CHECK report for r3Cseq on merida2
This page was generated on 2019-04-09 13:26:37 -0400 (Tue, 09 Apr 2019).
r3Cseq 1.29.1
Supat Thongjuea or
| Snapshot Date: 2019-04-08 17:01:18 -0400 (Mon, 08 Apr 2019) |
| URL: https://git.bioconductor.org/packages/r3Cseq |
| Branch: master |
| Last Commit: e4ca6f0 |
| Last Changed Date: 2018-12-20 05:21:23 -0400 (Thu, 20 Dec 2018) |
| malbec2 | Linux (Ubuntu 18.04.2 LTS) / x86_64 | OK | OK | OK | |  |
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | |
| celaya2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | |
| merida2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | [ OK ] | OK | |
Summary
Command output
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### Running command:
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### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:r3Cseq.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings r3Cseq_1.29.1.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/r3Cseq.Rcheck’
* using R Under development (unstable) (2018-11-27 r75683)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘r3Cseq/DESCRIPTION’ ... OK
* this is package ‘r3Cseq’ version ‘1.29.1’
* 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 ‘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 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 global function definition for
‘fitted’
assign3CseqSigContact: no visible binding for global variable
‘relative.position’
assign3CseqSigContact: no visible binding for global variable
‘chromosome’
excludeReadsNearViewpoint: no visible global function definition for
‘subjectHits’
generate3CseqReport: no visible global function definition for ‘pdf’
generate3CseqReport: no visible global function definition for
‘dev.off’
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’
getContrInteractionsInRefseq: no visible global function definition for
‘queryHits’
getContrInteractionsInRefseq: no visible global function definition for
‘subjectHits’
getExpInteractionsInRefseq: no visible global function definition for
‘queryHits’
getExpInteractionsInRefseq: no visible global function definition for
‘subjectHits’
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’
getPowerLawFittedCoeficient: no visible global function definition for
‘coefficients’
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’
makeInteractionMatrixNearCisPerWindow: no visible global function
definition for ‘fitted’
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 global function definition
for ‘par’
plotInteractionsNearViewpoint: no visible global function definition
for ‘plot’
plotInteractionsNearViewpoint: no visible global function definition
for ‘abline’
plotInteractionsNearViewpoint: no visible global function definition
for ‘text’
plotInteractionsNearViewpoint: no visible global function definition
for ‘lines’
plotInteractionsNearViewpoint: no visible global function definition
for ‘rect’
plotInteractionsNearViewpoint: no visible global function definition
for ‘legend’
plotInteractionsNearViewpoint: no visible global function definition
for ‘points’
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’
plotInteractionsPerChromosome: no visible global function definition
for ‘fitted’
plotInteractionsPerChromosome: no visible global function definition
for ‘plot’
plotInteractionsPerChromosome: no visible global function definition
for ‘abline’
plotInteractionsPerChromosome: no visible global function definition
for ‘lines’
plotInteractionsPerChromosome: no visible global function definition
for ‘legend’
plotInteractionsPerChromosome: no visible global function definition
for ‘par’
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’
plotOverviewInteractions: no visible global function definition for
‘plot’
plotOverviewInteractions: no visible global function definition for
‘axis’
plotOverviewInteractions: no visible global function definition for
‘polygon’
plotOverviewInteractions: no visible global function definition for
‘text’
plotOverviewInteractions: no visible global function definition for
‘rect’
plotOverviewInteractions: no visible global function definition for
‘legend’
getBatchInteractions,r3CseqInBatch: no visible global function
definition for ‘na.omit’
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’
plotDomainogramNearViewpoint,r3Cseq: no visible global function
definition for ‘par’
plotDomainogramNearViewpoint,r3Cseq: no visible global function
definition for ‘plot’
plotDomainogramNearViewpoint,r3Cseq: no visible global function
definition for ‘abline’
plotDomainogramNearViewpoint,r3Cseq: no visible global function
definition for ‘text’
plotDomainogramNearViewpoint,r3Cseq: no visible global function
definition for ‘lines’
plotDomainogramNearViewpoint,r3Cseq: no visible global function
definition for ‘rect’
plotDomainogramNearViewpoint,r3Cseq: no visible global function
definition for ‘legend’
plotDomainogramNearViewpoint,r3Cseq: no visible global function
definition for ‘points’
plotDomainogramNearViewpoint,r3Cseq: no visible global function
definition for ‘colorRampPalette’
plotDomainogramNearViewpoint,r3Cseq: no visible global function
definition for ‘image’
plotDomainogramNearViewpoint,r3Cseq: no visible global function
definition for ‘axis’
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 abline axis chromosome
coefficients colorRampPalette contr_RPMs dev.off enzyme enzyme.db
exp_RPMs fitted hg18refGene hg19refGene image legend lines log2fold
mm10refGene mm9refGene na.omit nr_reads num par pdf plot points
polygon queryHits rect relative.position rn5refGene subjectHits text
Consider adding
importFrom("grDevices", "colorRampPalette", "dev.off", "pdf")
importFrom("graphics", "abline", "axis", "image", "legend", "lines",
"par", "plot", "points", "polygon", "rect", "text")
importFrom("stats", "coefficients", "fitted", "na.omit")
to your NAMESPACE file.
* 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 files in ‘vignettes’ ... OK
* 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 vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: 2 NOTEs
See
‘/Users/biocbuild/bbs-3.9-bioc/meat/r3Cseq.Rcheck/00check.log’
for details.
Installation output
r3Cseq.Rcheck/00install.out
Tests output
Example timings
r3Cseq.Rcheck/r3Cseq-Ex.timings