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CHECK report for CellBench on tokay1

This page was generated on 2020-04-15 12:31:55 -0400 (Wed, 15 Apr 2020).

Package 240/1823HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
CellBench 1.2.0
Shian Su
Snapshot Date: 2020-04-14 16:46:13 -0400 (Tue, 14 Apr 2020)
URL: https://git.bioconductor.org/packages/CellBench
Branch: RELEASE_3_10
Last Commit: c725e05
Last Changed Date: 2019-10-29 13:11:30 -0400 (Tue, 29 Oct 2019)
malbec1 Linux (Ubuntu 18.04.4 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: CellBench
Version: 1.2.0
Command: C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:CellBench.install-out.txt --library=C:\Users\biocbuild\bbs-3.10-bioc\R\library --no-vignettes --timings CellBench_1.2.0.tar.gz
StartedAt: 2020-04-15 01:54:32 -0400 (Wed, 15 Apr 2020)
EndedAt: 2020-04-15 02:01:02 -0400 (Wed, 15 Apr 2020)
EllapsedTime: 389.2 seconds
RetCode: 0
Status:  OK  
CheckDir: CellBench.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:CellBench.install-out.txt --library=C:\Users\biocbuild\bbs-3.10-bioc\R\library --no-vignettes --timings CellBench_1.2.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.10-bioc/meat/CellBench.Rcheck'
* using R version 3.6.3 (2020-02-29)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'CellBench/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'CellBench' version '1.2.0'
* 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 'CellBench' 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
cellbench_case_study: no visible global function definition for
  'browseURL'
Undefined global functions or variables:
  browseURL
Consider adding
  importFrom("utils", "browseURL")
to your NAMESPACE file.
* 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-3.10-bioc/meat/CellBench.Rcheck/00check.log'
for details.



Installation output

CellBench.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.10/bioc/src/contrib/CellBench_1.2.0.tar.gz && rm -rf CellBench.buildbin-libdir && mkdir CellBench.buildbin-libdir && C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=CellBench.buildbin-libdir CellBench_1.2.0.tar.gz && C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD INSTALL CellBench_1.2.0.zip && rm CellBench_1.2.0.tar.gz CellBench_1.2.0.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 2122k    5  112k    0     0   336k      0  0:00:06 --:--:--  0:00:06  339k
100 2122k  100 2122k    0     0  4574k      0 --:--:-- --:--:-- --:--:-- 4603k

install for i386

* installing *source* package 'CellBench' ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'CellBench'
    finding HTML links ... done
    CellBench-package                       html  
    all_unique                              html  
    any_task_errors                         html  
    apply_methods                           html  
    arrow_sep                               html  
    as_pipeline_list                        html  
    cache_method                            html  
    cellbench_case_study                    html  
    cellbench_file                          html  
    check_class                             html  
    clear_cached_datasets                   html  
    clear_cellbench_cache                   html  
    data_list                               html  
    filter_zero_genes                       html  
    fn_arg_seq                              html  
    fn_list                                 html  
    is.task_error                           html  
    keep_high_count_cells                   html  
    keep_high_count_genes                   html  
    keep_high_var_genes                     html  
    load_all_data                           html  
    mhead                                   html  
    pipeline_collapse                       html  
    print.fn_arg_seq                        html  
    print.task_error                        html  
    sample_cells                            html  
    sample_genes                            html  
    sample_sce_data                         html  
    set_cellbench_bpparam                   html  
    set_cellbench_cache_path                html  
    set_cellbench_threads                   html  
    strip_timing                            html  
    summary.benchmark_tbl                   html  
    time_methods                            html  
    unpack_timing                           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 'CellBench' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'CellBench' as CellBench_1.2.0.zip
* DONE (CellBench)
* installing to library 'C:/Users/biocbuild/bbs-3.10-bioc/R/library'
package 'CellBench' successfully unpacked and MD5 sums checked

Tests output

CellBench.Rcheck/tests_i386/testthat.Rout


R version 3.6.3 (2020-02-29) -- "Holding the Windsock"
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(CellBench)
Loading required package: SingleCellExperiment
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

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, rowsum

Loading required package: magrittr

Attaching package: 'magrittr'

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

    equals, is_less_than, not

Loading required package: tibble
> 
> test_check("CellBench")
== testthat results  ===========================================================
[ OK: 101 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
  13.46    0.85   53.81 

CellBench.Rcheck/tests_x64/testthat.Rout


R version 3.6.3 (2020-02-29) -- "Holding the Windsock"
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(CellBench)
Loading required package: SingleCellExperiment
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

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, rowsum

Loading required package: magrittr

Attaching package: 'magrittr'

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

    equals, is_less_than, not

Loading required package: tibble
> 
> test_check("CellBench")
== testthat results  ===========================================================
[ OK: 101 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
  15.79    0.43   60.86 

Example timings

CellBench.Rcheck/examples_i386/CellBench-Ex.timings

nameusersystemelapsed
all_unique000
apply_methods0.060.030.09
arrow_sep0.020.000.02
as_pipeline_list0.060.000.06
cache_method000
cellbench_case_study000
cellbench_file000
check_class000
clear_cached_datasets000
clear_cellbench_cache000
data_list0.000.020.01
filter_zero_genes000
fn_arg_seq0.040.000.03
fn_list000
keep_high_count_cells0.320.010.35
keep_high_count_genes0.270.000.26
keep_high_var_genes0.120.020.14
load_all_data000
mhead000
pipeline_collapse0.080.000.08
print.fn_arg_seq000
sample_cells0.080.000.13
sample_genes0.110.000.34
set_cellbench_bpparam000
set_cellbench_cache_path000
set_cellbench_threads000
strip_timing000
summary.benchmark_tbl0.010.000.01
time_methods4.140.204.34
unpack_timing000

CellBench.Rcheck/examples_x64/CellBench-Ex.timings

nameusersystemelapsed
all_unique000
apply_methods0.090.000.09
arrow_sep000
as_pipeline_list0.050.010.07
cache_method000
cellbench_case_study000
cellbench_file000
check_class000
clear_cached_datasets000
clear_cellbench_cache000
data_list0.000.020.02
filter_zero_genes000
fn_arg_seq0.030.000.03
fn_list000
keep_high_count_cells0.30.00.3
keep_high_count_genes0.220.050.26
keep_high_var_genes0.20.00.2
load_all_data000
mhead000
pipeline_collapse0.070.000.07
print.fn_arg_seq0.010.000.01
sample_cells0.050.000.05
sample_genes0.110.000.11
set_cellbench_bpparam000
set_cellbench_cache_path000
set_cellbench_threads000
strip_timing000
summary.benchmark_tbl0.030.000.03
time_methods3.440.153.59
unpack_timing000