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CHECK report for BrainStars on riesling1

This page was generated on 2020-10-21 12:13:53 -0400 (Wed, 21 Oct 2020).

TO THE DEVELOPERS/MAINTAINERS OF THE BrainStars PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 198/1939HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
BrainStars 1.33.0
Itoshi NIKAIDO
Snapshot Date: 2020-10-20 14:40:34 -0400 (Tue, 20 Oct 2020)
URL: https://git.bioconductor.org/packages/BrainStars
Branch: master
Last Commit: e0111ee
Last Changed Date: 2020-04-27 14:29:00 -0400 (Mon, 27 Apr 2020)
malbec1 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
nebbiolo1 Linux (Ubuntu 20.04.1 LTS) / x86_64  OK  OK  OK 
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
riesling1 Windows Server 2019 Standard / x64  OK  OK [ OK ] OK 
merida1 macOS 10.14.6 Mojave / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: BrainStars
Version: 1.33.0
Command: D:\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:BrainStars.install-out.txt --library=D:\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings BrainStars_1.33.0.tar.gz
StartedAt: 2020-10-20 20:19:34 -0400 (Tue, 20 Oct 2020)
EndedAt: 2020-10-20 20:20:39 -0400 (Tue, 20 Oct 2020)
EllapsedTime: 64.1 seconds
RetCode: 0
Status:  OK  
CheckDir: BrainStars.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   D:\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:BrainStars.install-out.txt --library=D:\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings BrainStars_1.33.0.tar.gz
###
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* using log directory 'D:/biocbuild/bbs-3.12-bioc/meat/BrainStars.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 'BrainStars/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'BrainStars' version '1.33.0'
* 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 'BrainStars' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Package listed in more than one of Depends, Imports, Suggests, Enhances:
  'Biobase'
A package should be listed in only one of these fields.
* 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
Packages in Depends field not imported from:
  'RCurl' 'methods'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
.getBrainStarsExpression: no visible global function definition for
  'read.csv'
getBrainStars: no visible global function definition for 'getURL'
getBrainStarsExpression: no visible global function definition for
  'new'
getBrainStarsFigure: no visible global function definition for
  'getBinaryURL'
Undefined global functions or variables:
  getBinaryURL getURL new read.csv
Consider adding
  importFrom("methods", "new")
  importFrom("utils", "read.csv")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* 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
getBrainStarsFigure 0.05   0.02    11.3
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                    user system elapsed
getBrainStarsFigure    0      0   11.08
* 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: 3 NOTEs
See
  'D:/biocbuild/bbs-3.12-bioc/meat/BrainStars.Rcheck/00check.log'
for details.



Installation output

BrainStars.Rcheck/00install.out

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://172.29.0.3/BBS/3.12/bioc/src/contrib/BrainStars_1.33.0.tar.gz && rm -rf BrainStars.buildbin-libdir && mkdir BrainStars.buildbin-libdir && D:\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=BrainStars.buildbin-libdir BrainStars_1.33.0.tar.gz && D:\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL BrainStars_1.33.0.zip && rm BrainStars_1.33.0.tar.gz BrainStars_1.33.0.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  207k  100  207k    0     0  67.6M      0 --:--:-- --:--:-- --:--:-- 67.6M

install for i386

* installing *source* package 'BrainStars' ...
** using staged installation
** R
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'BrainStars'
    finding HTML links ... done
    BrainStars                              html  
    getBrainStars                           html  
    getBrainStarsFigure                     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 'BrainStars' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'BrainStars' as BrainStars_1.33.0.zip
* DONE (BrainStars)
* installing to library 'D:/biocbuild/bbs-3.12-bioc/R/library'
package 'BrainStars' successfully unpacked and MD5 sums checked

Tests output


Example timings

BrainStars.Rcheck/examples_i386/BrainStars-Ex.timings

nameusersystemelapsed
getBrainStars0.160.014.99
getBrainStarsFigure 0.05 0.0211.30

BrainStars.Rcheck/examples_x64/BrainStars-Ex.timings

nameusersystemelapsed
getBrainStars0.180.004.90
getBrainStarsFigure 0.00 0.0011.08