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CHECK report for iSEE on tokay1

This page was generated on 2019-04-13 11:29:00 -0400 (Sat, 13 Apr 2019).

Package 795/1649HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
iSEE 1.2.4
Charlotte Soneson
Snapshot Date: 2019-04-12 17:01:30 -0400 (Fri, 12 Apr 2019)
URL: https://git.bioconductor.org/packages/iSEE
Branch: RELEASE_3_8
Last Commit: a4018ef
Last Changed Date: 2019-04-09 18:43:33 -0400 (Tue, 09 Apr 2019)
malbec1 Linux (Ubuntu 16.04.6 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository
merida1 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: iSEE
Version: 1.2.4
Command: C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:iSEE.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings iSEE_1.2.4.tar.gz
StartedAt: 2019-04-13 03:15:54 -0400 (Sat, 13 Apr 2019)
EndedAt: 2019-04-13 03:24:34 -0400 (Sat, 13 Apr 2019)
EllapsedTime: 519.6 seconds
RetCode: 0
Status:  OK  
CheckDir: iSEE.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:iSEE.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings iSEE_1.2.4.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.8-bioc/meat/iSEE.Rcheck'
* using R version 3.5.3 (2019-03-11)
* 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 '1.2.4'
* checking package namespace information ... OK
* checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
  cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
 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 or elapsed time > 5s
                   user system elapsed
iSEE              12.29   0.95   13.32
annotateEnsembl    8.32   0.24    8.57
synchronizeAssays  8.08   0.41    8.48
modeGating         7.14   0.80    7.94
annotateEntrez     6.19   0.25    6.44
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                   user system elapsed
iSEE              12.03   1.11   13.20
synchronizeAssays  6.79   0.67    7.45
annotateEnsembl    7.09   0.19    7.28
modeGating         5.81   0.77    6.57
annotateEntrez     4.92   0.31    5.24
* 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-3.8-bioc/meat/iSEE.Rcheck/00check.log'
for details.



Installation output

iSEE.Rcheck/00install.out

##############################################################################
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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.8/bioc/src/contrib/iSEE_1.2.4.tar.gz && rm -rf iSEE.buildbin-libdir && mkdir iSEE.buildbin-libdir && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=iSEE.buildbin-libdir iSEE_1.2.4.tar.gz && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL iSEE_1.2.4.zip && rm iSEE_1.2.4.tar.gz iSEE_1.2.4.zip
###
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  % 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  172k  100  172k    0     0  4096k      0 --:--:-- --:--:-- --:--:-- 4549k

install for i386

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

    annotateEntrez                          html  
    availablePanelTypes                     html  
    colDataPlotDefaults                     html  
    colStatTableDefaults                    html  
    customDataPlotDefaults                  html  
    customStatTableDefaults                 html  
    featAssayPlotDefaults                   html  
    heatMapPlotDefaults                     html  
    iSEE-pkg                                html  
    iSEE                                    html  
    isColorMapCompatible                    html  
    jitterPoints                            html  
    lassoPoints                             html  
    modeGating                              html  
    pointDefaults                           html  
    redDimPlotDefaults                      html  
    rowDataPlotDefaults                     html  
    rowStatTableDefaults                    html  
    sampAssayPlotDefaults                   html  
    selectDefaults                          html  
    subsetPointsByGrid                      html  
    synchronizeAssays                       html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL

install for x64

* installing *source* package 'iSEE' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'iSEE' as iSEE_1.2.4.zip
* DONE (iSEE)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.8-bioc/R/library'
package 'iSEE' successfully unpacked and MD5 sums checked
In R CMD INSTALL

Tests output

iSEE.Rcheck/tests_i386/testthat.Rout


R version 3.5.3 (2019-03-11) -- "Great Truth"
Copyright (C) 2019 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, colMeans, colSums, colnames,
    dirname, do.call, duplicated, eval, evalq, get, grep, grepl,
    intersect, is.unsorted, lapply, lengths, mapply, match, mget,
    order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind,
    rowMeans, rowSums, 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

Loading required package: BiocParallel

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

Loading required package: SingleCellExperiment
> 
> test_check("iSEE")
Loading required package: scRNAseq
Loading required package: scater
Loading required package: ggplot2

Attaching package: 'scater'

The following object is masked from 'package:S4Vectors':

    rename

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

    filter

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: 1070 SKIPPED: 3 FAILED: 0
Warning message:
In .local(object, ...) : using library sizes as size factors
> 
> proc.time()
   user  system elapsed 
  73.10    5.48   78.79 

iSEE.Rcheck/tests_x64/testthat.Rout


R version 3.5.3 (2019-03-11) -- "Great Truth"
Copyright (C) 2019 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, colMeans, colSums, colnames,
    dirname, do.call, duplicated, eval, evalq, get, grep, grepl,
    intersect, is.unsorted, lapply, lengths, mapply, match, mget,
    order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind,
    rowMeans, rowSums, 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

Loading required package: BiocParallel

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

Loading required package: SingleCellExperiment
> 
> test_check("iSEE")
Loading required package: scRNAseq
Loading required package: scater
Loading required package: ggplot2

Attaching package: 'scater'

The following object is masked from 'package:S4Vectors':

    rename

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

    filter

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: 1070 SKIPPED: 3 FAILED: 0
Warning message:
In .local(object, ...) : using library sizes as size factors
> 
> proc.time()
   user  system elapsed 
  72.75    4.54   77.37 

Example timings

iSEE.Rcheck/examples_i386/iSEE-Ex.timings

nameusersystemelapsed
ExperimentColorMap-class0.050.010.06
annotateEnsembl8.320.248.57
annotateEntrez6.190.256.44
availablePanelTypes000
colDataPlotDefaults0.330.040.41
colStatTableDefaults0.090.000.09
customDataPlotDefaults0.110.000.11
customStatTableDefaults0.110.020.12
featAssayPlotDefaults0.220.000.22
heatMapPlotDefaults0.140.000.14
iSEE12.29 0.9513.32
isColorMapCompatible4.890.115.00
jitterPoints0.080.000.07
lassoPoints000
modeGating7.140.807.94
pointDefaults0.330.000.33
redDimPlotDefaults0.20.00.2
rowDataPlotDefaults0.220.000.22
rowStatTableDefaults0.110.000.11
sampAssayPlotDefaults0.20.00.2
selectDefaults0.240.000.23
subsetPointsByGrid0.170.000.18
synchronizeAssays8.080.418.48

iSEE.Rcheck/examples_x64/iSEE-Ex.timings

nameusersystemelapsed
ExperimentColorMap-class0.070.000.08
annotateEnsembl7.090.197.28
annotateEntrez4.920.315.24
availablePanelTypes000
colDataPlotDefaults0.830.050.87
colStatTableDefaults0.110.000.11
customDataPlotDefaults0.110.000.11
customStatTableDefaults0.120.000.13
featAssayPlotDefaults0.240.000.23
heatMapPlotDefaults0.150.000.16
iSEE12.03 1.1113.20
isColorMapCompatible3.490.163.64
jitterPoints0.080.010.10
lassoPoints000
modeGating5.810.776.57
pointDefaults0.360.000.36
redDimPlotDefaults0.220.000.22
rowDataPlotDefaults0.220.000.22
rowStatTableDefaults0.090.010.11
sampAssayPlotDefaults0.230.000.23
selectDefaults0.220.000.22
subsetPointsByGrid0.110.020.13
synchronizeAssays6.790.677.45