CAGEr 0.99.1
Vanja Haberle
| Snapshot Date: 2013-03-24 17:01:43 -0700 (Sun, 24 Mar 2013) | | URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/CAGEr | | Last Changed Rev: 74273 / Revision: 74774 | | Last Changed Date: 2013-03-13 06:31:35 -0700 (Wed, 13 Mar 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 Leopard (10.5.8) / i386 | OK | [ OK ] | OK |
* using log directory '/Users/biocbuild/bbs-2.12-bioc/meat/CAGEr.Rcheck'
* using R Under development (unstable) (2013-02-26 r62077)
* using platform: i386-apple-darwin9.8.0 (32-bit)
* using session charset: ASCII
* using option '--no-vignettes'
* checking for file 'CAGEr/DESCRIPTION' ... OK
* this is package 'CAGEr' version '0.99.1'
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Package which this enhances but not available for checking: 'multicore'
* 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 ... [21s/21s] 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'
.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'
.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'
.predefined.clusters: no visible binding for global variable 'tpm'
.summarize.clusters : <anonymous>: no visible binding for global
variable 'cluster'
.summarize.clusters: no visible binding for global variable 'nr_ctss'
.summarize.clusters: no visible binding for global variable 'tpm'
.summarize.clusters.predef : <anonymous>: no visible binding for global
variable 'cluster'
cumulativeCTSSdistribution,CAGEset: no visible binding for global
variable 'tpm'
extractExpressionClass,CAGEset: no visible binding for global variable
'expression_class'
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'
scoreShift,CAGEset-character-character : <anonymous>: no visible
binding for global variable 'consensus.cluster'
* 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' ... 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 ... [64s/64s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
importPublicData 22.099 1.207 23.470
quantilePositions 9.184 0.032 9.217
cumulativeCTSSdistribution 5.092 0.858 5.971
* 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 3 notes.
See
'/Users/biocbuild/bbs-2.12-bioc/meat/CAGEr.Rcheck/00check.log'
for details.