
iSet-class	0.057	0.002	0.108
image-methods	1.702	0.052	3.197
mz-methods	0.002	0.002	0.013
normalize-methods	0.461	0.003	0.842
peakAlign-methods	1.802	0.052	3.331
peakBin-methods	0.371	0.004	0.666
peakFilter-methods	1.869	0.028	3.387
peakPick-methods	0.489	0.010	0.896
pixelApply-methods	0.068	0.002	0.120
plot-methods	2.087	0.069	3.982
process-methods	0.389	0.004	0.737
reduceBaseline-methods	0.473	0.006	0.863
reduceDimension-methods	0.231	0.002	0.417
simulateSpectrum	0.731	0.030	1.375
smoothSignal-methods.R	0.533	0.005	0.990
spatialFastmap-methods	0.723	0.007	1.322
spatialKMeans-methods	1.790	0.067	3.384
spatialShrunkenCentroids-methods	2.534	0.028	4.632
standardizeRuns-methods	1.192	0.022	2.241
topLabels-methods	1.498	0.030	2.836