CAGEr 1.2.9
Vanja Haberle
| Snapshot Date: 2013-10-08 17:00:48 -0700 (Tue, 08 Oct 2013) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_12/madman/Rpacks/CAGEr | | Last Changed Rev: 79994 / Revision: 81334 | | Last Changed Date: 2013-09-02 08:08:14 -0700 (Mon, 02 Sep 2013) |
| george2 | Linux (Ubuntu 12.04.1 LTS) / x86_64 | OK | [ OK ] | |
| moscato2 | Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 | OK | OK | OK |
| petty | Mac OS X Snow Leopard (10.6.8) / x86_64 | OK | OK | OK |
* using log directory ‘/home/biocbuild/bbs-2.12-bioc/meat/CAGEr.Rcheck’
* using R version 3.0.1 (2013-05-16)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘CAGEr/DESCRIPTION’ ... OK
* this is package ‘CAGEr’ version ‘1.2.9’
* 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 ... [32s/33s] 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 ... OK
* 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’
.ctss2clusters : <anonymous>: no visible binding for global variable
‘chr’
.ctss2clusters.predef : <anonymous>: no visible binding for global
variable ‘chr’
.distclu: no visible binding for global variable ‘tpm’
.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’
.getCumsum : <anonymous>: no visible binding for global variable ‘chr’
.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 : <anonymous>: no visible binding for global variable ‘chr’
.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’
.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’
.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 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’
scoreShift,CAGEset-character-character : <anonymous>: no visible
binding for global variable ‘consensus.cluster’
scoreShift,CAGEset-character-character: no visible binding for global
variable ‘tagcount’
* 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’ ... 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 ... [107s/109s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
importPublicData 32.678 0.608 33.716
plotCorrelation 14.497 0.320 14.886
cumulativeCTSSdistribution 11.349 1.380 12.986
quantilePositions 8.821 0.028 8.930
clusterCTSS 6.480 0.716 7.323
scoreShift 5.548 0.004 5.920
* 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
NOTE: There were 2 notes.
See
‘/home/biocbuild/bbs-2.12-bioc/meat/CAGEr.Rcheck/00check.log’
for details.
* installing *source* package ‘CAGEr’ ...
** R
** data
** inst
** preparing package for lazy loading
Warning: replacing previous import ‘last’ when loading ‘data.table’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Warning: replacing previous import ‘last’ when loading ‘data.table’
* DONE (CAGEr)