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CHECK report for Cardinal on malbec2

This page was generated on 2019-10-16 12:06:07 -0400 (Wed, 16 Oct 2019).

Package 212/1741HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
Cardinal 2.2.6
Kylie A. Bemis
Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019)
URL: https://git.bioconductor.org/packages/Cardinal
Branch: RELEASE_3_9
Last Commit: 66fed1d
Last Changed Date: 2019-05-22 16:53:28 -0400 (Wed, 22 May 2019)
malbec2 Linux (Ubuntu 18.04.2 LTS) / x86_64  OK  OK [ OK ]UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
celaya2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: Cardinal
Version: 2.2.6
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
StartedAt: 2019-10-16 00:17:06 -0400 (Wed, 16 Oct 2019)
EndedAt: 2019-10-16 00:22:50 -0400 (Wed, 16 Oct 2019)
EllapsedTime: 343.8 seconds
RetCode: 0
Status:  OK 
CheckDir: Cardinal.Rcheck
Warnings: 0

Command output

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### 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
###
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* 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

Cardinal.Rcheck/00install.out

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###
### 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

Cardinal.Rcheck/tests/testthat.Rout


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

Cardinal.Rcheck/Cardinal-Ex.timings

nameusersystemelapsed
Hashmat-class0.2340.0050.246
IAnnotatedDataFrame-class0.1440.0000.144
ImageData-class0.0190.0000.019
ImageList-class0.4360.0240.461
ImagingExperiment-class0.0280.0000.027
MIAPE-Imaging-class0.0020.0000.002
MSImageData-class0.0950.0000.096
MSImageProcess-class0.0010.0000.000
MSImageSet-class0.2070.0070.214
MSImagingExperiment-class0.0790.0090.086
MSImagingInfo-class0.2160.0230.240
MassDataFrame-class0.0070.0000.007
PCA-methods1.7520.2081.956
PLS-methods0.6300.0120.641
PositionDataFrame-class0.010.000.01
SImageData-class0.0370.0040.041
SImageSet-class0.0620.0040.066
SparseImagingExperiment-class0.0240.0000.025
XDataFrame-class0.0060.0000.006
batchProcess-methods1.0130.0041.018
colocalized-methods1.1510.0041.155
colors-functions1.1350.0081.143
dplyr-methods1.1080.0081.117
findNeighbors-methods0.0420.0120.054
generateSpectrum1.0310.0001.031
iSet-class0.0270.0000.027
image-methods0.6740.0000.674
meansTest-methods4.2650.0324.297
mz-methods0.0020.0000.002
mzAlign-methods0.6470.0040.651
mzBin-methods0.3350.0000.335
normalize-methods0.3620.0040.366
peakAlign-methods0.6730.0120.685
peakBin-methods0.2430.0040.247
peakFilter-methods0.7720.0070.780
peakPick-methods0.2580.0000.257
pixelApply-methods0.9750.0080.984
plot-methods0.7870.0240.811
process-methods0.7870.0120.799
reduceBaseline-methods0.4750.0040.479
reduceDimension-methods0.1240.0000.124
simulateSpectrum0.6500.0080.707
slice-methods0.6220.0000.666
smoothSignal-methods.R0.4260.0000.430
spatialDGMM-methods6.1860.0486.310
spatialFastmap-methods0.7460.0000.746
spatialKMeans-methods1.5370.0151.762
spatialShrunkenCentroids-methods2.1130.0042.117
standardizeRuns-methods0.5310.0000.531
topFeatures-methods1.3910.0001.396