Multiple platform build/check report for BioC 3.9 - CHECK report for Cardinal on tokay2

Package: Cardinal

Version: 2.1.6

Command: C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:Cardinal.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings Cardinal_2.1.6.tar.gz

StartedAt: 2019-03-20 01:47:43 -0400 (Wed, 20 Mar 2019)

EndedAt: 2019-03-20 01:53:47 -0400 (Wed, 20 Mar 2019)

EllapsedTime: 363.7 seconds

RetCode: 0

Status: WARNINGS

CheckDir: Cardinal.Rcheck

Warnings: 2

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:Cardinal.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings Cardinal_2.1.6.tar.gz
###
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##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.9-bioc/meat/Cardinal.Rcheck'
* using R Under development (unstable) (2019-03-09 r76216)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* 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 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 for i386 is not available
Note: information on .o files for x64 is not available
File 'C:/Users/biocbuild/bbs-3.9-bioc/R/library/Cardinal/libs/i386/Cardinal.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
  Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
  Found 'printf', possibly from 'printf' (C)
File 'C:/Users/biocbuild/bbs-3.9-bioc/R/library/Cardinal/libs/x64/Cardinal.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
  Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
  Found 'printf', possibly from 'printf' (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 ...
** running examples for arch 'i386' ... OK
** running examples for arch 'x64' ... OK
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'testthat.R'
 OK
** running tests for arch 'x64' ...
  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
  'C:/Users/biocbuild/bbs-3.9-bioc/meat/Cardinal.Rcheck/00check.log'
for details.

##############################################################################
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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.9/bioc/src/contrib/Cardinal_2.1.6.tar.gz && rm -rf Cardinal.buildbin-libdir && mkdir Cardinal.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=Cardinal.buildbin-libdir Cardinal_2.1.6.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL Cardinal_2.1.6.zip && rm Cardinal_2.1.6.tar.gz Cardinal_2.1.6.zip
###
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  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100 1130k  100 1130k    0     0  16.3M      0 --:--:-- --:--:-- --:--:-- 18.0M

install for i386

* installing *source* package 'Cardinal' ...
** libs
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c DIP.cpp -o DIP.o
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c dynAlign.cpp -o dynAlign.o
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c imzML.cpp -o imzML.o
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c localMaxima.cpp -o localMaxima.o
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c pugixml.cpp -o pugixml.o
pugixml.cpp:221:18: warning: 'size_t pugi::impl::{anonymous}::strlength_wide(const wchar_t*)' defined but not used [-Wunused-function]
  PUGI__FN size_t strlength_wide(const wchar_t* s)
                  ^
pugixml.cpp:2258:18: warning: 'size_t pugi::impl::{anonymous}::as_utf8_begin(const wchar_t*, size_t)' defined but not used [-Wunused-function]
  PUGI__FN size_t as_utf8_begin(const wchar_t* str, size_t length)
                  ^
pugixml.cpp:2264:16: warning: 'void pugi::impl::{anonymous}::as_utf8_end(char*, size_t, const wchar_t*, size_t)' defined but not used [-Wunused-function]
  PUGI__FN void as_utf8_end(char* buffer, size_t size, const wchar_t* str, size_t length)
                ^
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c spatial.cpp -o spatial.o
spatial.cpp: In function 'SEXPREC* get_spatial_weights(SEXP, SEXP, double, bool) [with T1 = int; T2 = int; SEXP = SEXPREC*]':
spatial.cpp:214:6: warning: 'k' may be used uninitialized in this function [-Wmaybe-uninitialized]
  int k; // center pixel
      ^
spatial.cpp: In function 'SEXPREC* get_spatial_weights(SEXP, SEXP, double, bool) [with T1 = int; T2 = double; SEXP = SEXPREC*]':
spatial.cpp:214:6: warning: 'k' may be used uninitialized in this function [-Wmaybe-uninitialized]
spatial.cpp: In function 'SEXPREC* get_spatial_weights(SEXP, SEXP, double, bool) [with T1 = double; T2 = int; SEXP = SEXPREC*]':
spatial.cpp:214:6: warning: 'k' may be used uninitialized in this function [-Wmaybe-uninitialized]
spatial.cpp: In function 'SEXPREC* get_spatial_weights(SEXP, SEXP, double, bool) [with T1 = double; T2 = double; SEXP = SEXPREC*]':
spatial.cpp:214:6: warning: 'k' may be used uninitialized in this function [-Wmaybe-uninitialized]
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c utils.cpp -o utils.o
C:/Rtools/mingw_32/bin/g++ -shared -s -static-libgcc -o Cardinal.dll tmp.def DIP.o dynAlign.o imzML.o localMaxima.o pugixml.o spatial.o utils.o -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.9-bioc/meat/Cardinal.buildbin-libdir/00LOCK-Cardinal/00new/Cardinal/libs/i386
** 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
  converting help for package 'Cardinal'
    finding HTML links ... done
    Binmat-class                            html  
    finding level-2 HTML links ... done

    Cardinal-package                        html  
    Hashmat-class                           html  
    IAnnotatedDataFrame-class               html  
    ImageData-class                         html  
    ImageList-class                         html  
    ImagingExperiment-class                 html  
    MIAPE-Imaging-class                     html  
    MSContinuousImagingExperiment-class     html  
    MSImageData-class                       html  
    MSImageProcess-class                    html  
    MSImageSet-class                        html  
    MSImagingExperiment-class               html  
    MSImagingInfo-class                     html  
    MSProcessedImagingExperiment-class      html  
    MassDataFrame-class                     html  
    OPLS-methods                            html  
    PCA-methods                             html  
    PLS-methods                             html  
    PositionDataFrame-class                 html  
    ResultImagingExperiment-class           html  
    ResultSet-class                         html  
    SImageData-class                        html  
    SImageSet-class                         html  
    SparseImagingExperiment-class           html  
    XDataFrame-class                        html  
    batchProcess-methods                    html  
    colors-functions                        html  
    coregister-methods                      html  
    cvApply-methods                         html  
    deprecated                              html  
    filter-methods                          html  
    findNeighbors-methods                   html  
    generateSpectrum                        html  
    iSet-class                              html  
    image-methods                           html  
    mz-methods                              html  
    normalize-methods                       html  
    peakAlign-methods                       html  
    peakBin-methods                         html  
    peakFilter-methods                      html  
    peakPick-methods                        html  
    pixelApply-methods                      html  
    plot-methods                            html  
    process-methods                         html  
    readMSIData                             html  
    reduceBaseline-methods                  html  
    reduceDimension-methods                 html  
    reexports                               html  
    selectROI-methods                       html  
    simulateSpectrum                        html  
    smoothSignal-methods.R                  html  
    spatialFastmap-methods                  html  
    spatialKMeans-methods                   html  
    spatialShrunkenCentroids-methods        html  
    standardizeRuns-methods                 html  
    topLabels-methods                       html  
    writeMSIData                            html  
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path

install for x64

* installing *source* package 'Cardinal' ...
** libs
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c DIP.cpp -o DIP.o
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c dynAlign.cpp -o dynAlign.o
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c imzML.cpp -o imzML.o
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c localMaxima.cpp -o localMaxima.o
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c pugixml.cpp -o pugixml.o
pugixml.cpp:221:18: warning: 'size_t pugi::impl::{anonymous}::strlength_wide(const wchar_t*)' defined but not used [-Wunused-function]
  PUGI__FN size_t strlength_wide(const wchar_t* s)
                  ^
pugixml.cpp:2258:18: warning: 'size_t pugi::impl::{anonymous}::as_utf8_begin(const wchar_t*, size_t)' defined but not used [-Wunused-function]
  PUGI__FN size_t as_utf8_begin(const wchar_t* str, size_t length)
                  ^
pugixml.cpp:2264:16: warning: 'void pugi::impl::{anonymous}::as_utf8_end(char*, size_t, const wchar_t*, size_t)' defined but not used [-Wunused-function]
  PUGI__FN void as_utf8_end(char* buffer, size_t size, const wchar_t* str, size_t length)
                ^
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c spatial.cpp -o spatial.o
spatial.cpp: In function 'SEXPREC* get_spatial_weights(SEXP, SEXP, double, bool) [with T1 = int; T2 = int; SEXP = SEXPREC*]':
spatial.cpp:214:6: warning: 'k' may be used uninitialized in this function [-Wmaybe-uninitialized]
  int k; // center pixel
      ^
spatial.cpp: In function 'SEXPREC* get_spatial_weights(SEXP, SEXP, double, bool) [with T1 = int; T2 = double; SEXP = SEXPREC*]':
spatial.cpp:214:6: warning: 'k' may be used uninitialized in this function [-Wmaybe-uninitialized]
spatial.cpp: In function 'SEXPREC* get_spatial_weights(SEXP, SEXP, double, bool) [with T1 = double; T2 = int; SEXP = SEXPREC*]':
spatial.cpp:214:6: warning: 'k' may be used uninitialized in this function [-Wmaybe-uninitialized]
spatial.cpp: In function 'SEXPREC* get_spatial_weights(SEXP, SEXP, double, bool) [with T1 = double; T2 = double; SEXP = SEXPREC*]':
spatial.cpp:214:6: warning: 'k' may be used uninitialized in this function [-Wmaybe-uninitialized]
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c utils.cpp -o utils.o
C:/Rtools/mingw_64/bin/g++ -shared -s -static-libgcc -o Cardinal.dll tmp.def DIP.o dynAlign.o imzML.o localMaxima.o pugixml.o spatial.o utils.o -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.9-bioc/meat/Cardinal.buildbin-libdir/Cardinal/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'Cardinal' as Cardinal_2.1.6.zip
* DONE (Cardinal)
* installing to library 'C:/Users/biocbuild/bbs-3.9-bioc/R/library'
package 'Cardinal' successfully unpacked and MD5 sums checked


R Under development (unstable) (2019-03-09 r76216) -- "Unsuffered Consequences"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-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 
  39.93    1.12   41.07


R Under development (unstable) (2019-03-09 r76216) -- "Unsuffered Consequences"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (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 
  54.12    0.54   55.39

name	user	system	elapsed
Binmat-class	0	0	0
Hashmat-class	0.14	0.00	0.14
IAnnotatedDataFrame-class	0.14	0.00	0.14
ImageData-class	0.11	0.00	0.11
ImageList-class	0.11	0.00	0.11
ImagingExperiment-class	0.03	0.00	0.03
MIAPE-Imaging-class	0.02	0.00	0.02
MSImageData-class	0.53	0.02	0.54
MSImageProcess-class	0	0	0
MSImageSet-class	0.3	0.0	0.3
MSImagingExperiment-class	0.11	0.00	0.11
MSImagingInfo-class	0.20	0.05	0.25
MassDataFrame-class	0.02	0.00	0.02
OPLS-methods	0.12	0.01	0.14
PCA-methods	0.06	0.02	0.08
PLS-methods	0.11	0.01	0.12
PositionDataFrame-class	0.02	0.00	0.02
SImageData-class	0.06	0.02	0.07
SImageSet-class	0.06	0.05	0.11
SparseImagingExperiment-class	0.07	0.00	0.07
XDataFrame-class	0.01	0.00	0.01
batchProcess-methods	1.13	0.01	1.14
colors-functions	0.98	0.00	0.98
filter-methods	1.14	0.09	1.24
findNeighbors-methods	0.03	0.02	0.04
generateSpectrum	1.05	0.03	1.08
iSet-class	0.03	0.00	0.03
image-methods	0.83	0.00	0.83
mz-methods	0	0	0
normalize-methods	0.25	0.00	0.25
peakAlign-methods	0.72	0.00	0.72
peakBin-methods	0.17	0.00	0.17
peakFilter-methods	0.86	0.00	0.86
peakPick-methods	0.25	0.00	0.25
pixelApply-methods	0.03	0.00	0.03
plot-methods	1.06	0.08	1.20
process-methods	0.33	0.00	0.32
reduceBaseline-methods	0.23	0.00	0.24
reduceDimension-methods	0.11	0.00	0.11
simulateSpectrum	1.09	0.02	1.11
smoothSignal-methods.R	0.32	0.00	0.31
spatialFastmap-methods	0.34	0.00	0.34
spatialKMeans-methods	0.5	0.0	0.5
spatialShrunkenCentroids-methods	1.45	0.00	1.46
standardizeRuns-methods	0.66	0.00	0.65
topLabels-methods	0.66	0.00	0.66

name	user	system	elapsed
Binmat-class	0	0	0
Hashmat-class	0.24	0.03	0.33
IAnnotatedDataFrame-class	0.18	0.00	0.17
ImageData-class	0.04	0.00	0.05
ImageList-class	0.60	0.00	0.74
ImagingExperiment-class	0.04	0.00	0.07
MIAPE-Imaging-class	0.00	0.00	0.03
MSImageData-class	0.16	0.00	0.47
MSImageProcess-class	0	0	0
MSImageSet-class	0.26	0.04	0.31
MSImagingExperiment-class	0.11	0.02	0.13
MSImagingInfo-class	0.24	0.05	0.29
MassDataFrame-class	0	0	0
OPLS-methods	0.15	0.01	0.18
PCA-methods	0.08	0.00	0.07
PLS-methods	0.11	0.00	0.11
PositionDataFrame-class	0.03	0.00	0.03
SImageData-class	0.06	0.02	0.08
SImageSet-class	0.13	0.00	0.13
SparseImagingExperiment-class	0.04	0.00	0.04
XDataFrame-class	0.02	0.00	0.02
batchProcess-methods	1.09	0.00	1.09
colors-functions	1.14	0.00	1.14
filter-methods	1.77	0.01	1.80
findNeighbors-methods	0.09	0.00	0.09
generateSpectrum	1.79	0.00	1.78
iSet-class	0.04	0.00	0.05
image-methods	1.47	0.02	1.51
mz-methods	0.02	0.00	0.02
normalize-methods	0.39	0.00	0.39
peakAlign-methods	1.40	0.00	1.41
peakBin-methods	0.32	0.00	0.31
peakFilter-methods	1.40	0.02	1.53
peakPick-methods	0.31	0.02	0.32
pixelApply-methods	0.05	0.00	0.05
plot-methods	1.74	0.03	1.78
process-methods	0.28	0.00	0.28
reduceBaseline-methods	0.39	0.00	0.39
reduceDimension-methods	0.19	0.00	0.19
simulateSpectrum	1.15	0.01	1.17
smoothSignal-methods.R	0.42	0.00	0.42
spatialFastmap-methods	0.47	0.00	0.47
spatialKMeans-methods	0.71	0.00	0.71
spatialShrunkenCentroids-methods	1.78	0.00	1.78
standardizeRuns-methods	0.85	0.00	0.85
topLabels-methods	0.78	0.02	0.79

CHECK report for Cardinal on tokay2

Summary

Command output

Installation output

Tests output

Example timings