Multiple platform build/check report for BioC 3.11 - CHECK report for HCAExplorer on tokay2

Package: HCAExplorer

Version: 1.2.0

Command: C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:HCAExplorer.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings HCAExplorer_1.2.0.tar.gz

StartedAt: 2020-10-17 04:52:12 -0400 (Sat, 17 Oct 2020)

EndedAt: 2020-10-17 04:57:30 -0400 (Sat, 17 Oct 2020)

EllapsedTime: 318.0 seconds

RetCode: 0

Status: WARNINGS

CheckDir: HCAExplorer.Rcheck

Warnings: 1

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### Running command:
###
###   C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:HCAExplorer.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings HCAExplorer_1.2.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.11-bioc/meat/HCAExplorer.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 'HCAExplorer/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'HCAExplorer' 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 'HCAExplorer' 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: 'utils:::format.object_size'
  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 ... NOTE
.getManifest: no visible binding for global variable 'projectId'
.getManifestFileFormats: no visible binding for global variable
  'projectId'
.subset.HCAExplorer: no visible binding for global variable 'projectId'
[,HCAExplorer: no visible binding for global variable 'projectId'
getManifest,HCAExplorer: no visible binding for global variable
  'projectId'
getManifestFileFormats,HCAExplorer: no visible binding for global
  variable 'projectId'
Undefined global functions or variables:
  projectId
* 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 ... WARNING
Documented arguments not in \usage in documentation object 'values,HCAExplorer-method':
  '...'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
* 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
getManifest          11.75   0.18   39.58
filter.HCAExplorer    0.55   0.00    6.25
activate.HCAExplorer  0.53   0.01    9.31
resetQuery            0.53   0.00    6.29
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                     user system elapsed
getManifest          8.31   0.16   35.54
activate.HCAExplorer 0.58   0.00    9.33
filter.HCAExplorer   0.47   0.00    5.91
resetQuery           0.42   0.00    6.04
* 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 WARNING, 2 NOTEs
See
  'C:/Users/biocbuild/bbs-3.11-bioc/meat/HCAExplorer.Rcheck/00check.log'
for details.

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.11/bioc/src/contrib/HCAExplorer_1.2.0.tar.gz && rm -rf HCAExplorer.buildbin-libdir && mkdir HCAExplorer.buildbin-libdir && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=HCAExplorer.buildbin-libdir HCAExplorer_1.2.0.tar.gz && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL HCAExplorer_1.2.0.zip && rm HCAExplorer_1.2.0.tar.gz HCAExplorer_1.2.0.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 16172  100 16172    0     0   290k      0 --:--:-- --:--:-- --:--:--  336k

install for i386

* installing *source* package 'HCAExplorer' ...
** using staged installation
** R
** byte-compile and prepare package for lazy loading
Creating a generic function for 'fields' from package 'vctrs' in package 'HCAExplorer'
** help
*** installing help indices
  converting help for package 'HCAExplorer'
    finding HTML links ... done
    HCAExplorer-class                       html  
    HCAExplorer                             html  
    ProjectView-class                       html  
    activate.HCAExplorer                    html  
    fields-HCAExplorer-method               html  
    finding level-2 HTML links ... done

    filter.HCAExplorer                      html  
    getManifest                             html  
    getManifestFileFormats                  html  
    nextResults                             html  
    reexports                               html  
    resetQuery                              html  
    resetSelect                             html  
    results                                 html  
    select.HCAExplorer                      html  
    show-HCAExplorer-method                 html  
    sub-HCAExplorer-method                  html  
    undoQuery                               html  
    values-HCAExplorer-method               html  
    viewProjects                            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 'HCAExplorer' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'HCAExplorer' as HCAExplorer_1.2.0.zip
* DONE (HCAExplorer)
* installing to library 'C:/Users/biocbuild/bbs-3.11-bioc/R/library'
package 'HCAExplorer' successfully unpacked and MD5 sums checked


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(HCAExplorer)
Loading required package: dplyr

Attaching package: 'dplyr'

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

    matches

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

    filter, lag

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

    intersect, setdiff, setequal, union

> 
> test_check("HCAExplorer")
== testthat results  ===========================================================
[ OK: 1 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
   2.85    0.14    3.00


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(HCAExplorer)
Loading required package: dplyr

Attaching package: 'dplyr'

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

    matches

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

    filter, lag

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

    intersect, setdiff, setequal, union

> 
> test_check("HCAExplorer")
== testthat results  ===========================================================
[ OK: 1 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
   2.95    0.32    3.26

name	user	system	elapsed
HCAExplorer	0.35	0.03	2.53
activate.HCAExplorer	0.53	0.01	9.31
fields-HCAExplorer-method	0.11	0.00	2.22
filter.HCAExplorer	0.55	0.00	6.25
getManifest	11.75	0.18	39.58
getManifestFileFormats	0.28	0.02	3.25
nextResults	0.23	0.00	2.95
resetQuery	0.53	0.00	6.29
resetSelect	0.34	0.00	4.70
results	0.17	0.02	2.31
select.HCAExplorer	0.35	0.00	4.78
show-HCAExplorer-method	0.17	0.00	2.33
sub-HCAExplorer-method	0.23	0.00	2.83
undoQuery	0.41	0.00	4.89
values-HCAExplorer-method	0.11	0.00	2.28
viewProjects	0.47	0.01	4.88

name	user	system	elapsed
HCAExplorer	0.35	0.01	2.54
activate.HCAExplorer	0.58	0.00	9.33
fields-HCAExplorer-method	0.06	0.00	2.17
filter.HCAExplorer	0.47	0.00	5.91
getManifest	8.31	0.16	35.54
getManifestFileFormats	0.29	0.01	3.24
nextResults	0.26	0.00	2.83
resetQuery	0.42	0.00	6.04
resetSelect	0.28	0.00	4.58
results	0.19	0.00	2.33
select.HCAExplorer	0.35	0.00	4.67
show-HCAExplorer-method	0.14	0.00	2.38
sub-HCAExplorer-method	0.25	0.00	2.81
undoQuery	0.34	0.00	4.86
values-HCAExplorer-method	0.14	0.00	2.29
viewProjects	0.48	0.02	4.49

CHECK report for HCAExplorer on tokay2

Summary

Command output

Installation output

Tests output

Example timings