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CHECK report for iSEE on celaya2

This page was generated on 2020-01-16 13:50:37 -0500 (Thu, 16 Jan 2020).

Package 861/1818HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
iSEE 1.7.2
Charlotte Soneson
Snapshot Date: 2020-01-15 16:46:30 -0500 (Wed, 15 Jan 2020)
URL: https://git.bioconductor.org/packages/iSEE
Branch: master
Last Commit: d35a7c1
Last Changed Date: 2019-12-05 09:01:50 -0500 (Thu, 05 Dec 2019)
malbec2 Linux (Ubuntu 18.04.3 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: iSEE
Version: 1.7.2
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:iSEE.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings iSEE_1.7.2.tar.gz
StartedAt: 2020-01-16 05:41:56 -0500 (Thu, 16 Jan 2020)
EndedAt: 2020-01-16 05:51:48 -0500 (Thu, 16 Jan 2020)
EllapsedTime: 592.0 seconds
RetCode: 0
Status:  OK 
CheckDir: iSEE.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:iSEE.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings iSEE_1.7.2.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.11-bioc/meat/iSEE.Rcheck’
* using R Under development (unstable) (2019-12-14 r77572)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘iSEE/DESCRIPTION’ ... OK
* this is package ‘iSEE’ version ‘1.7.2’
* package encoding: UTF-8
* 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 ‘iSEE’ 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 ... NOTE
Unexported object imported by a ':::' call: ‘S4Vectors:::selectSome’
  See the note in ?`:::` about the use of this operator.
* 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                             user system elapsed
iSEE                       15.720  1.088  17.272
annotateEnsembl            15.001  1.365  17.065
synchronizeAssays          13.732  0.913  15.024
modeGating                 10.430  0.590  11.400
annotateEntrez              9.279  0.472  10.174
checkColormapCompatibility  9.012  0.389   9.939
* 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
  ‘/Users/biocbuild/bbs-3.11-bioc/meat/iSEE.Rcheck/00check.log’
for details.



Installation output

iSEE.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL iSEE
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/library’
* installing *source* package ‘iSEE’ ...
** using staged installation
** 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
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (iSEE)

Tests output

iSEE.Rcheck/tests/testthat.Rout


R Under development (unstable) (2019-12-14 r77572) -- "Unsuffered Consequences"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin15.6.0 (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(iSEE)
Loading required package: SummarizedExperiment
Loading required package: GenomicRanges
Loading required package: stats4
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: S4Vectors

Attaching package: 'S4Vectors'

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

    expand.grid

Loading required package: IRanges
Loading required package: GenomeInfoDb
Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

Loading required package: DelayedArray
Loading required package: matrixStats

Attaching package: 'matrixStats'

The following objects are masked from 'package:Biobase':

    anyMissing, rowMedians

Loading required package: BiocParallel

Attaching package: 'DelayedArray'

The following objects are masked from 'package:matrixStats':

    colMaxs, colMins, colRanges, rowMaxs, rowMins, rowRanges

The following objects are masked from 'package:base':

    aperm, apply, rowsum

Loading required package: SingleCellExperiment
> 
> test_check("iSEE")
Loading required package: scRNAseq
Loading required package: scater
Loading required package: ggplot2
snapshotDate(): 2020-01-08
see ?scRNAseq and browseVignettes('scRNAseq') for documentation
loading from cache
see ?scRNAseq and browseVignettes('scRNAseq') for documentation
loading from cache
see ?scRNAseq and browseVignettes('scRNAseq') for documentation
loading from cache
Class: ExperimentColorMap
assays(5): counts tophat_counts cufflinks_fpkm cufflinks_fpkm rsem_tpm
colData(1): passes_qc_checks_s
rowData(0):
all_discrete(0):
all_continuous(0):
global_discrete(1)
global_continuous(1)
══ testthat results  ═══════════════════════════════════════════════════════════
[ OK: 1126 | SKIPPED: 3 | WARNINGS: 15 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
178.632   4.737 184.054 

Example timings

iSEE.Rcheck/iSEE-Ex.timings

nameusersystemelapsed
ExperimentColorMap-class0.0670.0100.076
annotateEnsembl15.001 1.36517.065
annotateEntrez 9.279 0.47210.174
availablePanelTypes0.0000.0010.001
checkColormapCompatibility9.0120.3899.939
colDataPlotDefaults0.4620.0090.475
colStatTableDefaults0.2350.0040.239
customDataPlotDefaults0.2730.0210.295
customStatTableDefaults0.2590.0100.270
featAssayPlotDefaults0.5460.0160.562
heatMapPlotDefaults0.2140.0060.220
iSEE15.720 1.08817.272
jitterPoints0.1390.0230.161
lassoPoints0.0120.0020.012
modeEmpty0.2640.0070.271
modeGating10.43 0.5911.40
pointDefaults0.7210.0050.727
redDimPlotDefaults0.5490.0620.612
rowDataPlotDefaults0.4830.0030.486
rowStatTableDefaults0.1680.0030.169
sampAssayPlotDefaults0.6000.0040.604
selectDefaults0.6230.0610.682
subsetPointsByGrid0.2000.0470.246
synchronizeAssays13.732 0.91315.024