minfi 1.12.0
Kasper Daniel Hansen
| 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/minfi | | Last Changed Rev: 95439 / Revision: 102249 | | Last Changed Date: 2014-10-13 14:38:33 -0700 (Mon, 13 Oct 2014) |
| zin1 | Linux (Ubuntu 12.04.4 LTS) / x86_64 | OK | OK | OK | |
| moscato1 | Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 | OK | OK | OK | OK |
| perceval | Mac OS X Snow Leopard (10.6.8) / x86_64 | OK | OK | [ OK ] | OK |
| oaxaca | Mac OS X Mavericks (10.9.5) / x86_64 | OK | OK | OK | OK |
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### Running command:
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### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch minfi_1.12.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.0-bioc/meat/minfi.Rcheck’
* using R version 3.1.3 (2015-03-09)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘minfi/DESCRIPTION’ ... OK
* this is package ‘minfi’ version ‘1.12.0’
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Depends: includes the non-default packages:
‘BiocGenerics’ ‘Biobase’ ‘lattice’ ‘GenomicRanges’ ‘Biostrings’
‘bumphunter’
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 ‘minfi’ can be installed ... [30s/33s] 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 ‘digest’ in package code.
Please use :: or requireNamespace() instead.
See section 'Suggested packages' in the 'Writing R Extensions' manual.
Unexported objects imported by ':::' calls:
‘bumphunter:::.getEstimate’
‘GenomicRanges:::.ShallowSimpleListAssays’
‘GenomicRanges:::.valid.SummarizedExperiment.colData_dims’
‘GenomicRanges:::clone’
See the note in ?`:::` about the use of this operator.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
.digestMatrix: no visible global function definition for ‘digest’
blockFinder: no visible binding for global variable ‘locfitByCluster’
blockFinder: no visible global function definition for
‘bumphunterEngine’
cpgCollapseAnnotation: no visible global function definition for
‘seqlevels’
cpgCollapseAnnotation: no visible global function definition for
‘seqlevels<-’
getLocations: no visible global function definition for ‘seqlevels<-’
getLocations: no visible global function definition for ‘seqlevels’
getLocations: no visible global function definition for ‘genome<-’
MethylSet: no visible global function definition for ‘featureData<-’
MethylSet: no visible global function definition for
‘AnnotatedDataFrame’
preprocessNoob: no visible global function definition for ‘varMetadata’
preprocessNoob: no visible global function definition for
‘varMetadata<-’
* 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [426s/427s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
bumphunter 86.093 20.155 106.456
preprocessFunnorm 79.127 12.093 91.249
preprocessNoob 36.730 6.089 42.831
preprocessQuantile 29.238 3.335 32.608
detectionP 28.946 1.694 30.691
read.450k.exp 13.439 0.658 14.101
read.450k 11.576 0.718 12.335
densityBeanPlot 10.645 0.713 11.374
minfiQC 10.027 1.167 11.199
densityPlot 9.077 0.978 10.067
preprocessIllumina 8.466 0.602 9.069
getSex 7.717 0.886 8.608
preprocessRaw 6.973 0.475 7.500
IlluminaMethylationManifest-class 5.627 0.363 5.992
* checking for unstated dependencies in tests ... OK
* checking tests ...
Running ‘runTests.R’ [242s/348s]
[242s/348s] 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
‘/Users/biocbuild/bbs-3.0-bioc/meat/minfi.Rcheck/00check.log’
for details.