Back to Multiple platform build/check report for BioC 3.10
AB[C]DEFGHIJKLMNOPQRSTUVWXYZ

CHECK report for Cardinal on malbec1

This page was generated on 2020-04-15 12:09:41 -0400 (Wed, 15 Apr 2020).

Package 226/1823HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
Cardinal 2.4.0
Kylie A. Bemis
Snapshot Date: 2020-04-14 16:46:13 -0400 (Tue, 14 Apr 2020)
URL: https://git.bioconductor.org/packages/Cardinal
Branch: RELEASE_3_10
Last Commit: 5f5c0c9
Last Changed Date: 2019-10-29 13:09:08 -0400 (Tue, 29 Oct 2019)
malbec1 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK [ OK ]UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
merida1 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: Cardinal
Version: 2.4.0
Command: /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD check --install=check:Cardinal.install-out.txt --library=/home/biocbuild/bbs-3.10-bioc/R/library --no-vignettes --timings Cardinal_2.4.0.tar.gz
StartedAt: 2020-04-15 02:47:32 -0400 (Wed, 15 Apr 2020)
EndedAt: 2020-04-15 02:52:24 -0400 (Wed, 15 Apr 2020)
EllapsedTime: 292.7 seconds
RetCode: 0
Status:  OK 
CheckDir: Cardinal.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD check --install=check:Cardinal.install-out.txt --library=/home/biocbuild/bbs-3.10-bioc/R/library --no-vignettes --timings Cardinal_2.4.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.10-bioc/meat/Cardinal.Rcheck’
* using R version 3.6.3 (2020-02-29)
* 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 ‘2.4.0’
* 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 ... 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
* 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 NOTE
See
  ‘/home/biocbuild/bbs-3.10-bioc/meat/Cardinal.Rcheck/00check.log’
for details.



Installation output

Cardinal.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD INSTALL Cardinal
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.10-bioc/R/library’
* installing *source* package ‘Cardinal’ ...
** using staged installation
** libs
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.10-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-3.10-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-3.10-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-3.10-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-3.10-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-3.10-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-3.10-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-3.10-bioc/R/lib -L/usr/local/lib -o Cardinal.so DIP.o dynAlign.o imzML.o init.o pugixml.o spatial.o utils.o -L/home/biocbuild/bbs-3.10-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.10-bioc/R/library/00LOCK-Cardinal/00new/Cardinal/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** 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

Cardinal.Rcheck/tests/testthat.Rout


R version 3.6.3 (2020-02-29) -- "Holding the Windsock"
Copyright (C) 2020 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

Attaching package: 'ProtGenerics'

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

    smooth


Attaching package: 'Cardinal'

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

    filter

> 
> test_check("Cardinal")
══ testthat results  ═══════════════════════════════════════════════════════════
[ OK: 479 | SKIPPED: 8 | WARNINGS: 0 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
 62.216   1.004  64.007 

Example timings

Cardinal.Rcheck/Cardinal-Ex.timings

nameusersystemelapsed
AnnotatedImagingExperiment-class0.1440.0040.222
Hashmat-class0.1040.0080.113
IAnnotatedDataFrame-class0.1400.0040.153
ImageData-class0.0320.0000.033
ImageList-class0.0960.0000.095
ImagingExperiment-class0.0440.0080.054
MIAPE-Imaging-class0.0000.0000.003
MSImageData-class0.1680.0120.184
MSImageProcess-class0.0000.0000.001
MSImageSet-class0.3320.0160.352
MSImagingExperiment-class0.1280.0000.130
MSImagingInfo-class0.4040.0000.408
MassDataFrame-class0.0040.0000.008
PCA-methods1.7640.2562.096
PLS-methods0.9440.0080.953
PositionDataFrame-class0.0160.0000.017
SImageData-class0.0560.0040.059
SImageSet-class0.1280.0040.131
SparseImagingExperiment-class0.0480.0040.050
XDataFrame-class0.0120.0000.010
colocalized-methods1.4160.0361.493
colors-functions1.0200.0001.033
dplyr-methods1.3280.0161.378
findNeighbors-methods0.0560.0120.068
iSet-class0.0360.0000.037
image-methods0.8880.0000.939
meansTest-methods3.5840.0523.679
mz-methods0.0000.0000.002
mzAlign-methods1.0040.0041.009
mzBin-methods0.4160.0000.413
mzFilter-methods1.1520.0041.186
normalize-methods0.3520.0000.353
peakAlign-methods0.6760.0040.681
peakBin-methods0.4400.0000.445
peakPick-methods0.3800.0000.383
pixelApply-methods1.4640.0201.493
plot-methods1.2840.0081.298
process-methods1.7560.0201.824
reduceBaseline-methods0.5120.0000.514
simulateSpectrum0.7840.0000.789
slice-methods0.6360.0040.716
smoothSignal-methods0.4760.0000.477
spatialDGMM-methods2.0680.0122.119
spatialFastmap-methods0.7560.0040.767
spatialKMeans-methods1.4720.0201.497
spatialShrunkenCentroids-methods1.8720.0081.886
topFeatures-methods0.8920.0000.893