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CHECK report for scone on celaya2

This page was generated on 2019-04-09 13:17:28 -0400 (Tue, 09 Apr 2019).

Package 1444/1703HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
scone 1.7.1
Michael Cole
Snapshot Date: 2019-04-08 17:01:18 -0400 (Mon, 08 Apr 2019)
URL: https://git.bioconductor.org/packages/scone
Branch: master
Last Commit: 56f9c5f
Last Changed Date: 2019-01-04 13:48:53 -0400 (Fri, 04 Jan 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  WARNINGS  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
merida2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK 

Summary

Package: scone
Version: 1.7.1
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:scone.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings scone_1.7.1.tar.gz
StartedAt: 2019-04-09 05:20:13 -0400 (Tue, 09 Apr 2019)
EndedAt: 2019-04-09 05:31:41 -0400 (Tue, 09 Apr 2019)
EllapsedTime: 687.7 seconds
RetCode: 0
Status:  OK 
CheckDir: scone.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:scone.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings scone_1.7.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/scone.Rcheck’
* using R Under development (unstable) (2019-03-18 r76245)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘scone/DESCRIPTION’ ... OK
* this is package ‘scone’ version ‘1.7.1’
* 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 ‘scone’ 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
sconeReport: no visible global function definition for
  ‘visNetworkOutput’
sconeReport: no visible global function definition for ‘plotlyOutput’
sconeReport : server: no visible global function definition for
  ‘renderVisNetwork’
sconeReport : server: no visible global function definition for ‘%>%’
sconeReport : server: no visible global function definition for
  ‘visNetwork’
sconeReport : server: no visible global function definition for
  ‘visHierarchicalLayout’
sconeReport : server: no visible global function definition for
  ‘visGroups’
sconeReport : server: no visible global function definition for
  ‘visEdges’
sconeReport : server: no visible global function definition for
  ‘visOptions’
sconeReport : server: no visible global function definition for
  ‘visLegend’
sconeReport : server: no visible global function definition for
  ‘visNetworkProxy’
sconeReport : server: no visible global function definition for
  ‘visSelectNodes’
sconeReport : server: no visible global function definition for
  ‘plot_ly’
sconeReport : server: no visible global function definition for
  ‘ggplot’
sconeReport : server: no visible global function definition for ‘aes’
sconeReport : server: no visible global function definition for
  ‘geom_bar’
sconeReport : server: no visible global function definition for ‘ylim’
sconeReport : server: no visible global function definition for ‘labs’
sconeReport : server: no visible global function definition for ‘theme’
sconeReport : server: no visible global function definition for
  ‘element_blank’
sconeReport : server: no visible global function definition for
  ‘ggplotly’
sconeReport : server: no visible global function definition for
  ‘geom_violin’
sconeReport : server: no visible global function definition for
  ‘coord_cartesian’
sconeReport : server: no visible global function definition for
  ‘scale_fill_manual’
sconeReport : server: no visible global function definition for
  ‘geom_point’
sconeReport : server: no visible global function definition for
  ‘guides’
Undefined global functions or variables:
  %>% aes coord_cartesian element_blank geom_bar geom_point geom_violin
  ggplot ggplotly guides labs plot_ly plotlyOutput renderVisNetwork
  scale_fill_manual theme visEdges visGroups visHierarchicalLayout
  visLegend visNetwork visNetworkOutput visNetworkProxy visOptions
  visSelectNodes ylim
* 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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* 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
  ‘/Users/biocbuild/bbs-3.9-bioc/meat/scone.Rcheck/00check.log’
for details.



Installation output

scone.Rcheck/00install.out

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


* installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library’
* installing *source* package ‘scone’ ...
** using staged installation
** R
** data
** 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 (scone)

Tests output

scone.Rcheck/tests/testthat.Rout


R Under development (unstable) (2019-03-18 r76245) -- "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.

> Sys.setenv("R_TESTS" = "")
> 
> library(testthat)
> library(scone)
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, colMeans, colSums, 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, rowMeans, rowSums,
    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

> 
> test_check("scone")

SubmitJobs |+                                                |   0% (00:00:00)
SubmitJobs |+                                                |   0% (00:00:00)
SubmitJobs |++++++++++++++++++++++++                         |  50% (00:00:05)
SubmitJobs |+++++++++++++++++++++++++++++++++++++++++++++++++| 100% (00:00:00)

Waiting                   |+                                 |   0% (00:00:00)
Waiting [S:0 D:3 E:0 R:0] |++++++++++++++++++++++++++++++++++| 100% (00:00:00)


SubmitJobs |+                                                |   0% (00:00:00)
SubmitJobs |+                                                |   0% (00:00:00)
SubmitJobs |++++++++++++++++++++++++                         |  50% (00:00:05)
SubmitJobs |+++++++++++++++++++++++++++++++++++++++++++++++++| 100% (00:00:00)

Waiting                   |+                                 |   0% (00:00:00)
Waiting [S:0 D:3 E:0 R:0] |++++++++++++++++++++++++++++++++++| 100% (00:00:00)


SubmitJobs |+                                                |   0% (00:00:00)
SubmitJobs |+                                                |   0% (00:00:00)
SubmitJobs |++++++++++++++++++++++++                         |  50% (00:00:05)
SubmitJobs |+++++++++++++++++++++++++++++++++++++++++++++++++| 100% (00:00:00)

Waiting                   |+                                 |   0% (00:00:00)
Waiting [S:0 D:3 E:0 R:0] |++++++++++++++++++++++++++++++++++| 100% (00:00:00)


SubmitJobs |+                                                |   0% (00:00:00)
SubmitJobs |+                                                |   0% (00:00:00)
SubmitJobs |++++++++++++++++++++++++                         |  50% (00:00:37)
SubmitJobs |+++++++++++++++++++++++++++++++++++++++++++++++++| 100% (00:00:00)

Waiting                   |+                                 |   0% (00:00:00)
Waiting [S:0 D:36 E:0 R:0] |++++++++++++++++++++++++++++++++++| 100% (00:00:00)

══ testthat results  ═══════════════════════════════════════════════════════════
OK: 315 SKIPPED: 0 FAILED: 0
> 
> proc.time()
   user  system elapsed 
172.783  12.202 274.274 

Example timings

scone.Rcheck/scone-Ex.timings

nameusersystemelapsed
CLR_FN0.0020.0000.002
DESEQ_FN0.0020.0010.003
FQ_FN0.0030.0010.003
SCRAN_FN1.9830.1682.150
SUM_FN0.0010.0000.001
SconeExperiment-class0.5770.0930.670
TMM_FN0.0070.0010.008
UQ_FN0.0030.0000.004
biplot_color0.0160.0020.017
biplot_interactive0.4920.0360.527
control_genes0.0210.0290.050
estimate_ziber0.0600.0040.064
factor_sample_filter0.0820.0050.089
fast_estimate_ziber0.0740.0010.076
get_bio0.0760.0000.076
get_design1.1570.0141.171
get_negconruv0.0960.0010.096
get_normalized0.0930.0010.093
get_params0.0500.0000.051
get_qc0.0860.0010.089
get_scores0.0950.0010.097
impute_expectation0.0030.0000.003
impute_null0.0000.0000.001
lm_adjust0.0070.0000.007
make_design0.0030.0000.004
metric_sample_filter0.0110.0020.016
scone0.1650.0040.170
sconeReport0.0680.0020.069
scone_easybake0.0690.0020.071
score_matrix0.0050.0010.006
select_methods0.0630.0010.063
simple_FNR_params0.0420.0000.042