Multiple platform build/check report for BioC 3.9 - CHECK report for Cardinal on malbec2

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:Cardinal.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings Cardinal_2.2.6.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.9-bioc/meat/Cardinal.Rcheck’
* using R version 3.6.1 (2019-07-05)
* 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 ‘2.2.6’
* 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                     user system elapsed
spatialDGMM-methods 6.186  0.048    6.31
* 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
  ‘/home/biocbuild/bbs-3.9-bioc/meat/Cardinal.Rcheck/00check.log’
for details.

Installation output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD INSTALL Cardinal
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.9-bioc/R/library’
* installing *source* package ‘Cardinal’ ...
** using staged installation
** libs
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG   -I/usr/local/include  -fpic  -g -O2  -Wall -c DIP.cpp -o DIP.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG   -I/usr/local/include  -fpic  -g -O2  -Wall -c dynAlign.cpp -o dynAlign.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG   -I/usr/local/include  -fpic  -g -O2  -Wall -c imzML.cpp -o imzML.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG   -I/usr/local/include  -fpic  -g -O2  -Wall -c init.cpp -o init.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG   -I/usr/local/include  -fpic  -g -O2  -Wall -c localMaxima.cpp -o localMaxima.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG   -I/usr/local/include  -fpic  -g -O2  -Wall -c pugixml.cpp -o pugixml.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG   -I/usr/local/include  -fpic  -g -O2  -Wall -c spatial.cpp -o spatial.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG   -I/usr/local/include  -fpic  -g -O2  -Wall -c utils.cpp -o utils.o
g++ -std=gnu++11 -shared -L/home/biocbuild/bbs-3.9-bioc/R/lib -L/usr/local/lib -o Cardinal.so DIP.o dynAlign.o imzML.o init.o localMaxima.o pugixml.o spatial.o utils.o -L/home/biocbuild/bbs-3.9-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.9-bioc/R/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)

Tests output


R version 3.6.1 (2019-07-05) -- "Action of the Toes"
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, 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 
134.567   1.765 137.570

Example timings

name	user	system	elapsed
Hashmat-class	0.234	0.005	0.246
IAnnotatedDataFrame-class	0.144	0.000	0.144
ImageData-class	0.019	0.000	0.019
ImageList-class	0.436	0.024	0.461
ImagingExperiment-class	0.028	0.000	0.027
MIAPE-Imaging-class	0.002	0.000	0.002
MSImageData-class	0.095	0.000	0.096
MSImageProcess-class	0.001	0.000	0.000
MSImageSet-class	0.207	0.007	0.214
MSImagingExperiment-class	0.079	0.009	0.086
MSImagingInfo-class	0.216	0.023	0.240
MassDataFrame-class	0.007	0.000	0.007
PCA-methods	1.752	0.208	1.956
PLS-methods	0.630	0.012	0.641
PositionDataFrame-class	0.01	0.00	0.01
SImageData-class	0.037	0.004	0.041
SImageSet-class	0.062	0.004	0.066
SparseImagingExperiment-class	0.024	0.000	0.025
XDataFrame-class	0.006	0.000	0.006
batchProcess-methods	1.013	0.004	1.018
colocalized-methods	1.151	0.004	1.155
colors-functions	1.135	0.008	1.143
dplyr-methods	1.108	0.008	1.117
findNeighbors-methods	0.042	0.012	0.054
generateSpectrum	1.031	0.000	1.031
iSet-class	0.027	0.000	0.027
image-methods	0.674	0.000	0.674
meansTest-methods	4.265	0.032	4.297
mz-methods	0.002	0.000	0.002
mzAlign-methods	0.647	0.004	0.651
mzBin-methods	0.335	0.000	0.335
normalize-methods	0.362	0.004	0.366
peakAlign-methods	0.673	0.012	0.685
peakBin-methods	0.243	0.004	0.247
peakFilter-methods	0.772	0.007	0.780
peakPick-methods	0.258	0.000	0.257
pixelApply-methods	0.975	0.008	0.984
plot-methods	0.787	0.024	0.811
process-methods	0.787	0.012	0.799
reduceBaseline-methods	0.475	0.004	0.479
reduceDimension-methods	0.124	0.000	0.124
simulateSpectrum	0.650	0.008	0.707
slice-methods	0.622	0.000	0.666
smoothSignal-methods.R	0.426	0.000	0.430
spatialDGMM-methods	6.186	0.048	6.310
spatialFastmap-methods	0.746	0.000	0.746
spatialKMeans-methods	1.537	0.015	1.762
spatialShrunkenCentroids-methods	2.113	0.004	2.117
standardizeRuns-methods	0.531	0.000	0.531
topFeatures-methods	1.391	0.000	1.396

CHECK report for Cardinal on malbec2

Summary

Command output

Installation output

Tests output

Example timings