CAGEr 1.13.0
Vanja Haberle
| Snapshot Date: 2015-10-26 20:20:04 -0400 (Mon, 26 Oct 2015) | | URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/CAGEr | | Last Changed Rev: 109592 / Revision: 109948 | | 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 | OK | OK | [ OK ] | |  |
| windows2.bioconductor.org | Windows Server 2012 R2 Enterprise SP1 (64-bit) / x64 | OK | OK | OK | OK | |
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### Running command:
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### /home/biocbuild/bbs-3.3-bioc/R/bin/R CMD check --no-vignettes --timings CAGEr_1.13.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.3-bioc/meat/CAGEr.Rcheck’
* using R Under development (unstable) (2015-09-09 r69333)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘CAGEr/DESCRIPTION’ ... OK
* this is package ‘CAGEr’ version ‘1.13.0’
* 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 ‘CAGEr’ can be installed ... [12s/12s] 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' call to ‘parallel’ in package code.
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
.cluster.ctss.strand: no visible binding for global variable ‘tpm’
.cluster.ctss.strand: no visible global function definition for ‘Rle’
.ctss2clusters: no visible global function definition for ‘detectCores’
.ctss2clusters: no visible global function definition for ‘mclapply’
.ctss2clusters : <anonymous>: no visible binding for global variable
‘chr’
.ctss2clusters.predef: no visible global function definition for
‘detectCores’
.ctss2clusters.predef: no visible global function definition for
‘mclapply’
.ctss2clusters.predef : <anonymous>: no visible binding for global
variable ‘chr’
.distclu: no visible binding for global variable ‘tpm’
.distclu: no visible global function definition for ‘mclapply’
.estimate.G.addition.and.correct: no visible binding for global
variable ‘removedG’
.estimate.G.addition.and.correct: no visible binding for global
variable ‘pos’
.estimate.G.addition.and.correct: no visible binding for global
variable ‘V1’
.estimate.G.addition.and.correct: no visible binding for global
variable ‘V2’
.estimate.G.addition.and.correct: no visible binding for global
variable ‘nr_tags’
.fit.power.law.to.reverse.cumulative: no visible binding for global
variable ‘num’
.fit.power.law.to.reverse.cumulative: no visible binding for global
variable ‘nr_tags’
.get.quant.pos: no visible global function definition for ‘detectCores’
.get.quant.pos: no visible global function definition for ‘mclapply’
.getCumsum: no visible global function definition for ‘detectCores’
.getCumsum: no visible global function definition for ‘mclapply’
.getCumsum : <anonymous>: no visible binding for global variable ‘chr’
.getCumsumChr: no visible global function definition for ‘Rle’
.getCumsumChr2: no visible binding for global variable ‘chr’
.getTotalTagCount: no visible binding for global variable ‘tpm’
.getTotalTagCount: no visible binding for global variable
‘consensus.cluster’
.make.consensus.clusters: no visible binding for global variable ‘tpm’
.paraclu: no visible binding for global variable ‘tpm’
.paraclu3: no visible global function definition for ‘detectCores’
.paraclu3 : <anonymous>: no visible binding for global variable ‘chr’
.paraclu3: no visible global function definition for ‘mclapply’
.paraclu3: no visible binding for global variable ‘chr’
.paraclu3: no visible binding for global variable ‘max_d’
.paraclu3: no visible binding for global variable ‘min_d’
.paraclu3: no visible binding for global variable ‘tpm’
.plotReverseCumulative: no visible binding for global variable ‘num’
.plotReverseCumulative: no visible binding for global variable
‘nr_tags’
.predefined.clusters: no visible binding for global variable ‘tpm’
.predefined.clusters: no visible global function definition for
‘mclapply’
.remove.added.G : <anonymous>: no visible binding for global variable
‘chr’
.remove.added.G: no visible binding for global variable ‘removedG’
.remove.added.G: no visible binding for global variable ‘chr’
.remove.added.G: no visible binding for global variable ‘pos’
.remove.added.G: no visible binding for global variable ‘nr_tags’
.remove.added.G: no visible binding for global variable ‘tag_count’
.reverse.cumsum: no visible global function definition for
‘detectCores’
.reverse.cumsum: no visible global function definition for ‘mclapply’
.score.promoter.shifting: no visible global function definition for
‘detectCores’
.score.promoter.shifting: no visible global function definition for
‘mclapply’
.summarize.clusters: no visible binding for global variable ‘chr’
.summarize.clusters: no visible binding for global variable ‘pos’
.summarize.clusters: no visible binding for global variable ‘tpm’
.summarize.clusters: no visible binding for global variable ‘cluster’
.summarize.clusters: no visible binding for global variable ‘nr_ctss’
.summarize.clusters.predef: no visible binding for global variable
‘chr’
.summarize.clusters.predef: no visible binding for global variable
‘pos’
.summarize.clusters.predef: no visible binding for global variable
‘tpm’
.summarize.clusters.predef: no visible binding for global variable
‘cluster’
aggregateTagClusters,CAGEset: no visible binding for global variable
‘consensus.cluster’
aggregateTagClusters,CAGEset: no visible binding for global variable
‘chr’
aggregateTagClusters,CAGEset: no visible binding for global variable
‘tpm’
cumulativeCTSSdistribution,CAGEset: no visible binding for global
variable ‘tpm’
extractExpressionClass,CAGEset: no visible binding for global variable
‘expression_class’
getCTSS,CAGEset: no visible global function definition for ‘seqlengths’
getCTSS,CAGEset: no visible binding for global variable ‘tag_count’
getCTSS,CAGEset: no visible binding for global variable ‘chr’
getCTSS,CAGEset: no visible binding for global variable ‘pos’
getShiftingPromoters,CAGEset: no visible binding for global variable
‘groupX.tpm’
getShiftingPromoters,CAGEset: no visible binding for global variable
‘groupY.tpm’
getShiftingPromoters,CAGEset: no visible binding for global variable
‘shifting.score’
getShiftingPromoters,CAGEset: no visible binding for global variable
‘fdr.KS’
importPublicData,character-character-ANY-character: no visible binding
for global variable ‘ENCODEtissueCAGEfly’
importPublicData,character-character-ANY-character: no visible binding
for global variable ‘ENCODEhumanCellLinesSamples’
importPublicData,character-character-ANY-character: no visible binding
for global variable ‘FANTOMhumanSamples’
importPublicData,character-character-ANY-character: no visible binding
for global variable ‘FANTOMmouseSamples’
importPublicData,character-character-ANY-character: no visible binding
for global variable ‘FANTOM5humanSamples’
importPublicData,character-character-ANY-character: no visible binding
for global variable ‘FANTOM5mouseSamples’
importPublicData,character-character-ANY-character: no visible binding
for global variable ‘ZebrafishSamples’
importPublicData,character-character-ANY-character: no visible binding
for global variable ‘ZebrafishCAGE’
scoreShift,CAGEset-character-character: no visible global function
definition for ‘detectCores’
scoreShift,CAGEset-character-character: no visible global function
definition for ‘mclapply’
scoreShift,CAGEset-character-character : <anonymous>: no visible
binding for global variable ‘consensus.cluster’
scoreShift,CAGEset-character-character : <anonymous> : <anonymous>: no
visible global function definition for ‘Rle’
scoreShift,CAGEset-character-character: no visible binding for global
variable ‘tagcount’
Undefined global functions or variables:
ENCODEhumanCellLinesSamples ENCODEtissueCAGEfly FANTOM5humanSamples
FANTOM5mouseSamples FANTOMhumanSamples FANTOMmouseSamples Rle V1 V2
ZebrafishCAGE ZebrafishSamples chr cluster consensus.cluster
detectCores expression_class fdr.KS groupX.tpm groupY.tpm max_d
mclapply min_d nr_ctss nr_tags num pos removedG seqlengths
shifting.score tag_count tagcount tpm
* 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 ... [70s/74s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
importPublicData 36.975 0.412 41.650
scoreShift 5.534 0.000 5.538
cumulativeCTSSdistribution 5.215 0.252 5.479
plotCorrelation 5.273 0.048 5.324
* 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
‘/home/biocbuild/bbs-3.3-bioc/meat/CAGEr.Rcheck/00check.log’
for details.