Back to the "Multiple platform build/check report" A  B [C] D  E  F  G  H  I  J  K  L  M  N  O  P  Q  R  S  T  U  V  W  X  Y  Z 

BioC 3.6: CHECK report for cellbaseR on veracruz1

This page was generated on 2017-08-16 13:50:26 -0400 (Wed, 16 Aug 2017).

Package 183/1410HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
cellbaseR 1.1.1
Mohammed OE Abdallah
Snapshot Date: 2017-08-15 17:18:21 -0400 (Tue, 15 Aug 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/cellbaseR
Last Changed Rev: 129266 / Revision: 131943
Last Changed Date: 2017-04-28 17:17:39 -0400 (Fri, 28 Apr 2017)
malbec1 Linux (Ubuntu 16.04.1 LTS) / x86_64  NotNeeded  ERROR  skipped 
tokay1 Windows Server 2012 R2 Standard / x64  NotNeeded  ERROR  skipped  skipped 
veracruz1 OS X 10.11.6 El Capitan / x86_64  NotNeeded  OK [ WARNINGS ] OK UNNEEDED, same version exists in internal repository

Summary

Package: cellbaseR
Version: 1.1.1
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings cellbaseR_1.1.1.tar.gz
StartedAt: 2017-08-16 00:50:49 -0400 (Wed, 16 Aug 2017)
EndedAt: 2017-08-16 00:53:18 -0400 (Wed, 16 Aug 2017)
EllapsedTime: 149.0 seconds
RetCode: 0
Status:  WARNINGS 
CheckDir: cellbaseR.Rcheck
Warnings: 1

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings cellbaseR_1.1.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.6-bioc/meat/cellbaseR.Rcheck’
* using R version 3.4.1 (2017-06-30)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘cellbaseR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘cellbaseR’ version ‘1.1.1’
* 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 ‘cellbaseR’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* 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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... WARNING
Found the following significant warnings:

  Warning: 'rbind.pages' is deprecated.
  Warning: 'rbind.pages' is deprecated.
  Warning: 'rbind.pages' is deprecated.
  Warning: 'rbind.pages' is deprecated.
  Warning: 'rbind.pages' is deprecated.
  Warning: 'rbind.pages' is deprecated.
  Warning: 'rbind.pages' is deprecated.
  Warning: 'rbind.pages' is deprecated.
  Warning: 'rbind.pages' is deprecated.
  Warning: 'rbind.pages' is deprecated.
  Warning: 'rbind.pages' is deprecated.
  Warning: 'rbind.pages' is deprecated.
  Warning: 'rbind.pages' is deprecated.
  Warning: 'rbind.pages' is deprecated.
  Warning: 'rbind.pages' is deprecated.
  Warning: 'rbind.pages' is deprecated.
  Warning: 'rbind.pages' is deprecated.
  Warning: 'rbind.pages' is deprecated.
  Warning: 'rbind.pages' is deprecated.
  Warning: 'rbind.pages' is deprecated.
  Warning: 'rbind.pages' is deprecated.
  Warning: 'rbind.pages' is deprecated.
  Warning: 'rbind.pages' is deprecated.
  Warning: 'rbind.pages' is deprecated.
  Warning: 'rbind.pages' is deprecated.
  Warning: 'rbind.pages' is deprecated.
  Warning: 'rbind.pages' is deprecated.
  Warning: 'rbind.pages' is deprecated.
  Warning: 'rbind.pages' is deprecated.
  Warning: 'rbind.pages' is deprecated.
  Warning: 'rbind.pages' is deprecated.
  Warning: 'rbind.pages' is deprecated.
  Warning: 'rbind.pages' is deprecated.
  Warning: 'rbind.pages' is deprecated.
  Warning: 'rbind.pages' is deprecated.
  Warning: 'rbind.pages' is deprecated.
  Warning: 'rbind.pages' is deprecated.
  Warning: 'rbind.pages' is deprecated.
  Warning: 'rbind.pages' is deprecated.
  Warning: 'rbind.pages' is deprecated.
  Warning: 'rbind.pages' is deprecated.
  Warning: 'rbind.pages' is deprecated.
  Warning: 'rbind.pages' is deprecated.
  Warning: 'rbind.pages' is deprecated.
  Warning: 'rbind.pages' is deprecated.
  Warning: 'rbind.pages' is deprecated.
  Warning: 'rbind.pages' is deprecated.
  Warning: 'rbind.pages' is deprecated.
  Warning: 'rbind.pages' is deprecated.
  Warning: 'rbind.pages' is deprecated.
  Warning: 'rbind.pages' is deprecated.
  Warning: 'rbind.pages' is deprecated.
  Warning: 'rbind.pages' is deprecated.
  Warning: 'rbind.pages' is deprecated.
  Warning: 'rbind.pages' is deprecated.
  Warning: 'rbind.pages' is deprecated.
  Warning: 'rbind.pages' is deprecated.
  Warning: 'rbind.pages' is deprecated.
  Warning: 'rbind.pages' is deprecated.
  Warning: 'rbind.pages' is deprecated.
  Warning: 'rbind.pages' is deprecated.
  Warning: 'rbind.pages' is deprecated.
  Warning: 'rbind.pages' is deprecated.
  Warning: 'rbind.pages' is deprecated.
  Warning: 'rbind.pages' is deprecated.
  Warning: 'rbind.pages' is deprecated.
  Warning: 'rbind.pages' is deprecated.
  Warning: 'rbind.pages' is deprecated.
  Warning: 'rbind.pages' is deprecated.
  Warning: 'rbind.pages' is deprecated.
  Warning: 'rbind.pages' is deprecated.
  Warning: 'rbind.pages' is deprecated.
  Warning: 'rbind.pages' is deprecated.
  Warning: 'rbind.pages' is deprecated.
  Warning: 'rbind.pages' is deprecated.
  Warning: 'rbind.pages' is deprecated.
  Warning: 'rbind.pages' is deprecated.
  Warning: 'rbind.pages' is deprecated.
Deprecated functions may be defunct as soon as of the next release of
R.
See ?Deprecated.
Examples with CPU or elapsed time > 5s
                               user system elapsed
getClinical-CellBaseR-method 12.030  0.128  15.709
getClinicalByRegion           4.809  0.034   6.447
AnnotateVcf-CellBaseR-method  3.013  0.794  13.352
* 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: 1 WARNING
See
  ‘/Users/biocbuild/bbs-3.6-bioc/meat/cellbaseR.Rcheck/00check.log’
for details.

cellbaseR.Rcheck/00install.out:

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

cellbaseR.Rcheck/cellbaseR-Ex.timings:

nameusersystemelapsed
AnnotateVcf-CellBaseR-method 3.013 0.79413.352
CellBaseParam0.0020.0000.002
CellBaseR0.3310.0290.661
createGeneModel0.5090.0251.173
getCaddScores0.1430.0020.677
getCellBase-CellBaseR-method0.1160.0010.600
getCellBaseResourceHelp0.2490.0020.830
getChromosomeInfo-CellBaseR-method0.1220.0020.984
getClinical-CellBaseR-method12.030 0.12815.709
getClinicalByGene1.7860.0212.676
getClinicalByRegion4.8090.0346.447
getConservationByRegion0.2050.0130.878
getGene-CellBaseR-method0.1530.0080.814
getGeneInfo0.1410.0090.649
getMeta-CellBaseR-method0.1260.0020.624
getProtein-CellBaseR-method0.1900.0020.771
getProteinInfo0.1820.0020.771
getRegion-CellBaseR-method0.1750.0030.862
getRegulatoryByRegion0.1910.0041.022
getSnp-CellBaseR-method0.1190.0010.597
getSnpByGene0.1240.0030.609
getTf-CellBaseR-method0.0950.0012.523
getTfbsByRegion0.1090.0020.616
getTranscript-CellBaseR-method0.0920.0010.603
getTranscriptByGene0.0860.0010.572
getVariant-CellBaseR-method0.1580.0030.848
getVariantAnnotation0.1440.0020.785
getXref-CellBaseR-method0.1280.0010.595