Multiple platform build/check report for BioC 3.14 - CHECK results for scone on tokay2

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo2	Linux (Ubuntu 20.04.4 LTS)	x86_64	4.1.3 (2022-03-10) -- "One Push-Up"	4324
tokay2	Windows Server 2012 R2 Standard	x64	4.1.3 (2022-03-10) -- "One Push-Up"	4077
machv2	macOS 10.14.6 Mojave	x86_64	4.1.3 (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*

Package: scone

Version: 1.18.0

Command: C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:scone.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings scone_1.18.0.tar.gz

StartedAt: 2022-04-13 02:29:52 -0400 (Wed, 13 Apr 2022)

EndedAt: 2022-04-13 02:46:28 -0400 (Wed, 13 Apr 2022)

EllapsedTime: 995.6 seconds

RetCode: 0

Status: OK

CheckDir: scone.Rcheck

Warnings: 0

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:scone.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings scone_1.18.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.14-bioc/meat/scone.Rcheck'
* using R version 4.1.3 (2022-03-10)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* 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 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 ...
** running examples for arch 'i386' ... OK
** running examples for arch 'x64' ... OK
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'testthat.R'
 OK
** running tests for arch 'x64' ...
  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
  'C:/Users/biocbuild/bbs-3.14-bioc/meat/scone.Rcheck/00check.log'
for details.

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.14/bioc/src/contrib/scone_1.18.0.tar.gz && rm -rf scone.buildbin-libdir && mkdir scone.buildbin-libdir && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=scone.buildbin-libdir scone_1.18.0.tar.gz && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL scone_1.18.0.zip && rm scone_1.18.0.tar.gz scone_1.18.0.zip
###
##############################################################################
##############################################################################


  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100  113k  100  113k    0     0   206k      0 --:--:-- --:--:-- --:--:--  206k

install for i386

* installing *source* package 'scone' ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'scone'
    finding HTML links ... done
    CLR_FN                                  html  
    DESEQ_FN                                html  
    FQ_FN                                   html  
    PSINORM_FN                              html  
    PsiNorm                                 html  
    SCRAN_FN                                html  
    SUM_FN                                  html  
    SconeExperiment-class                   html  
    finding level-2 HTML links ... done

    TMM_FN                                  html  
    UQ_FN                                   html  
    biplot_color                            html  
    biplot_interactive                      html  
    control_genes                           html  
    dot-likfn                               html  
    dot-parse_row                           html  
    dot-pzfn                                html  
    estimate_ziber                          html  
    factor_sample_filter                    html  
    fast_estimate_ziber                     html  
    get_bio                                 html  
    get_design                              html  
    get_negconruv                           html  
    get_normalized                          html  
    get_params                              html  
    get_qc                                  html  
    get_scores                              html  
    impute_expectation                      html  
    impute_null                             html  
    lm_adjust                               html  
    make_design                             html  
    metric_sample_filter                    html  
    scone                                   html  
    sconeReport                             html  
    scone_easybake                          html  
    score_matrix                            html  
    select_methods                          html  
    simple_FNR_params                       html  
** 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

install for x64

* installing *source* package 'scone' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'scone' as scone_1.18.0.zip
* DONE (scone)
* installing to library 'C:/Users/biocbuild/bbs-3.14-bioc/R/library'
package 'scone' successfully unpacked and MD5 sums checked


R version 4.1.3 (2022-03-10) -- "One Push-Up"
Copyright (C) 2022 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-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

Attaching package: 'IRanges'

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

    windows

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% (00:00:03)
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% (00:00:33)
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 62 ]
> 
> proc.time()
   user  system elapsed 
  130.4     3.0   283.0 
> 
> > 
>


R version 4.1.3 (2022-03-10) -- "One Push-Up"
Copyright (C) 2022 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (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

Attaching package: 'IRanges'

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

    windows

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% (00:00:03)
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% (00:00:34)
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 62 ]
> 
> proc.time()
   user  system elapsed 
 144.09    1.34  302.90 
> 
> > 
>

name	user	system	elapsed
CLR_FN	0	0	0
DESEQ_FN	0	0	0
FQ_FN	0	0	0
PSINORM_FN	0	0	0
PsiNorm	0.46	0.14	0.59
SCRAN_FN	0.92	0.11	1.03
SUM_FN	0	0	0
SconeExperiment-class	0.22	0.00	0.22
TMM_FN	0	0	0
UQ_FN	0	0	0
biplot_color	0.01	0.00	0.02
biplot_interactive	0.41	0.04	0.43
control_genes	0.00	0.03	0.04
estimate_ziber	0.03	0.00	0.03
factor_sample_filter	0.05	0.00	0.04
fast_estimate_ziber	0.03	0.00	0.03
get_bio	0.08	0.00	0.08
get_design	1.29	0.07	1.38
get_negconruv	0.10	0.00	0.09
get_normalized	0.11	0.00	0.11
get_params	0.08	0.00	0.08
get_qc	0.09	0.00	0.09
get_scores	0.09	0.00	0.10
impute_expectation	0	0	0
impute_null	0	0	0
lm_adjust	0	0	0
make_design	0	0	0
metric_sample_filter	0	0	0
scone	0.22	0.15	0.36
sconeReport	0.15	0.06	0.22
scone_easybake	0.11	0.09	0.20
score_matrix	0	0	0
select_methods	0.16	0.08	0.24
simple_FNR_params	0.03	0.00	0.03

name	user	system	elapsed
CLR_FN	0	0	0
DESEQ_FN	0	0	0
FQ_FN	0	0	0
PSINORM_FN	0	0	0
PsiNorm	0.53	0.00	0.53
SCRAN_FN	1.04	0.08	1.13
SUM_FN	0	0	0
SconeExperiment-class	0.29	0.00	0.30
TMM_FN	0.02	0.00	0.01
UQ_FN	0	0	0
biplot_color	0.01	0.00	0.02
biplot_interactive	0.35	0.00	0.34
control_genes	0.00	0.03	0.03
estimate_ziber	0.04	0.00	0.05
factor_sample_filter	0.05	0.00	0.05
fast_estimate_ziber	0.05	0.00	0.04
get_bio	0.11	0.00	0.11
get_design	0.56	0.03	0.60
get_negconruv	0.11	0.00	0.11
get_normalized	0.14	0.00	0.14
get_params	0.11	0.00	0.11
get_qc	0.12	0.00	0.13
get_scores	0.14	0.01	0.15
impute_expectation	0	0	0
impute_null	0	0	0
lm_adjust	0	0	0
make_design	0	0	0
metric_sample_filter	0	0	0
scone	0.29	0.00	0.30
sconeReport	0.17	0.00	0.17
scone_easybake	0.15	0.02	0.16
score_matrix	0.01	0.00	0.01
select_methods	0.17	0.00	0.18
simple_FNR_params	0.17	0.00	0.17

CHECK results for scone on tokay2

Summary

Command output

Installation output

Tests output

Example timings