r3Cseq 1.17.0
Supat Thongjuea
| Snapshot Date: 2015-10-21 20:20:05 -0400 (Wed, 21 Oct 2015) | | URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/r3Cseq | | Last Changed Rev: 109592 / Revision: 109826 | | Last Changed Date: 2015-10-13 15:59:53 -0400 (Tue, 13 Oct 2015) |
| linux2.bioconductor.org | Linux (Ubuntu 14.04.2 LTS) / x86_64 | NotNeeded | OK | OK | |  |
| windows2.bioconductor.org | Windows Server 2012 R2 Enterprise SP1 (64-bit) / x64 | NotNeeded | OK | OK | OK | |
| morelia | Mac OS X Mavericks (10.9.5) / x86_64 | NotNeeded | OK | [ OK ] | OK | |
##############################################################################
##############################################################################
###
### Running command:
###
### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings r3Cseq_1.17.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.3-bioc/meat/r3Cseq.Rcheck’
* using R Under development (unstable) (2015-10-08 r69496)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘r3Cseq/DESCRIPTION’ ... OK
* this is package ‘r3Cseq’ version ‘1.17.0’
* 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 ... [14s/14s] 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 ... NOTE
'library' or 'require' calls in package code:
‘BSgenome.Hsapiens.UCSC.hg18.masked’
‘BSgenome.Hsapiens.UCSC.hg19.masked’
‘BSgenome.Mmusculus.UCSC.mm10.masked’
‘BSgenome.Mmusculus.UCSC.mm9.masked’
‘BSgenome.Rnorvegicus.UCSC.rn5.masked’
Please use :: or requireNamespace() instead.
See section 'Suggested packages' in 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
assign3CseqSigContact: no visible binding for global variable
‘relative.position’
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’
get3CseqRefGene: no visible binding for global variable ‘mm10refGene’
get3CseqRefGene: no visible binding for global variable ‘rn5refGene’
getFragmentsPerWindow: no visible binding for global variable
‘BSgenome.Hsapiens.UCSC.hg18.masked’
getFragmentsPerWindow: no visible binding for global variable
‘BSgenome.Hsapiens.UCSC.hg19.masked’
getFragmentsPerWindow: no visible binding for global variable
‘BSgenome.Mmusculus.UCSC.mm9.masked’
getFragmentsPerWindow: no visible binding for global variable
‘BSgenome.Mmusculus.UCSC.mm10.masked’
getFragmentsPerWindow: no visible binding for global variable
‘BSgenome.Rnorvegicus.UCSC.rn5.masked’
getPowerLawFittedCoeficient: no visible binding for global variable
‘num’
getPowerLawFittedCoeficient: no visible binding for global variable
‘nr_reads’
getViewpoint: no visible binding for global variable
‘BSgenome.Hsapiens.UCSC.hg18.masked’
getViewpoint: no visible global function definition for ‘DNAString’
getViewpoint: no visible binding for global variable
‘BSgenome.Hsapiens.UCSC.hg19.masked’
getViewpoint: no visible binding for global variable
‘BSgenome.Mmusculus.UCSC.mm9.masked’
getViewpoint: no visible binding for global variable
‘BSgenome.Mmusculus.UCSC.mm10.masked’
getViewpoint: no visible binding for global variable
‘BSgenome.Rnorvegicus.UCSC.rn5.masked’
makeInteractionMatrixNearCisPerWindow: no visible binding for global
variable ‘BSgenome.Hsapiens.UCSC.hg19.masked’
makeInteractionMatrixNearCisPerWindow: no visible binding for global
variable ‘BSgenome.Hsapiens.UCSC.hg18.masked’
makeInteractionMatrixNearCisPerWindow: no visible binding for global
variable ‘BSgenome.Mmusculus.UCSC.mm9.masked’
makeInteractionMatrixNearCisPerWindow: no visible binding for global
variable ‘BSgenome.Mmusculus.UCSC.mm10.masked’
makeInteractionMatrixNearCisPerWindow: no visible binding for global
variable ‘BSgenome.Rnorvegicus.UCSC.rn5.masked’
plotInteractionsNearViewpoint: no visible binding for global variable
‘BSgenome.Hsapiens.UCSC.hg18.masked’
plotInteractionsNearViewpoint: no visible binding for global variable
‘BSgenome.Hsapiens.UCSC.hg19.masked’
plotInteractionsNearViewpoint: no visible binding for global variable
‘BSgenome.Mmusculus.UCSC.mm9.masked’
plotInteractionsNearViewpoint: no visible binding for global variable
‘BSgenome.Mmusculus.UCSC.mm10.masked’
plotInteractionsNearViewpoint: no visible binding for global variable
‘BSgenome.Rnorvegicus.UCSC.rn5.masked’
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’
plotInteractionsNearViewpoint: no visible binding for global variable
‘log2fold’
plotInteractionsPerChromosome: no visible binding for global variable
‘BSgenome.Hsapiens.UCSC.hg18.masked’
plotInteractionsPerChromosome: no visible binding for global variable
‘BSgenome.Hsapiens.UCSC.hg19.masked’
plotInteractionsPerChromosome: no visible binding for global variable
‘BSgenome.Mmusculus.UCSC.mm9.masked’
plotInteractionsPerChromosome: no visible binding for global variable
‘BSgenome.Mmusculus.UCSC.mm10.masked’
plotInteractionsPerChromosome: no visible binding for global variable
‘BSgenome.Rnorvegicus.UCSC.rn5.masked’
plotOverviewInteractions: no visible binding for global variable
‘BSgenome.Hsapiens.UCSC.hg18.masked’
plotOverviewInteractions: no visible binding for global variable
‘BSgenome.Hsapiens.UCSC.hg19.masked’
plotOverviewInteractions: no visible binding for global variable
‘BSgenome.Mmusculus.UCSC.mm9.masked’
plotOverviewInteractions: no visible binding for global variable
‘BSgenome.Mmusculus.UCSC.mm10.masked’
plotOverviewInteractions: no visible binding for global variable
‘BSgenome.Rnorvegicus.UCSC.rn5.masked’
getEnzymeRestrictionPositionInSelectedGenome,repbaseEnzyme: no visible
binding for global variable ‘BSgenome.Hsapiens.UCSC.hg18.masked’
getEnzymeRestrictionPositionInSelectedGenome,repbaseEnzyme: no visible
binding for global variable ‘BSgenome.Hsapiens.UCSC.hg19.masked’
getEnzymeRestrictionPositionInSelectedGenome,repbaseEnzyme: no visible
binding for global variable ‘BSgenome.Mmusculus.UCSC.mm9.masked’
getEnzymeRestrictionPositionInSelectedGenome,repbaseEnzyme: no visible
binding for global variable ‘BSgenome.Mmusculus.UCSC.mm10.masked’
getEnzymeRestrictionPositionInSelectedGenome,repbaseEnzyme: no visible
binding for global variable ‘BSgenome.Rnorvegicus.UCSC.rn5.masked’
getEnzymeRestrictionSequences,repbaseEnzyme-character: no visible
binding for global variable ‘enzyme’
initialize,repbaseEnzyme: no visible binding for global variable
‘enzyme.db’
plotDomainogramNearViewpoint,r3Cseq: no visible binding for global
variable ‘BSgenome.Hsapiens.UCSC.hg18.masked’
plotDomainogramNearViewpoint,r3Cseq: no visible binding for global
variable ‘BSgenome.Hsapiens.UCSC.hg19.masked’
plotDomainogramNearViewpoint,r3Cseq: no visible binding for global
variable ‘BSgenome.Mmusculus.UCSC.mm9.masked’
plotDomainogramNearViewpoint,r3Cseq: no visible binding for global
variable ‘BSgenome.Mmusculus.UCSC.mm10.masked’
plotDomainogramNearViewpoint,r3Cseq: no visible binding for global
variable ‘BSgenome.Rnorvegicus.UCSC.rn5.masked’
plotDomainogramNearViewpoint,r3Cseq: no visible binding for global
variable ‘chromosome’
Undefined global functions or variables:
BSgenome.Hsapiens.UCSC.hg18.masked BSgenome.Hsapiens.UCSC.hg19.masked
BSgenome.Mmusculus.UCSC.mm10.masked
BSgenome.Mmusculus.UCSC.mm9.masked
BSgenome.Rnorvegicus.UCSC.rn5.masked DNAString chromosome contr_RPMs
enzyme enzyme.db exp_RPMs hg18refGene hg19refGene log2fold
mm10refGene mm9refGene nr_reads num relative.position rn5refGene
* 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [7s/7s] 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: 2 NOTEs
See
‘/Users/biocbuild/bbs-3.3-bioc/meat/r3Cseq.Rcheck/00check.log’
for details.
* installing *source* package ‘r3Cseq’ ...
** R
** data
** inst
** preparing package for lazy loading
No methods found in "Biostrings" for requests: DNAString
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
No methods found in "Biostrings" for requests: DNAString
* DONE (r3Cseq)