Package: Cardinal

Version: 2.0.4

Command: /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD check --install=check:Cardinal.install-out.txt --library=/home/biocbuild/bbs-3.8-bioc/R/library --no-vignettes --timings Cardinal_2.0.4.tar.gz

StartedAt: 2019-04-15 22:40:21 -0400 (Mon, 15 Apr 2019)

EndedAt: 2019-04-15 22:43:52 -0400 (Mon, 15 Apr 2019)

EllapsedTime: 210.7 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: Cardinal.Rcheck

Warnings: 1

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### Running command:
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###   /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD check --install=check:Cardinal.install-out.txt --library=/home/biocbuild/bbs-3.8-bioc/R/library --no-vignettes --timings Cardinal_2.0.4.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.8-bioc/meat/Cardinal.Rcheck’
* using R version 3.5.3 (2019-03-11)
* using platform: x86_64-pc-linux-gnu (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 ‘2.0.4’
* 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 ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... WARNING
Undocumented code objects:
  ‘filter’
All user-level objects in a package should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* 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 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
  ‘/home/biocbuild/bbs-3.8-bioc/meat/Cardinal.Rcheck/00check.log’
for details.

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### Running command:
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###   /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD INSTALL Cardinal
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* installing to library ‘/home/biocbuild/bbs-3.8-bioc/R/library’
* installing *source* package ‘Cardinal’ ...
** libs
gcc -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c dynamicAlign.c -o dynamicAlign.o
gcc -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c fastmap.c -o fastmap.o
fastmap.c: In function ‘choose_distant_objects’:
fastmap.c:59:24: warning: ‘o_b’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  pivot_objects->b[col] = o_b;
                        ^
g++  -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c imzML.cpp -o imzML.o
g++  -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c localMaxima.cpp -o localMaxima.o
g++  -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c pugixml.cpp -o pugixml.o
gcc -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c smooth.c -o smooth.o
gcc -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c spatial.c -o spatial.o
g++  -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c utils.cpp -o utils.o
g++ -shared -L/home/biocbuild/bbs-3.8-bioc/R/lib -L/usr/local/lib -o Cardinal.so dynamicAlign.o fastmap.o imzML.o localMaxima.o pugixml.o smooth.o spatial.o utils.o -L/home/biocbuild/bbs-3.8-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.8-bioc/R/library/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
* DONE (Cardinal)

R version 3.5.3 (2019-03-11) -- "Great Truth"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (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, lengths, 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 2.0.4)

    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: 380 SKIPPED: 0 FAILED: 0
> 
> proc.time()
   user  system elapsed 
 47.228   0.548  47.972 

name	user	system	elapsed
Binmat-class	0	0	0
Hashmat-class	0.176	0.004	0.181
IAnnotatedDataFrame-class	0.188	0.008	0.230
ImageData-class	0.016	0.000	0.019
ImageList-class	0.064	0.000	0.066
ImagingExperiment-class	0.024	0.000	0.023
MIAPE-Imaging-class	0.004	0.000	0.002
MSImageData-class	0.112	0.000	0.112
MSImageProcess-class	0.000	0.000	0.001
MSImageSet-class	0.184	0.012	0.195
MSImagingExperiment-class	0.092	0.000	0.090
MSImagingInfo-class	0.236	0.004	0.240
MassDataFrame-class	0.012	0.000	0.012
OPLS-methods	0.196	0.000	0.197
PCA-methods	0.076	0.000	0.074
PLS-methods	0.112	0.000	0.113
PositionDataFrame-class	0.02	0.00	0.02
SImageData-class	0.076	0.000	0.077
SImageSet-class	0.104	0.004	0.110
SparseImagingExperiment-class	0.044	0.000	0.046
XDataFrame-class	0.016	0.000	0.014
batchProcess-methods	1.060	0.008	1.067
colors-functions	1.216	0.060	1.276
filter-methods	1.468	0.640	1.440
generateImage	1.188	0.112	1.303
generateSpectrum	0.040	0.004	0.043
iSet-class	0.048	0.000	0.045
image-methods	0.876	0.008	0.887
mz-methods	0.000	0.000	0.001
normalize-methods	0.160	0.000	0.159
peakAlign-methods	0.564	0.000	0.566
peakFilter-methods	1.104	0.000	1.110
peakPick-methods	0.132	0.000	0.130
pixelApply-methods	0.032	0.000	0.034
plot-methods	0.684	0.004	0.685
process-methods	0.540	0.184	0.608
reduceBaseline-methods	0.140	0.028	0.170
reduceDimension-methods	0.132	0.008	0.139
smoothSignal-methods.R	0.116	0.004	0.122
spatialKMeans-methods	0.552	0.004	0.556
spatialShrunkenCentroids-methods	2.120	0.008	2.131
standardizeRuns-methods	0.440	0.000	0.441
topLabels-methods	1.208	0.028	1.251