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CHECK report for BiocCaseStudies on tokay1

This page was generated on 2019-04-13 11:20:35 -0400 (Sat, 13 Apr 2019).

Package 133/1649HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
BiocCaseStudies 1.44.0
Bioconductor Package Maintainer
Snapshot Date: 2019-04-12 17:01:30 -0400 (Fri, 12 Apr 2019)
URL: https://git.bioconductor.org/packages/BiocCaseStudies
Branch: RELEASE_3_8
Last Commit: 2b671b5
Last Changed Date: 2018-10-30 11:41:44 -0400 (Tue, 30 Oct 2018)
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: BiocCaseStudies
Version: 1.44.0
Command: C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:BiocCaseStudies.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings BiocCaseStudies_1.44.0.tar.gz
StartedAt: 2019-04-13 00:45:11 -0400 (Sat, 13 Apr 2019)
EndedAt: 2019-04-13 00:46:44 -0400 (Sat, 13 Apr 2019)
EllapsedTime: 92.4 seconds
RetCode: 0
Status:  OK  
CheckDir: BiocCaseStudies.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:BiocCaseStudies.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings BiocCaseStudies_1.44.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.8-bioc/meat/BiocCaseStudies.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 'BiocCaseStudies/DESCRIPTION' ... OK
* this is package 'BiocCaseStudies' version '1.44.0'
* 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 '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 'plot'
resample: no visible global function definition for 'segments'
Undefined global functions or variables:
  capture.output is pData packageDescription plot sd segments
  sessionInfo strbreak
Consider adding
  importFrom("graphics", "plot", "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-3.8-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/3.8/bioc/src/contrib/BiocCaseStudies_1.44.0.tar.gz && rm -rf BiocCaseStudies.buildbin-libdir && mkdir BiocCaseStudies.buildbin-libdir && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=BiocCaseStudies.buildbin-libdir BiocCaseStudies_1.44.0.tar.gz && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL BiocCaseStudies_1.44.0.zip && rm BiocCaseStudies_1.44.0.tar.gz BiocCaseStudies_1.44.0.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  6971  100  6971    0     0   174k      0 --:--:-- --:--:-- --:--:--  194k

install for i386

* installing *source* package 'BiocCaseStudies' ...
** 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
In R CMD INSTALL

install for x64

* installing *source* package 'BiocCaseStudies' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'BiocCaseStudies' as BiocCaseStudies_1.44.0.zip
* DONE (BiocCaseStudies)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.8-bioc/R/library'
package 'BiocCaseStudies' successfully unpacked and MD5 sums checked
In R CMD INSTALL

Tests output


Example timings

BiocCaseStudies.Rcheck/examples_i386/BiocCaseStudies-Ex.timings

nameusersystemelapsed
fixedWidthCat0.020.000.02
requiredPackages000

BiocCaseStudies.Rcheck/examples_x64/BiocCaseStudies-Ex.timings

nameusersystemelapsed
fixedWidthCat0.000.010.02
requiredPackages000