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Package 485/631HostnameOS / ArchBUILDCHECKBUILD BIN
r3Cseq 1.5.0
Supat Thongjuea
Snapshot Date: 2013-01-15 17:01:14 -0800 (Tue, 15 Jan 2013)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/r3Cseq
Last Changed Rev: 71760 / Revision: 72575
Last Changed Date: 2012-12-10 04:16:58 -0800 (Mon, 10 Dec 2012)
george2 Linux (Ubuntu 12.04.1 LTS) / x86_64  OK  WARNINGS 
lamb2 Linux (openSUSE 11.4) / x86_64  OK [ WARNINGS ]
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  WARNINGS  OK 
petty Mac OS X Leopard (10.5.8) / i386  OK  WARNINGS  OK 

Summary

Package: r3Cseq
Version: 1.5.0
Command: /home/biocbuild/bbs-2.12-bioc/R/bin/R CMD check --no-vignettes --timings r3Cseq_1.5.0.tar.gz
StartedAt: 2013-01-16 05:36:15 -0800 (Wed, 16 Jan 2013)
EndedAt: 2013-01-16 05:40:13 -0800 (Wed, 16 Jan 2013)
EllapsedTime: 237.9 seconds
RetCode: 0
Status:  WARNINGS 
CheckDir: r3Cseq.Rcheck
Warnings: 2

Command output

* using log directory ‘/loc/home/biocbuild/bbs-2.12-bioc/meat/r3Cseq.Rcheck’
* using R Under development (unstable) (2012-12-17 r61365)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘r3Cseq/DESCRIPTION’ ... OK
* this is package ‘r3Cseq’ version ‘1.5.0’
* 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 ‘r3Cseq’ can be installed ... OK
* checking installed package size ... OK
* checking package 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 for unstated dependencies in R code ... WARNING
‘library’ or ‘require’ calls not declared from:
  ‘BSgenome.Hsapiens.UCSC.hg18’ ‘BSgenome.Hsapiens.UCSC.hg19’
package ‘methods’ is used but not declared
See the information on DESCRIPTION files in the chapter ‘Creating R
packages’ of the ‘Writing R Extensions’ manual.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
plotDomainogramNearViewpoint,r3Cseq: warning in axis(1, at = c(seq(0,
  1, by = 0.1)), lab = c(seq(-distance, distance, distance/5)),
  cex.axis = 0.8, las = 2): partial argument match of 'lab' to 'labels'
plotDomainogramNearViewpoint,r3Cseq: warning in axis(2, at = c(0, 1),
  lab = c(paste(maximum_window/1000, "Kb"), "2 Kb"), cex.axis = 0.8,
  las = 2): partial argument match of 'lab' to 'labels'
assign3CseqSigContact: no visible binding for global variable
  ‘chromosome’
get3CseqRefGene: no visible binding for global variable ‘hg18refGene’
get3CseqRefGene: no visible binding for global variable ‘hg19refGene’
get3CseqRefGene: no visible binding for global variable ‘mm9refGene’
getFragmentsPerWindow: no visible binding for global variable
  ‘Hsapiens’
getPowerLawFittedCoeficient: no visible binding for global variable
  ‘num’
getPowerLawFittedCoeficient: no visible binding for global variable
  ‘nr_reads’
getViewpoint: no visible binding for global variable ‘Hsapiens’
makeInteractionMatrixNearCisPerWindow: no visible binding for global
  variable ‘Hsapiens’
plotInteractionsNearViewpoint: no visible binding for global variable
  ‘Hsapiens’
plotInteractionsNearViewpoint: no visible binding for global variable
  ‘chromosome’
plotInteractionsNearViewpoint: no visible binding for global variable
  ‘exp_RPMs’
plotInteractionsNearViewpoint: no visible binding for global variable
  ‘contr_RPMs’
plotInteractionsPerChromosome: no visible binding for global variable
  ‘Hsapiens’
plotOverviewInteractions: no visible binding for global variable
  ‘Hsapiens’
export3CseqRawReads2bedGraph,r3Cseq: no visible binding for global
  variable ‘Hsapiens’
getBatchReadCountPerRestrictionFragment,r3CseqInBatch: no visible
  binding for global variable ‘exp.read.length’
getEnzymeRestrictionPositionInSelectedGenome,repbaseEnzyme: no visible
  binding for global variable ‘Hsapiens’
plotDomainogramNearViewpoint,r3Cseq: no visible binding for global
  variable ‘Hsapiens’
plotDomainogramNearViewpoint,r3Cseq: no visible binding for global
  variable ‘chromosome’
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... WARNING
Undocumented code objects:
  ‘contrRawData<-’ ‘expRawData<-’
All user-level objects in a package should have documentation entries.
See the chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* 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’ ... NOTE
The following directories should probably not be installed:
  ‘images’

Consider the use of a .Rinstignore file: see ‘Writing R Extensions’,
or move the vignette sources from ‘inst/doc’ to ‘vignettes’.
* 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 vignettes ... SKIPPED
* checking PDF version of manual ... OK

WARNING: There were 2 warnings.
NOTE: There were 2 notes.
See
  ‘/loc/home/biocbuild/bbs-2.12-bioc/meat/r3Cseq.Rcheck/00check.log’
for details.

r3Cseq.Rcheck/00install.out:

* installing *source* package ‘r3Cseq’ ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
   ‘r3Cseq.Rnw’ 
** testing if installed package can be loaded

* DONE (r3Cseq)

r3Cseq.Rcheck/r3Cseq-Ex.timings:

nameusersystemelapsed
calculateBatchRPM0.0040.0040.006
calculateRPM0.0000.0080.006
contrInteractionRegions0.0040.0000.007
contrRPM0.0040.0040.007
contrRawData0.0080.0000.008
contrReadCount0.0080.0000.008
expInteractionRegions0.0040.0040.008
expRPM0.0040.0040.008
expRawData0.0080.0000.008
expReadCount0.0040.0040.008
export3Cseq2bedGraph0.0040.0040.008
export3CseqRawReads2bedGraph0.0040.0040.008
exportBatchInteractions2text0.0080.0000.009
exportInteractions2text0.0080.0000.008
generate3CseqReport0.0040.0040.009
getBatchInteractions0.0080.0000.008
getBatchRawReads0.4080.0000.406
getBatchReadCountPerRestrictionFragment0.0080.0000.010
getBatchReadCountPerWindow0.0080.0000.006
getContrInteractionsInRefseq0.0080.0000.006
getExpInteractionsInRefseq0.0080.0000.008
getInteractions0.0040.0040.007
getRawReads0.0040.0000.006
getReadCountPerRestrictionFragment0.0040.0000.007
getReadCountPerWindow0.0040.0040.006
getViewpoint0.0040.0000.006
plotDomainogramNearViewpoint0.0040.0000.007
plotInteractionsNearViewpoint0.0040.0040.007
plotInteractionsPerChromosome0.0040.0040.007
plotOverviewInteractions0.0040.0040.007
r3Cseq-class0.0040.0040.007
r3CseqCommon-class0.0080.0000.008
r3CseqInBatch-class0.0080.0000.007