r3Cseq 1.12.1
Supat Thongjuea
| Snapshot Date: 2015-04-09 16:20:12 -0700 (Thu, 09 Apr 2015) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_0/madman/Rpacks/r3Cseq | | Last Changed Rev: 97464 / Revision: 102249 | | Last Changed Date: 2014-12-07 15:30:30 -0800 (Sun, 07 Dec 2014) |
| zin1 | Linux (Ubuntu 12.04.4 LTS) / x86_64 | NotNeeded | OK | [ OK ] | |
| moscato1 | Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 | NotNeeded | OK | OK | OK |
| perceval | Mac OS X Snow Leopard (10.6.8) / x86_64 | NotNeeded | OK | OK | OK |
| oaxaca | Mac OS X Mavericks (10.9.5) / x86_64 | NotNeeded | OK | OK | OK |
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### Running command:
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### /home/biocbuild/bbs-3.0-bioc/R/bin/R CMD check --no-vignettes --timings r3Cseq_1.12.1.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.0-bioc/meat/r3Cseq.Rcheck’
* using R version 3.1.3 (2015-03-09)
* 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 ‘1.12.1’
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Depends: includes the non-default packages:
‘GenomicRanges’ ‘Rsamtools’ ‘data.table’ ‘rtracklayer’ ‘VGAM’
‘qvalue’ ‘RColorBrewer’ ‘sqldf’
Adding so many packages to the search path is excessive and importing
selectively is preferable.
* 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 ... [21s/22s] 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.mm9.masked’
Please use :: or requireNamespace() instead.
See section 'Suggested packages' in the 'Writing R Extensions' manual.
Packages in Depends field not imported from:
‘GenomicRanges’ ‘RColorBrewer’ ‘Rsamtools’ ‘VGAM’ ‘data.table’
‘methods’ ‘qvalue’ ‘rtracklayer’ ‘sqldf’
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
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 global function definition for
‘space’
assign3CseqSigContact: no visible global function definition for
‘vsmooth.spline’
assign3CseqSigContact: no visible global function definition for
‘qvalue’
assign3CseqSigContact: no visible binding for global variable
‘relative.position’
assign3CseqSigContact: no visible binding for global variable
‘chromosome’
assign3CseqSigContact: no visible global function definition for
‘RangedData’
assign3CseqSigContact: no visible global function definition for
‘IRanges’
excludeReadsNearViewpoint: no visible global function definition for
‘space’
excludeReadsNearViewpoint: no visible global function definition for
‘RangedData’
excludeReadsNearViewpoint: no visible global function definition for
‘IRanges’
excludeReadsNearViewpoint: no visible global function definition for
‘subjectHits’
excludeReadsNearViewpoint: no visible global function definition for
‘findOverlaps’
generate3CseqReport: no visible global function definition for ‘space’
get3CseqRefGene: no visible binding for global variable ‘hg18refGene’
get3CseqRefGene: no visible binding for global variable ‘hg19refGene’
get3CseqRefGene: no visible binding for global variable ‘mm9refGene’
getContrInteractionsInRefseq: no visible global function definition for
‘GRanges’
getContrInteractionsInRefseq: no visible global function definition for
‘space’
getContrInteractionsInRefseq: no visible global function definition for
‘IRanges’
getContrInteractionsInRefseq: no visible global function definition for
‘findOverlaps’
getContrInteractionsInRefseq: no visible global function definition for
‘queryHits’
getContrInteractionsInRefseq: no visible global function definition for
‘subjectHits’
getContrInteractionsInRefseq: no visible global function definition for
‘sqldf’
getExpInteractionsInRefseq: no visible global function definition for
‘GRanges’
getExpInteractionsInRefseq: no visible global function definition for
‘space’
getExpInteractionsInRefseq: no visible global function definition for
‘IRanges’
getExpInteractionsInRefseq: no visible global function definition for
‘findOverlaps’
getExpInteractionsInRefseq: no visible global function definition for
‘queryHits’
getExpInteractionsInRefseq: no visible global function definition for
‘subjectHits’
getExpInteractionsInRefseq: no visible global function definition for
‘sqldf’
getFragmentsPerWindow: no visible binding for global variable
‘BSgenome.Hsapiens.UCSC.hg18.masked’
getFragmentsPerWindow: no visible global function definition for
‘seqlengths’
getFragmentsPerWindow: no visible global function definition for
‘RangedData’
getFragmentsPerWindow: no visible global function definition for
‘IRanges’
getFragmentsPerWindow: no visible binding for global variable
‘BSgenome.Hsapiens.UCSC.hg19.masked’
getFragmentsPerWindow: no visible binding for global variable
‘BSgenome.Mmusculus.UCSC.mm9.masked’
getPowerLawFittedCoeficient: no visible global function definition for
‘data.table’
getPowerLawFittedCoeficient: no visible binding for global variable
‘num’
getPowerLawFittedCoeficient: no visible binding for global variable
‘nr_reads’
getPowerLawFittedCoeficient: no visible global function definition for
‘setkey’
getPowerLawFittedCoeficient: no visible global function definition for
‘setnames’
getViewpoint: no visible binding for global variable
‘BSgenome.Hsapiens.UCSC.hg18.masked’
getViewpoint: no visible global function definition for ‘matchPattern’
getViewpoint: no visible global function definition for ‘DNAString’
getViewpoint: no visible global function definition for
‘reverseComplement’
getViewpoint: no visible global function definition for ‘RangedData’
getViewpoint: no visible global function definition for ‘IRanges’
getViewpoint: no visible binding for global variable
‘BSgenome.Hsapiens.UCSC.hg19.masked’
getViewpoint: no visible binding for global variable
‘BSgenome.Mmusculus.UCSC.mm9.masked’
makeInteractionMatrixNearCisPerWindow: no visible global function
definition for ‘space’
makeInteractionMatrixNearCisPerWindow: no visible global function
definition for ‘seqnames’
makeInteractionMatrixNearCisPerWindow: no visible binding for global
variable ‘BSgenome.Hsapiens.UCSC.hg19.masked’
makeInteractionMatrixNearCisPerWindow: no visible global function
definition for ‘seqlengths’
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 global function
definition for ‘RangedData’
makeInteractionMatrixNearCisPerWindow: no visible global function
definition for ‘IRanges’
makeInteractionMatrixNearCisPerWindow: no visible global function
definition for ‘countOverlaps’
makeInteractionMatrixNearCisPerWindow: no visible global function
definition for ‘vsmooth.spline’
makeInteractionMatrixNearCisPerWindow: no visible global function
definition for ‘qvalue’
plotInteractionsNearViewpoint: no visible global function definition
for ‘space’
plotInteractionsNearViewpoint: no visible binding for global variable
‘BSgenome.Hsapiens.UCSC.hg18.masked’
plotInteractionsNearViewpoint: no visible global function definition
for ‘seqlengths’
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
‘chromosome’
plotInteractionsNearViewpoint: no visible global function definition
for ‘brewer.pal’
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 global function definition
for ‘seqlengths’
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 global function definition
for ‘space’
plotInteractionsPerChromosome: no visible global function definition
for ‘brewer.pal’
plotOverviewInteractions: no visible binding for global variable
‘BSgenome.Hsapiens.UCSC.hg18.masked’
plotOverviewInteractions: no visible global function definition for
‘seqlengths’
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 global function definition for
‘brewer.pal’
plotOverviewInteractions: no visible global function definition for
‘space’
powerLawFittedRPM: no visible global function definition for ‘zeta’
calculateBatchRPM,r3CseqInBatch: no visible global function definition
for ‘space’
calculateBatchRPM,r3CseqInBatch: no visible global function definition
for ‘RangedData’
calculateBatchRPM,r3CseqInBatch: no visible global function definition
for ‘IRanges’
export3Cseq2bedGraph,r3Cseq: no visible global function definition for
‘space’
export3Cseq2bedGraph,r3Cseq: no visible global function definition for
‘RangedData’
export3Cseq2bedGraph,r3Cseq: no visible global function definition for
‘IRanges’
export3Cseq2bedGraph,r3Cseq: no visible global function definition for
‘export’
export3CseqRawReads2bedGraph,r3Cseq: no visible global function
definition for ‘RleList’
export3CseqRawReads2bedGraph,r3Cseq: no visible binding for global
variable ‘BSgenome.Hsapiens.UCSC.hg18.masked’
export3CseqRawReads2bedGraph,r3Cseq: no visible global function
definition for ‘seqlengths’
export3CseqRawReads2bedGraph,r3Cseq: no visible global function
definition for ‘seqlevels<-’
export3CseqRawReads2bedGraph,r3Cseq: no visible global function
definition for ‘seqlengths<-’
export3CseqRawReads2bedGraph,r3Cseq: no visible global function
definition for ‘coverage’
export3CseqRawReads2bedGraph,r3Cseq: no visible binding for global
variable ‘BSgenome.Hsapiens.UCSC.hg19.masked’
export3CseqRawReads2bedGraph,r3Cseq: no visible binding for global
variable ‘BSgenome.Mmusculus.UCSC.mm9.masked’
export3CseqRawReads2bedGraph,r3Cseq: no visible global function
definition for ‘export’
exportBatchInteractions2text,r3CseqInBatch: no visible global function
definition for ‘space’
exportInteractions2text,r3Cseq: no visible global function definition
for ‘space’
getBatchInteractions,r3CseqInBatch: no visible global function
definition for ‘space’
getBatchInteractions,r3CseqInBatch: no visible global function
definition for ‘qvalue’
getBatchInteractions,r3CseqInBatch: no visible global function
definition for ‘RangedData’
getBatchInteractions,r3CseqInBatch: no visible global function
definition for ‘IRanges’
getBatchRawReads,r3CseqInBatch: no visible global function definition
for ‘ScanBamParam’
getBatchRawReads,r3CseqInBatch: no visible global function definition
for ‘scanBamFlag’
getBatchRawReads,r3CseqInBatch: no visible global function definition
for ‘scanBam’
getBatchRawReads,r3CseqInBatch: no visible global function definition
for ‘width’
getBatchRawReads,r3CseqInBatch: no visible global function definition
for ‘GRanges’
getBatchRawReads,r3CseqInBatch: no visible global function definition
for ‘IRanges’
getBatchReadCountPerRestrictionFragment,r3CseqInBatch: no visible
global function definition for ‘RangedData’
getBatchReadCountPerRestrictionFragment,r3CseqInBatch: no visible
global function definition for ‘IRanges’
getBatchReadCountPerRestrictionFragment,r3CseqInBatch: no visible
global function definition for ‘space’
getBatchReadCountPerRestrictionFragment,r3CseqInBatch: no visible
global function definition for ‘countOverlaps’
getBatchReadCountPerWindow,r3CseqInBatch: no visible global function
definition for ‘space’
getBatchReadCountPerWindow,r3CseqInBatch: no visible global function
definition for ‘countOverlaps’
getBatchReadCountPerWindow,r3CseqInBatch: no visible global function
definition for ‘RangedData’
getBatchReadCountPerWindow,r3CseqInBatch: no visible global function
definition for ‘IRanges’
getEnzymeRestrictionPositionInSelectedGenome,repbaseEnzyme: no visible
binding for global variable ‘BSgenome.Hsapiens.UCSC.hg18.masked’
getEnzymeRestrictionPositionInSelectedGenome,repbaseEnzyme: no visible
global function definition for ‘matchPattern’
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’
getEnzymeRestrictionSequences,repbaseEnzyme-character: no visible
binding for global variable ‘enzyme’
getRawReads,r3Cseq: no visible global function definition for
‘ScanBamParam’
getRawReads,r3Cseq: no visible global function definition for
‘scanBamFlag’
getRawReads,r3Cseq: no visible global function definition for ‘scanBam’
getRawReads,r3Cseq: no visible global function definition for ‘width’
getRawReads,r3Cseq: no visible global function definition for ‘GRanges’
getRawReads,r3Cseq: no visible global function definition for ‘IRanges’
getReadCountPerRestrictionFragment,r3Cseq: no visible global function
definition for ‘RangedData’
getReadCountPerRestrictionFragment,r3Cseq: no visible global function
definition for ‘IRanges’
getReadCountPerRestrictionFragment,r3Cseq: no visible global function
definition for ‘countOverlaps’
getReadCountPerRestrictionFragment,r3Cseq: no visible global function
definition for ‘space’
getReadCountPerWindow,r3Cseq: no visible global function definition for
‘countOverlaps’
getReadCountPerWindow,r3Cseq: no visible global function definition for
‘RangedData’
getReadCountPerWindow,r3Cseq: no visible global function definition for
‘space’
getReadCountPerWindow,r3Cseq: no visible global function definition for
‘IRanges’
plotDomainogramNearViewpoint,r3Cseq: no visible global function
definition for ‘space’
plotDomainogramNearViewpoint,r3Cseq: no visible binding for global
variable ‘BSgenome.Hsapiens.UCSC.hg18.masked’
plotDomainogramNearViewpoint,r3Cseq: no visible global function
definition for ‘seqlengths’
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 ‘chromosome’
plotDomainogramNearViewpoint,r3Cseq: no visible global function
definition for ‘brewer.pal’
* 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 ... [10s/10s] 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
NOTE: There were 3 notes.
See
‘/home/biocbuild/bbs-3.0-bioc/meat/r3Cseq.Rcheck/00check.log’
for details.