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BioC 3.2: CHECK report for Rcade on linux1.bioconductor.org

This page was generated on 2015-10-27 17:25:39 -0400 (Tue, 27 Oct 2015).

Package 848/1104HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
Rcade 1.12.0
Jonathan Cairns
Snapshot Date: 2015-10-26 19:24:07 -0400 (Mon, 26 Oct 2015)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_2/madman/Rpacks/Rcade
Last Changed Rev: 109589 / Revision: 109947
Last Changed Date: 2015-10-13 15:36:05 -0400 (Tue, 13 Oct 2015)
linux1.bioconductor.org Linux (Ubuntu 14.04.2 LTS) / x86_64  NotNeeded  OK [ OK ]UNNEEDED, same version exists in internal repository
windows1.bioconductor.org Windows Server 2012 R2 Enterprise SP1 (64-bit) / x64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository
perceval Mac OS X Snow Leopard (10.6.8) / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: Rcade
Version: 1.12.0
Command: /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings Rcade_1.12.0.tar.gz
StartedAt: 2015-10-27 07:15:34 -0400 (Tue, 27 Oct 2015)
EndedAt: 2015-10-27 07:17:42 -0400 (Tue, 27 Oct 2015)
EllapsedTime: 128.1 seconds
RetCode: 0
Status:  OK 
CheckDir: Rcade.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings Rcade_1.12.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.2-bioc/meat/Rcade.Rcheck’
* using R version 3.2.2 (2015-08-14)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘Rcade/DESCRIPTION’ ... OK
* this is package ‘Rcade’ version ‘1.12.0’
* 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:
  .BBSoptions
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 ‘Rcade’ can be installed ... [10s/10s] OK
* checking installed package size ... NOTE
  installed size is  5.6Mb
  sub-directories of 1Mb or more:
    extdata   5.2Mb
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Title field: should not end in a period.
* 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
Namespaces in Imports field not imported from:
  ‘graphics’ ‘plotrix’
  All declared Imports should be used.
Packages in Depends field not imported from:
  ‘GenomicRanges’ ‘Rsamtools’ ‘baySeq’ ‘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
RcadeAnalysis: no visible global function definition for ‘values’
constructRcadeTable: no visible global function definition for
  ‘elementMetadata’
countReads: no visible global function definition for ‘ScanBamParam’
countReads: no visible global function definition for ‘seqlevels’
countReads: no visible global function definition for ‘scanBam’
countReads: no visible global function definition for ‘seqlevels<-’
countReads: no visible global function definition for ‘strand’
countReads: no visible global function definition for ‘start<-’
countReads: no visible global function definition for ‘width<-’
countReads: no visible global function definition for ‘countOverlaps’
defineBins: no visible global function definition for ‘IRanges’
defineBins: no visible global function definition for ‘GRanges’
defineBins: no visible global function definition for ‘DataFrame’
defineBins: no visible global function definition for ‘values<-’
describeGR: no visible global function definition for ‘elementMetadata’
diffCountsBaySeq: no visible global function definition for ‘width’
diffCountsBaySeq: no visible binding for global variable ‘getLibsizes’
diffCountsBaySeq: no visible global function definition for
  ‘libsizes<-’
diffCountsBaySeq: no visible binding for global variable ‘getPriors.NB’
diffCountsBaySeq: no visible binding for global variable
  ‘getLikelihoods’
getBamChrs: no visible global function definition for ‘scanBamHeader’
plotBBB,Rcade : .local: no visible global function definition for
  ‘decorate3d’
plotMM,Rcade : .local: no visible global function definition for
  ‘color.legend’
* 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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [22s/22s] OK
Examples with CPU or elapsed time > 5s
                  user system elapsed
diffCountsBaySeq 7.956  0.060   8.082
RcadeAnalysis    6.389  0.032   6.434
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.R’ [6s/6s]
 [6s/6s] 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: 5 NOTEs
See
  ‘/home/biocbuild/bbs-3.2-bioc/meat/Rcade.Rcheck/00check.log’
for details.


Rcade.Rcheck/00install.out:

* installing *source* package ‘Rcade’ ...
** 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 (Rcade)

Rcade.Rcheck/Rcade-Ex.timings:

nameusersystemelapsed
Rcade-class0.7910.0370.839
RcadeAnalysis6.3890.0326.434
RcadeSTAT10.0020.0000.002
constructRcadeTable0.0060.0000.006
countReads1.2230.0041.231
defineBins0.0180.0000.017
diffCountsBaySeq7.9560.0608.082
exportRcade-methods0.0020.0000.002