Back to Multiple platform build/check report for BioC 3.14
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This page was generated on 2022-04-13 12:08:45 -0400 (Wed, 13 Apr 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.1.3 (2022-03-10) -- "One Push-Up" 4324
tokay2Windows Server 2012 R2 Standardx644.1.3 (2022-03-10) -- "One Push-Up" 4077
machv2macOS 10.14.6 Mojavex86_644.1.3 (2022-03-10) -- "One Push-Up" 4137
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

CHECK results for scone on machv2


To the developers/maintainers of the scone package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/scone.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 1733/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
scone 1.18.0  (landing page)
Davide Risso
Snapshot Date: 2022-04-12 01:55:07 -0400 (Tue, 12 Apr 2022)
git_url: https://git.bioconductor.org/packages/scone
git_branch: RELEASE_3_14
git_last_commit: 80329bd
git_last_commit_date: 2021-10-26 12:32:11 -0400 (Tue, 26 Oct 2021)
nebbiolo2Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: scone
Version: 1.18.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:scone.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings scone_1.18.0.tar.gz
StartedAt: 2022-04-12 18:14:01 -0400 (Tue, 12 Apr 2022)
EndedAt: 2022-04-12 18:28:29 -0400 (Tue, 12 Apr 2022)
EllapsedTime: 867.1 seconds
RetCode: 0
Status:   OK  
CheckDir: scone.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:scone.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings scone_1.18.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.14-bioc/meat/scone.Rcheck’
* using R version 4.1.3 (2022-03-10)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘scone/DESCRIPTION’ ... OK
* this is package ‘scone’ version ‘1.18.0’
* 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 ‘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-3.14-bioc/meat/scone.Rcheck/00check.log’
for details.



Installation output

scone.Rcheck/00install.out

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


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.1/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 version 4.1.3 (2022-03-10) -- "One Push-Up"
Copyright (C) 2022 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin17.0 (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: MatrixGenerics
Loading required package: matrixStats

Attaching package: 'MatrixGenerics'

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

    colAlls, colAnyNAs, colAnys, colAvgsPerRowSet, colCollapse,
    colCounts, colCummaxs, colCummins, colCumprods, colCumsums,
    colDiffs, colIQRDiffs, colIQRs, colLogSumExps, colMadDiffs,
    colMads, colMaxs, colMeans2, colMedians, colMins, colOrderStats,
    colProds, colQuantiles, colRanges, colRanks, colSdDiffs, colSds,
    colSums2, colTabulates, colVarDiffs, colVars, colWeightedMads,
    colWeightedMeans, colWeightedMedians, colWeightedSds,
    colWeightedVars, rowAlls, rowAnyNAs, rowAnys, rowAvgsPerColSet,
    rowCollapse, rowCounts, rowCummaxs, rowCummins, rowCumprods,
    rowCumsums, rowDiffs, rowIQRDiffs, rowIQRs, rowLogSumExps,
    rowMadDiffs, rowMads, rowMaxs, rowMeans2, rowMedians, rowMins,
    rowOrderStats, rowProds, rowQuantiles, rowRanges, rowRanks,
    rowSdDiffs, rowSds, rowSums2, rowTabulates, rowVarDiffs, rowVars,
    rowWeightedMads, rowWeightedMeans, rowWeightedMedians,
    rowWeightedSds, rowWeightedVars

Loading required package: GenomicRanges
Loading required package: stats4
Loading required package: BiocGenerics

Attaching package: 'BiocGenerics'

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.max, which.min

Loading required package: S4Vectors

Attaching package: 'S4Vectors'

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

    I, expand.grid, unname

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")'.


Attaching package: 'Biobase'

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

    rowMedians

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

    anyMissing, rowMedians

> 
> 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% (00:00:03)
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% (00:00:04)
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% (00:00:39)
SubmitJobs |+++++++++++++++++++++++++++++++++++++++++++++++++| 100% (00:00:00)

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

[ FAIL 0 | WARN 0 | SKIP 0 | PASS 64 ]
> 
> proc.time()
   user  system elapsed 
192.304   7.875 408.070 

Example timings

scone.Rcheck/scone-Ex.timings

nameusersystemelapsed
CLR_FN0.0030.0000.003
DESEQ_FN0.0020.0010.002
FQ_FN0.0040.0010.005
PSINORM_FN0.0020.0010.002
PsiNorm0.8820.0080.891
SCRAN_FN1.5500.1181.669
SUM_FN0.0010.0000.001
SconeExperiment-class0.3320.0010.333
TMM_FN0.0030.0000.004
UQ_FN0.0010.0000.001
biplot_color0.0130.0020.015
biplot_interactive0.4560.0090.466
control_genes0.0200.0070.027
estimate_ziber0.0500.0020.052
factor_sample_filter0.0750.0060.082
fast_estimate_ziber0.0410.0020.043
get_bio0.3460.0030.350
get_design0.9490.0040.954
get_negconruv1.2620.0021.265
get_normalized0.2380.0010.239
get_params0.1690.0000.170
get_qc0.1380.0000.138
get_scores0.2130.0010.215
impute_expectation0.0010.0000.001
impute_null000
lm_adjust0.0050.0010.005
make_design0.0020.0000.002
metric_sample_filter0.0080.0010.010
scone0.4560.0210.478
sconeReport0.2170.0220.238
scone_easybake0.2530.0220.274
score_matrix0.0050.0010.007
select_methods0.2690.0220.292
simple_FNR_params0.0490.0050.054