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BioC 3.5: CHECK report for cellbaseR on veracruz2

This page was generated on 2017-09-22 13:54:35 -0400 (Fri, 22 Sep 2017).

Package 182/1381HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
cellbaseR 1.0.0
Mohammed OE Abdallah
Snapshot Date: 2017-09-21 17:18:06 -0400 (Thu, 21 Sep 2017)
URL: https://git.bioconductor.org/packages/cellbaseR
Last Commit: 691e84e
Last Changed Date: 2017-04-24 15:45:44 -0400 (Mon, 24 Apr 2017)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  NotNeeded  OK  WARNINGS UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  NotNeeded  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository
veracruz2 OS X 10.11.6 El Capitan / x86_64  NotNeeded  OK [ WARNINGS ] OK UNNEEDED, same version exists in internal repository

Summary

Package: cellbaseR
Version: 1.0.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings cellbaseR_1.0.0.tar.gz
StartedAt: 2017-09-22 00:44:01 -0400 (Fri, 22 Sep 2017)
EndedAt: 2017-09-22 00:46:39 -0400 (Fri, 22 Sep 2017)
EllapsedTime: 157.5 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_1.0.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.5-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 ‘1.0.0’
* 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 ‘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 12.604  0.154  15.414
getClinicalByRegion           5.861  0.063   7.542
AnnotateVcf-CellBaseR-method  3.350  0.793  17.849
* 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-3.5-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 3.350 0.79317.849
CellBaseParam0.0020.0000.003
CellBaseR0.3450.0310.674
createGeneModel0.4420.0201.089
getCaddScores0.1180.0020.601
getCellBase-CellBaseR-method0.1140.0020.620
getCellBaseResourceHelp0.2370.0020.835
getChromosomeInfo-CellBaseR-method0.1290.0020.617
getClinical-CellBaseR-method12.604 0.15415.414
getClinicalByGene1.4360.0172.304
getClinicalByRegion5.8610.0637.542
getConservationByRegion0.1400.0030.875
getGene-CellBaseR-method0.1740.0030.807
getGeneInfo0.1090.0020.590
getMeta-CellBaseR-method0.1130.0020.593
getProtein-CellBaseR-method0.1790.0020.784
getProteinInfo0.1780.0020.768
getRegion-CellBaseR-method0.1560.0030.880
getRegulatoryByRegion0.1600.0051.094
getSnp-CellBaseR-method0.0980.0010.585
getSnpByGene0.1230.0020.705
getTf-CellBaseR-method0.1200.0023.568
getTfbsByRegion0.1460.0010.662
getTranscript-CellBaseR-method0.1130.0020.605
getTranscriptByGene0.0970.0020.594
getVariant-CellBaseR-method0.1850.0030.824
getVariantAnnotation0.1640.0020.814
getXref-CellBaseR-method0.1060.0010.583