Back to Multiple platform build/check report for BioC 3.14
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This page was generated on 2021-10-20 12:05:25 -0400 (Wed, 20 Oct 2021).

CHECK results for scone on riesling1

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? here 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 1724/2072HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
scone 1.17.2  (landing page)
Davide Risso
Snapshot Date: 2021-10-19 14:50:04 -0400 (Tue, 19 Oct 2021)
git_url: https://git.bioconductor.org/packages/scone
git_branch: master
git_last_commit: 21cbec3
git_last_commit_date: 2021-09-16 05:00:34 -0400 (Thu, 16 Sep 2021)
nebbiolo2Linux (Ubuntu 20.04.2 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
riesling1Windows Server 2019 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    NA  

Summary

Package: scone
Version: 1.17.2
Command: D:\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:scone.install-out.txt --library=D:\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings scone_1.17.2.tar.gz
StartedAt: 2021-10-20 03:39:17 -0400 (Wed, 20 Oct 2021)
EndedAt: 2021-10-20 03:52:02 -0400 (Wed, 20 Oct 2021)
EllapsedTime: 765.4 seconds
RetCode: 0
Status:   OK  
CheckDir: scone.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   D:\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:scone.install-out.txt --library=D:\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings scone_1.17.2.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'D:/biocbuild/bbs-3.14-bioc/meat/scone.Rcheck'
* using R version 4.1.1 (2021-08-10)
* 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 '1.17.2'
* 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 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
  'D:/biocbuild/bbs-3.14-bioc/meat/scone.Rcheck/00check.log'
for details.



Installation output

scone.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.14/bioc/src/contrib/scone_1.17.2.tar.gz && rm -rf scone.buildbin-libdir && mkdir scone.buildbin-libdir && D:\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=scone.buildbin-libdir scone_1.17.2.tar.gz && D:\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL scone_1.17.2.zip && rm scone_1.17.2.tar.gz scone_1.17.2.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
 81  113k   81 94527    0     0   491k      0 --:--:-- --:--:-- --:--:--  488k
100  113k  100  113k    0     0   599k      0 --:--:-- --:--:-- --:--:--  599k

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_1.17.2.zip
* DONE (scone)
* installing to library 'D:/biocbuild/bbs-3.14-bioc/R/library'
package 'scone' successfully unpacked and MD5 sums checked

Tests output

scone.Rcheck/tests_i386/testthat.Rout


R version 4.1.1 (2021-08-10) -- "Kick Things"
Copyright (C) 2021 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% (00:00:03)
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% (00:00:02)
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% (00:00:01)
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% (00:00:21)
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 
  86.48    1.18  143.65 
> 
> > 
> 

scone.Rcheck/tests_x64/testthat.Rout


R version 4.1.1 (2021-08-10) -- "Kick Things"
Copyright (C) 2021 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% (00:00:04)
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% (00:00:02)
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% (00:00:26)
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 
 102.34    1.21  163.14 
> 
> > 
> 

Example timings

scone.Rcheck/examples_i386/scone-Ex.timings

nameusersystemelapsed
CLR_FN000
DESEQ_FN000
FQ_FN000
PSINORM_FN000
PsiNorm0.360.060.42
SCRAN_FN0.890.141.03
SUM_FN000
SconeExperiment-class0.170.000.17
TMM_FN000
UQ_FN000
biplot_color0.020.000.02
biplot_interactive0.20.00.2
control_genes0.030.020.05
estimate_ziber0.140.000.14
factor_sample_filter0.040.000.03
fast_estimate_ziber0.010.000.01
get_bio0.060.000.07
get_design0.330.000.32
get_negconruv0.740.000.74
get_normalized0.070.000.08
get_params0.050.000.04
get_qc0.060.000.07
get_scores0.080.000.07
impute_expectation000
impute_null000
lm_adjust000
make_design000
metric_sample_filter000
scone0.160.000.16
sconeReport0.080.000.08
scone_easybake0.070.010.09
score_matrix000
select_methods0.110.000.11
simple_FNR_params0.020.000.02

scone.Rcheck/examples_x64/scone-Ex.timings

nameusersystemelapsed
CLR_FN000
DESEQ_FN000
FQ_FN000
PSINORM_FN000
PsiNorm1.010.001.02
SCRAN_FN0.660.080.73
SUM_FN000
SconeExperiment-class0.150.000.16
TMM_FN000
UQ_FN000
biplot_color0.020.000.01
biplot_interactive0.250.000.25
control_genes0.000.030.04
estimate_ziber0.030.000.03
factor_sample_filter0.030.000.03
fast_estimate_ziber0.030.000.03
get_bio0.070.000.06
get_design0.340.000.35
get_negconruv0.080.000.07
get_normalized0.090.020.11
get_params0.050.010.07
get_qc0.060.030.09
get_scores0.070.000.08
impute_expectation000
impute_null000
lm_adjust000
make_design000
metric_sample_filter000
scone0.180.000.17
sconeReport0.090.000.10
scone_easybake0.080.000.08
score_matrix000
select_methods0.110.000.11
simple_FNR_params0.010.000.01