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This page was generated on 2021-08-02 15:05:54 -0400 (Mon, 02 Aug 2021).

CHECK results for RbcBook1 on machv2

To the developers/maintainers of the RbcBook1 package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/RbcBook1.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 1505/2041HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
RbcBook1 1.60.0  (landing page)
Vince Carey
Snapshot Date: 2021-08-01 04:50:10 -0400 (Sun, 01 Aug 2021)
URL: https://git.bioconductor.org/packages/RbcBook1
Branch: RELEASE_3_13
Last Commit: f563f7a
Last Changed Date: 2021-05-19 11:38:15 -0400 (Wed, 19 May 2021)
nebbiolo1Linux (Ubuntu 20.04.2 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: RbcBook1
Version: 1.60.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:RbcBook1.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings RbcBook1_1.60.0.tar.gz
StartedAt: 2021-08-01 22:26:59 -0400 (Sun, 01 Aug 2021)
EndedAt: 2021-08-01 22:27:46 -0400 (Sun, 01 Aug 2021)
EllapsedTime: 46.1 seconds
RetCode: 0
Status:   OK  
CheckDir: RbcBook1.Rcheck
Warnings: 0

Command output

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:RbcBook1.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings RbcBook1_1.60.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.13-bioc/meat/RbcBook1.Rcheck’
* using R version 4.1.0 (2021-05-18)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘RbcBook1/DESCRIPTION’ ... OK
* this is package ‘RbcBook1’ version ‘1.60.0’
* 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 ... NOTE
Found the following hidden files and directories:
  .git_fetch_output.txt
  .git_merge_output.txt
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘RbcBook1’ can be installed ... OK
* checking installed package size ... NOTE
  installed size is  6.5Mb
  sub-directories of 1Mb or more:
    data   6.4Mb
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Description field: should contain one or more complete sentences.
* 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
* 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
'library' or 'require' call to ‘graph’ which was already attached by Depends.
  Please remove these calls from your code.
Packages in Depends field not imported from:
  ‘Biobase’ ‘graph’ ‘rpart’
  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
bcSweave: no visible global function definition for
  ‘Sweave’
remapAff: no visible binding for global variable
  ‘hgu95av2SYMBOL’
rpart2gNEL: no visible global function definition for
  ‘new’
rpart2gNEL: no visible global function definition for
  ‘edgemode<-’
rpart2gNEL: no visible global function definition for
  ‘addEdge’
Undefined global functions or variables:
  Sweave addEdge edgemode<- hgu95av2SYMBOL new
Consider adding
  importFrom("methods", "new")
  importFrom("utils", "Sweave")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* checking Rd files ... NOTE
prepare_Rd: requireAllBook1.Rd:9-10: Dropping empty section \arguments
* 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... 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: 6 NOTEs
See
  ‘/Users/biocbuild/bbs-3.13-bioc/meat/RbcBook1.Rcheck/00check.log’
for details.



Installation output

RbcBook1.Rcheck/00install.out

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL RbcBook1
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.1/Resources/library’
* installing *source* package ‘RbcBook1’ ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** 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
* DONE (RbcBook1)

Tests output


Example timings

RbcBook1.Rcheck/RbcBook1-Ex.timings

nameusersystemelapsed
bcStangle0.0000.0010.000
bcSweave0.0000.0000.001
bcr0.8100.0370.847
checkVerbatimLines0.0180.0030.021
imageSize000
perf0.0010.0020.003
requireAllBook10.0000.0010.000
rpart2gNEL0.1390.0110.151