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BioC 3.5: CHECK report for randPack on toluca2

This page was generated on 2017-04-23 14:35:49 -0400 (Sun, 23 Apr 2017).

Package 1056/1377HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
randPack 1.21.0
Robert Gentleman
Snapshot Date: 2017-04-22 17:18:01 -0400 (Sat, 22 Apr 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/randPack
Last Changed Rev: 122712 / Revision: 129046
Last Changed Date: 2016-10-17 15:10:43 -0400 (Mon, 17 Oct 2016)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  NotNeeded  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository
toluca2 Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK [ OK ] OK 
veracruz2 OS X 10.11.6 El Capitan / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: randPack
Version: 1.21.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings randPack_1.21.0.tar.gz
StartedAt: 2017-04-23 08:35:44 -0400 (Sun, 23 Apr 2017)
EndedAt: 2017-04-23 08:36:18 -0400 (Sun, 23 Apr 2017)
EllapsedTime: 34.1 seconds
RetCode: 0
Status:  OK 
CheckDir: randPack.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings randPack_1.21.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/randPack.Rcheck’
* using R Under development (unstable) (2017-02-15 r72187)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘randPack/DESCRIPTION’ ... OK
* this is package ‘randPack’ version ‘1.21.0’
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘randPack’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Non-standard license specification:
  Artistic 2.0
Standardizable: TRUE
Standardized license specification:
  Artistic-2.0
* 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 loading without being on the library search path ... OK
* checking dependencies in R code ... NOTE
Package in Depends field not imported from: ‘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
.checkRand2CT : <anonymous>: no visible global function definition for
  ‘is’
.newEBC: no visible global function definition for ‘is’
.newPBlock: no visible global function definition for ‘is’
.newUrn: no visible global function definition for ‘is’
addPData: no visible global function definition for ‘is’
createTrial: no visible global function definition for ‘new’
getCovariates : <anonymous> : <anonymous>: no visible binding for
  global variable ‘slot’
getEnrolleeInfo: no visible global function definition for ‘is’
getTreatment: no visible global function definition for ‘is’
makeRandomizer: no visible global function definition for ‘is’
makeRandomizer: no visible global function definition for ‘new’
trtAlloc: no visible global function definition for ‘is’
validPID: no visible global function definition for ‘is’
show,ClinicalTrial: no visible global function definition for ‘show’
Undefined global functions or variables:
  is new show slot
Consider adding
  importFrom("methods", "is", "new", "show", "slot")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* checking Rd files ... NOTE
prepare_Rd: getTreatment.Rd:20-21: Dropping empty section \details
prepare_Rd: getTreatment.Rd:22-23: Dropping empty section \value
prepare_Rd: makeRandomizer.Rd:40-41: Dropping empty section \examples
* 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 installed files from ‘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: 4 NOTEs
See
  ‘/Users/biocbuild/bbs-3.5-bioc/meat/randPack.Rcheck/00check.log’
for details.


randPack.Rcheck/00install.out:

* installing *source* package ‘randPack’ ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (randPack)

randPack.Rcheck/randPack-Ex.timings:

nameusersystemelapsed
CT10.0180.0020.023
ClinicalExperiment-class0.0030.0010.006
ClinicalTrial-class0.0250.0030.029
PatientData-class0.0010.0000.001
PatientID-class0.0020.0000.005
Randomizer-class0.0010.0000.002
SampleData0.0070.0010.010
createTrial0.0040.0000.006
getEnrolleeInfo0.0020.0000.004
getTreatment0.0060.0010.010
minimizePocSim0.0040.0010.004
simPats0.0040.0000.004
treatmentNames0.0020.0010.002