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CHECK report for BiocCaseStudies on tokay1

This page was generated on 2020-08-07 11:58:02 -0400 (Fri, 07 Aug 2020).

TO THE DEVELOPERS/MAINTAINERS OF THE BiocCaseStudies PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 148/1882HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
BiocCaseStudies 1.51.0
Bioconductor Package Maintainer
Snapshot Date: 2020-08-06 14:50:46 -0400 (Thu, 06 Aug 2020)
URL: https://git.bioconductor.org/packages/BiocCaseStudies
Branch: master
Last Commit: 436d015
Last Changed Date: 2020-04-27 14:16:09 -0400 (Mon, 27 Apr 2020)
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 macOS 10.14.6 Mojave / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: BiocCaseStudies
Version: 1.51.0
Command: C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:BiocCaseStudies.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings BiocCaseStudies_1.51.0.tar.gz
StartedAt: 2020-08-06 23:57:44 -0400 (Thu, 06 Aug 2020)
EndedAt: 2020-08-06 23:58:23 -0400 (Thu, 06 Aug 2020)
EllapsedTime: 39.1 seconds
RetCode: 0
Status:  OK  
CheckDir: BiocCaseStudies.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:BiocCaseStudies.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings BiocCaseStudies_1.51.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.12-bioc/meat/BiocCaseStudies.Rcheck'
* using R version 4.0.2 (2020-06-22)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'BiocCaseStudies/DESCRIPTION' ... OK
* this is package 'BiocCaseStudies' version '1.51.0'
* 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 'BiocCaseStudies' can be installed ... OK
* checking installed package size ... OK
* checking package 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:
  'Biobase' 'methods' 'tools'
  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
fixedWidthCat: no visible global function definition for
  'capture.output'
fixedWidthCat: no visible global function definition for 'strbreak'
mySessionInfo: no visible global function definition for 'sessionInfo'
packages2install : <anonymous>: no visible global function definition
  for 'packageDescription'
packages2install : <anonymous>: no visible global function definition
  for 'is'
parseLibVers: no visible global function definition for
  'packageDescription'
requiredPackages : <anonymous>: no visible global function definition
  for 'packageDescription'
requiredPackages : <anonymous>: no visible global function definition
  for 'is'
resample: no visible global function definition for 'pData'
resample: no visible binding for global variable 'sd'
resample: no visible global function definition for 'segments'
Undefined global functions or variables:
  capture.output is pData packageDescription sd segments sessionInfo
  strbreak
Consider adding
  importFrom("graphics", "segments")
  importFrom("methods", "is")
  importFrom("stats", "sd")
  importFrom("utils", "capture.output", "packageDescription",
             "sessionInfo")
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 examples ...
** running examples for arch 'i386' ... OK
** running examples for arch 'x64' ... OK
* checking PDF version of manual ... OK
* DONE

Status: 3 NOTEs
See
  'C:/Users/biocbuild/bbs-3.12-bioc/meat/BiocCaseStudies.Rcheck/00check.log'
for details.



Installation output

BiocCaseStudies.Rcheck/00install.out

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.12/bioc/src/contrib/BiocCaseStudies_1.51.0.tar.gz && rm -rf BiocCaseStudies.buildbin-libdir && mkdir BiocCaseStudies.buildbin-libdir && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=BiocCaseStudies.buildbin-libdir BiocCaseStudies_1.51.0.tar.gz && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL BiocCaseStudies_1.51.0.zip && rm BiocCaseStudies_1.51.0.tar.gz BiocCaseStudies_1.51.0.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  6979  100  6979    0     0   198k      0 --:--:-- --:--:-- --:--:--  219k

install for i386

* installing *source* package 'BiocCaseStudies' ...
** using staged installation
** R
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'BiocCaseStudies'
    finding HTML links ... done
    fixedWidthCat                           html  
    markup                                  html  
    mySessionInfo                           html  
    parseLibVers                            html  
    requiredPackages                        html  
    resample                                html  
** building package indices
** 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 'BiocCaseStudies' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'BiocCaseStudies' as BiocCaseStudies_1.51.0.zip
* DONE (BiocCaseStudies)
* installing to library 'C:/Users/biocbuild/bbs-3.12-bioc/R/library'
package 'BiocCaseStudies' successfully unpacked and MD5 sums checked

Tests output


Example timings

BiocCaseStudies.Rcheck/examples_i386/BiocCaseStudies-Ex.timings

nameusersystemelapsed
fixedWidthCat000
requiredPackages000

BiocCaseStudies.Rcheck/examples_x64/BiocCaseStudies-Ex.timings

nameusersystemelapsed
fixedWidthCat000
requiredPackages000