ChIPpeakAnno 3.2.2
Lihua Julie Zhu , Jianhong Ou
| Snapshot Date: 2015-10-08 17:20:21 -0700 (Thu, 08 Oct 2015) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_1/madman/Rpacks/ChIPpeakAnno | | Last Changed Rev: 103921 / Revision: 109384 | | Last Changed Date: 2015-05-18 07:59:06 -0700 (Mon, 18 May 2015) |
| zin2 | Linux (Ubuntu 14.04.2 LTS) / x86_64 | OK | OK | [ OK ] | |  |
| moscato2 | Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 | OK | OK | OK | OK | |
| petty | Mac OS X Snow Leopard (10.6.8) / x86_64 | OK | OK | OK | OK | |
| morelia | Mac OS X Mavericks (10.9.5) / x86_64 | OK | OK | OK | OK | |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.1-bioc/R/bin/R CMD check --no-vignettes --timings ChIPpeakAnno_3.2.2.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.1-bioc/meat/ChIPpeakAnno.Rcheck’
* using R version 3.2.2 (2015-08-14)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘ChIPpeakAnno/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘ChIPpeakAnno’ version ‘3.2.2’
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Depends: includes the non-default packages:
‘grid’ ‘VennDiagram’ ‘biomaRt’ ‘IRanges’ ‘Biostrings’ ‘GenomicRanges’
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 ‘ChIPpeakAnno’ can be installed ... [15s/21s] OK
* checking installed package size ... NOTE
installed size is 11.6Mb
sub-directories of 1Mb or more:
data 9.7Mb
extdata 1.0Mb
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Title field: should not end in a period.
Malformed Description field: should contain one or more complete sentences.
* 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
annotatePeakInBatch: no visible global function definition for
‘seqlevels’
assignChromosomeRegion : formatSeqnames: no visible global function
definition for ‘seqlevels’
assignChromosomeRegion: no visible global function definition for
‘seqlengths’
assignChromosomeRegion: no visible global function definition for
‘seqlevels’
assignChromosomeRegion: no visible global function definition for
‘keepSeqlevels’
findOverlappingPeaks: no visible global function definition for
‘DataFrame’
formatSeqnames: no visible global function definition for ‘seqlevels’
getAllPeakSequence: no visible global function definition for
‘seqlevels’
getAllPeakSequence: no visible global function definition for
‘seqlengths’
getAllPeakSequence: no visible global function definition for
‘seqlengths<-’
getEnrichedGO: no visible global function definition for ‘mappedkeys’
getEnrichedGO : <anonymous>: no visible global function definition for
‘GOID’
getEnrichedGO : <anonymous>: no visible global function definition for
‘Term’
getEnrichedGO : <anonymous>: no visible global function definition for
‘Definition’
getEnrichedGO : <anonymous>: no visible global function definition for
‘Ontology’
getEnrichedPATH: no visible global function definition for ‘mappedkeys’
* 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’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [21s/27s] OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘runTests.R’ [42s/65s]
[43s/66s] 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
Status: 4 NOTEs
See
‘/home/biocbuild/bbs-3.1-bioc/meat/ChIPpeakAnno.Rcheck/00check.log’
for details.
* installing *source* package ‘ChIPpeakAnno’ ...
** R
** data
** inst
** preparing package for lazy loading
Creating a generic function for ‘nchar’ from package ‘base’ in package ‘S4Vectors’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Creating a generic function for ‘nchar’ from package ‘base’ in package ‘S4Vectors’
* DONE (ChIPpeakAnno)