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CHECK report for iSEE on tokay2

This page was generated on 2020-10-17 11:56:54 -0400 (Sat, 17 Oct 2020).

TO THE DEVELOPERS/MAINTAINERS OF THE iSEE PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 895/1905HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
iSEE 2.0.0
Charlotte Soneson
Snapshot Date: 2020-10-16 14:40:19 -0400 (Fri, 16 Oct 2020)
URL: https://git.bioconductor.org/packages/iSEE
Branch: RELEASE_3_11
Last Commit: 0d82c2a
Last Changed Date: 2020-04-27 15:14:42 -0400 (Mon, 27 Apr 2020)
malbec2 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK  WARNINGS 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
machv2 macOS 10.14.6 Mojave / x86_64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository

Summary

Package: iSEE
Version: 2.0.0
Command: C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:iSEE.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings iSEE_2.0.0.tar.gz
StartedAt: 2020-10-17 05:18:40 -0400 (Sat, 17 Oct 2020)
EndedAt: 2020-10-17 05:30:38 -0400 (Sat, 17 Oct 2020)
EllapsedTime: 718.3 seconds
RetCode: 0
Status:  WARNINGS  
CheckDir: iSEE.Rcheck
Warnings: 2

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:iSEE.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings iSEE_2.0.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.11-bioc/meat/iSEE.Rcheck'
* using R version 4.0.3 (2020-10-10)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'iSEE/DESCRIPTION' ... OK
* this is package 'iSEE' version '2.0.0'
* 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 '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
* 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 ... 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 ...
** running examples for arch 'i386' ... WARNING
Found the following significant warnings:

  Warning: 'redDimPlotDefaults' is deprecated.
  Warning: 'featAssayPlotDefaults' is deprecated.
  Warning: 'colDataPlotDefaults' is deprecated.
  Warning: 'rowStatTableDefaults' is deprecated.
  Warning: 'colStatTableDefaults' is deprecated.
  Warning: 'rowDataPlotDefaults' is deprecated.
  Warning: 'sampAssayPlotDefaults' is deprecated.
  Warning: 'heatMapPlotDefaults' is deprecated.
Deprecated functions may be defunct as soon as of the next release of
R.
See ?Deprecated.
Examples with CPU (user + system) or elapsed time > 5s
                            user system elapsed
checkColormapCompatibility 12.00   1.78   14.46
iSEE                       13.06   0.69   14.11
synchronizeAssays          11.94   0.59   12.95
** running examples for arch 'x64' ... WARNING
Found the following significant warnings:

  Warning: 'redDimPlotDefaults' is deprecated.
  Warning: 'featAssayPlotDefaults' is deprecated.
  Warning: 'colDataPlotDefaults' is deprecated.
  Warning: 'rowStatTableDefaults' is deprecated.
  Warning: 'colStatTableDefaults' is deprecated.
  Warning: 'rowDataPlotDefaults' is deprecated.
  Warning: 'sampAssayPlotDefaults' is deprecated.
  Warning: 'heatMapPlotDefaults' is deprecated.
Deprecated functions may be defunct as soon as of the next release of
R.
See ?Deprecated.
Examples with CPU (user + system) or elapsed time > 5s
                            user system elapsed
iSEE                       16.98   0.81   18.18
synchronizeAssays          13.71   0.75   14.90
checkColormapCompatibility 12.11   1.47   14.14
* 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: 2 WARNINGs, 1 NOTE
See
  'C:/Users/biocbuild/bbs-3.11-bioc/meat/iSEE.Rcheck/00check.log'
for details.



Installation output

iSEE.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.11/bioc/src/contrib/iSEE_2.0.0.tar.gz && rm -rf iSEE.buildbin-libdir && mkdir iSEE.buildbin-libdir && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=iSEE.buildbin-libdir iSEE_2.0.0.tar.gz && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL iSEE_2.0.0.zip && rm iSEE_2.0.0.tar.gz iSEE_2.0.0.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
  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100 2489k  100 2489k    0     0  6881k      0 --:--:-- --:--:-- --:--:-- 6991k

install for i386

* installing *source* package 'iSEE' ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'iSEE'
    finding HTML links ... done
    ColumnDataPlot-class                    html  
    finding level-2 HTML links ... done

    ColumnDataTable-class                   html  
    ColumnDotPlot-class                     html  
    ColumnTable-class                       html  
    ComplexHeatmapPlot-class                html  
    DotPlot-class                           html  
    ExperimentColorMap-class                html  
    FeatureAssayPlot-class                  html  
    Panel-class                             html  
    ReducedDimensionPlot-class              html  
    RowDataPlot-class                       html  
    RowDataTable-class                      html  
    RowDotPlot-class                        html  
    RowTable-class                          html  
    SampleAssayPlot-class                   html  
    Table-class                             html  
    addMultiSelectionCommands               html  
    aes-utils                               html  
    checkColormapCompatibility              html  
    class-utils                             html  
    collapseBox                             html  
    createCustomPanels                      html  
    createLandingPage                       html  
    createProtectedParameterObservers       html  
    dataframe-utils                         html  
    defaults                                html  
    filterDTColumn                          html  
    getEncodedName                          html  
    getPanelColor                           html  
    iSEE-pkg                                html  
    iSEE                                    html  
    iSEEOptions                             html  
    interface-generics                      html  
    jitterPoints                            html  
    labs-utils                              html  
    lassoPoints                             html  
    manage_commands                         html  
    metadata-plot-generics                  html  
    multi-select-generics                   html  
    observer-generics                       html  
    output-generics                         html  
    plot-generics                           html  
    plot-utils                              html  
    processMultiSelections                  html  
    retrieveOutput                          html  
    setCachedCommonInfo                     html  
    setup-generics                          html  
    single-select-generics                  html  
    subsetPointsByGrid                      html  
    synchronizeAssays                       html  
    table-generics                          html  
    track-utils                             html  
    visual-parameters-generics              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 'iSEE' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'iSEE' as iSEE_2.0.0.zip
* DONE (iSEE)
* installing to library 'C:/Users/biocbuild/bbs-3.11-bioc/R/library'
package 'iSEE' successfully unpacked and MD5 sums checked

Tests output

iSEE.Rcheck/tests_i386/testthat.Rout


R version 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out"
Copyright (C) 2020 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.

> 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

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")'.

Loading required package: DelayedArray
Loading required package: matrixStats

Attaching package: 'matrixStats'

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

    anyMissing, rowMedians


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(): 2020-04-27
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: 1094 | SKIPPED: 4 | WARNINGS: 28 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
  91.64    4.46   96.71 

iSEE.Rcheck/tests_x64/testthat.Rout


R version 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out"
Copyright (C) 2020 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.

> 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

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")'.

Loading required package: DelayedArray
Loading required package: matrixStats

Attaching package: 'matrixStats'

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

    anyMissing, rowMedians


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(): 2020-04-27
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: 1094 | SKIPPED: 4 | WARNINGS: 28 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
  91.73    2.64   96.00 

Example timings

iSEE.Rcheck/examples_i386/iSEE-Ex.timings

nameusersystemelapsed
ColumnDataPlot-class1.830.071.89
ColumnDataTable-class0.330.000.32
ComplexHeatmapPlot-class1.340.011.36
ExperimentColorMap-class0.030.000.03
FeatureAssayPlot-class0.780.000.78
ReducedDimensionPlot-class1.760.081.84
RowDataPlot-class0.770.010.78
RowDataTable-class0.500.020.52
SampleAssayPlot-class0.480.030.51
aes-utils000
checkColormapCompatibility12.00 1.7814.46
class-utils0.020.000.01
collapseBox0.010.000.02
createCustomPanels0.050.000.05
createLandingPage0.090.000.09
dataframe-utils0.050.000.05
defaults1.420.001.47
filterDTColumn000
getPanelColor0.020.000.02
iSEE13.06 0.6914.11
iSEEOptions000
jitterPoints0.080.000.07
labs-utils000
lassoPoints000
manage_commands000
plot-utils0.010.000.01
setCachedCommonInfo000
subsetPointsByGrid0.560.000.57
synchronizeAssays11.94 0.5912.95

iSEE.Rcheck/examples_x64/iSEE-Ex.timings

nameusersystemelapsed
ColumnDataPlot-class3.030.033.06
ColumnDataTable-class0.580.020.59
ComplexHeatmapPlot-class0.870.040.92
ExperimentColorMap-class0.030.000.03
FeatureAssayPlot-class1.640.031.67
ReducedDimensionPlot-class0.920.020.94
RowDataPlot-class0.700.030.73
RowDataTable-class0.540.000.53
SampleAssayPlot-class0.810.030.85
aes-utils000
checkColormapCompatibility12.11 1.4714.14
class-utils000
collapseBox0.030.000.03
createCustomPanels0.060.000.06
createLandingPage0.130.000.13
dataframe-utils0.040.000.04
defaults2.140.002.18
filterDTColumn000
getPanelColor0.020.000.02
iSEE16.98 0.8118.18
iSEEOptions000
jitterPoints0.120.000.13
labs-utils000
lassoPoints0.000.000.01
manage_commands000
plot-utils0.020.000.02
setCachedCommonInfo0.020.000.02
subsetPointsByGrid101
synchronizeAssays13.71 0.7514.90