Back to Multiple platform build/check report for BioC 3.14
ABCDEFGH[I]JKLMNOPQRSTUVWXYZ

This page was generated on 2022-04-13 12:06:45 -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 iSEE on tokay2


To the developers/maintainers of the iSEE package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/iSEE.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 957/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
iSEE 2.6.0  (landing page)
Kevin Rue-Albrecht
Snapshot Date: 2022-04-12 01:55:07 -0400 (Tue, 12 Apr 2022)
git_url: https://git.bioconductor.org/packages/iSEE
git_branch: RELEASE_3_14
git_last_commit: 9c0e8e0
git_last_commit_date: 2021-10-26 12:42:43 -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: iSEE
Version: 2.6.0
Command: C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:iSEE.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings iSEE_2.6.0.tar.gz
StartedAt: 2022-04-12 21:39:34 -0400 (Tue, 12 Apr 2022)
EndedAt: 2022-04-12 21:51:37 -0400 (Tue, 12 Apr 2022)
EllapsedTime: 723.3 seconds
RetCode: 0
Status:   OK  
CheckDir: iSEE.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:iSEE.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings iSEE_2.6.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.14-bioc/meat/iSEE.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 'iSEE/DESCRIPTION' ... OK
* this is package 'iSEE' version '2.6.0'
* 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' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                            user system elapsed
checkColormapCompatibility 19.55   3.62   24.75
iSEE                       17.01   0.56   18.45
synchronizeAssays          14.99   0.57   16.53
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                            user system elapsed
checkColormapCompatibility 21.44   2.19   25.09
iSEE                       16.61   0.41   17.94
synchronizeAssays          15.23   0.45   16.64
* 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/iSEE.Rcheck/00check.log'
for details.



Installation output

iSEE.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.14/bioc/src/contrib/iSEE_2.6.0.tar.gz && rm -rf iSEE.buildbin-libdir && mkdir iSEE.buildbin-libdir && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=iSEE.buildbin-libdir iSEE_2.6.0.tar.gz && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL iSEE_2.6.0.zip && rm iSEE_2.6.0.tar.gz iSEE_2.6.0.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
  5 4769k    5  243k    0     0   717k      0  0:00:06 --:--:--  0:00:06  716k
 39 4769k   39 1878k    0     0  1401k      0  0:00:03  0:00:01  0:00:02 1401k
 91 4769k   91 4375k    0     0  1893k      0  0:00:02  0:00:02 --:--:-- 1893k
100 4769k  100 4769k    0     0  1943k      0  0:00:02  0:00:02 --:--:-- 1942k

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  
    addCustomLabelsCommands                 html  
    addLabelCentersCommands                 html  
    addMultiSelectionCommands               html  
    addTourStep                             html  
    aes-utils                               html  
    cache-utils                             html  
    checkColormapCompatibility              html  
    class-utils                             html  
    cleanDataset                            html  
    collapseBox                             html  
    conditional-utils                       html  
    createCustomDimnamesModalObservers      html  
    createCustomPanels                      html  
    createLandingPage                       html  
    createProtectedParameterObservers       html  
    defaultTour                             html  
    documentation-generics                  html  
    extractAssaySubmatrix                   html  
    filterDTColumn                          html  
    getEncodedName                          html  
    getPanelColor                           html  
    iSEE-pkg                                html  
    iSEE                                    html  
    iSEEOptions                             html  
    interface-generics                      html  
    interface-wrappers                      html  
    jitterPoints                            html  
    labs-utils                              html  
    lassoPoints                             html  
    manage_commands                         html  
    metadata-plot-generics                  html  
    multi-select-generics                   html  
    multiSelectionToFactor                  html  
    observer-generics                       html  
    output-generics                         html  
    panelDefaults                           html  
    plot-generics                           html  
    plot-utils                              html  
    processMultiSelections                  html  
    registerAppOptions                      html  
    replaceMissingWithFirst                 html  
    requestUpdate                           html  
    retrieveOutput                          html  
    selectionColorMap                       html  
    setCachedCommonInfo                     html  
    setup-generics                          html  
    single-select-generics                  html  
    specific-tours                          html  
    subsetPointsByGrid                      html  
    synchronizeAssays                       html  
    table-generics                          html  
    track-utils                             html  
    validate-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_2.6.0.zip
* DONE (iSEE)
* installing to library 'C:/Users/biocbuild/bbs-3.14-bioc/R/library'
package 'iSEE' successfully unpacked and MD5 sums checked

Tests output

iSEE.Rcheck/tests_i386/testthat.Rout


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.

> library(testthat)
> library(iSEE)
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

Loading required package: SingleCellExperiment
> 
> test_check("iSEE")
Loading required package: scRNAseq
Loading required package: scater
Loading required package: scuttle
Loading required package: ggplot2
snapshotDate(): 2021-10-19
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
Warning in (function (A, nv = 5, nu = nv, maxit = 1000, work = nv + 7, reorth = TRUE,  :
  You're computing too large a percentage of total singular values, use a standard svd instead.
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)
[ FAIL 0 | WARN 4 | SKIP 2 | PASS 1453 ]

== Skipped tests ===============================================================
* empty test (1)
* waiting for a fix to the SCE itself (1)

[ FAIL 0 | WARN 4 | SKIP 2 | PASS 1453 ]
> 
> proc.time()
   user  system elapsed 
  82.51    3.90   91.65 

iSEE.Rcheck/tests_x64/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-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: 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

Loading required package: SingleCellExperiment
> 
> test_check("iSEE")
Loading required package: scRNAseq
Loading required package: scater
Loading required package: scuttle
Loading required package: ggplot2
snapshotDate(): 2021-10-19
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
Warning in (function (A, nv = 5, nu = nv, maxit = 1000, work = nv + 7, reorth = TRUE,  :
  You're computing too large a percentage of total singular values, use a standard svd instead.
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)
[ FAIL 0 | WARN 4 | SKIP 2 | PASS 1453 ]

== Skipped tests ===============================================================
* empty test (1)
* waiting for a fix to the SCE itself (1)

[ FAIL 0 | WARN 4 | SKIP 2 | PASS 1453 ]
> 
> proc.time()
   user  system elapsed 
  94.25    2.96   99.07 

Example timings

iSEE.Rcheck/examples_i386/iSEE-Ex.timings

nameusersystemelapsed
ColumnDataPlot-class3.200.193.39
ColumnDataTable-class0.880.000.87
ComplexHeatmapPlot-class1.250.001.25
ExperimentColorMap-class0.030.000.03
FeatureAssayPlot-class1.130.011.14
ReducedDimensionPlot-class1.470.031.50
RowDataPlot-class1.470.051.52
RowDataTable-class0.70.00.7
SampleAssayPlot-class1.250.001.25
aes-utils000
cache-utils0.050.000.05
checkColormapCompatibility19.55 3.6224.75
class-utils0.010.000.02
cleanDataset0.250.000.25
collapseBox0.050.000.04
createCustomPanels0.140.020.16
createLandingPage0.250.000.25
defaultTour000
filterDTColumn000
getPanelColor0.390.020.41
iSEE17.01 0.5618.45
iSEEOptions000
jitterPoints0.060.000.06
labs-utils000
lassoPoints0.020.000.02
manage_commands000
multiSelectionToFactor000
panelDefaults000
plot-utils0.010.000.01
registerAppOptions000
selectionColorMap0.020.000.02
setCachedCommonInfo0.010.000.01
subsetPointsByGrid0.550.010.57
synchronizeAssays14.99 0.5716.53

iSEE.Rcheck/examples_x64/iSEE-Ex.timings

nameusersystemelapsed
ColumnDataPlot-class3.590.113.70
ColumnDataTable-class0.780.020.80
ComplexHeatmapPlot-class1.220.101.31
ExperimentColorMap-class0.020.000.02
FeatureAssayPlot-class1.300.011.31
ReducedDimensionPlot-class2.140.022.16
RowDataPlot-class1.120.031.16
RowDataTable-class0.970.000.96
SampleAssayPlot-class1.780.011.80
aes-utils000
cache-utils0.050.000.05
checkColormapCompatibility21.44 2.1925.09
class-utils0.010.000.02
cleanDataset0.280.000.28
collapseBox0.050.000.04
createCustomPanels0.110.020.13
createLandingPage0.200.010.22
defaultTour0.020.000.01
filterDTColumn000
getPanelColor0.470.000.47
iSEE16.61 0.4117.94
iSEEOptions000
jitterPoints0.070.000.08
labs-utils000
lassoPoints0.020.000.06
manage_commands000
multiSelectionToFactor000
panelDefaults000
plot-utils0.030.000.03
registerAppOptions0.020.000.02
selectionColorMap000
setCachedCommonInfo0.010.000.01
subsetPointsByGrid0.800.030.83
synchronizeAssays15.23 0.4516.64