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 |
* 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.