methylPipe 1.6.2
Kamal Kishore
| Snapshot Date: 2016-10-12 17:20:15 -0700 (Wed, 12 Oct 2016) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_3/madman/Rpacks/methylPipe | | Last Changed Rev: 117513 / Revision: 122332 | | Last Changed Date: 2016-05-15 13:18:19 -0700 (Sun, 15 May 2016) |
| zin2 | Linux (Ubuntu 14.04.2 LTS) / x86_64 | OK | OK | [ ERROR ] | | |
| moscato2 | Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 | OK | OK | WARNINGS | OK |  |
| oaxaca | Mac OS X Mavericks (10.9.5) / x86_64 | OK | ERROR | skipped | skipped | |
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### Running command:
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### /home/biocbuild/bbs-3.3-bioc/R/bin/R CMD check --no-vignettes --timings methylPipe_1.6.2.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.3-bioc/meat/methylPipe.Rcheck’
* using R version 3.3.1 (2016-06-21)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘methylPipe/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘methylPipe’ version ‘1.6.2’
* 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 ‘methylPipe’ can be installed ... 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
BSprepare : binomTestMulti: no visible global function definition for
'binom.test'
BSprepare : binomTestMulti : pVfun: no visible global function
definition for 'binom.test'
BSprepare : binomTestMulti: no visible global function definition for
'p.adjust'
chiCombP: no visible global function definition for 'pchisq'
consolidateDMRs: no visible global function definition for 'p.adjust'
plotMeth: no visible global function definition for 'rainbow'
process.hmc: no visible global function definition for 'write.table'
findDMR,BSdataSet : DMRchr: no visible global function definition for
'kruskal.test'
findDMR,BSdataSet : DMRchr: no visible global function definition for
'wilcox.test'
findDMR,BSdataSet: no visible global function definition for
'stopCluster'
findPMDs,BSdata : PMDchr: no visible global function definition for
'segmentPMDs'
mCsmoothing,BSdata: no visible global function definition for
'smooth.spline'
mCsmoothing,BSdata: no visible global function definition for 'box'
mCsmoothing,BSdata: no visible global function definition for 'axis'
mCsmoothing,BSdata: no visible global function definition for 'mtext'
methstats,BSdataSet: no visible global function definition for
'stopCluster'
methstats,BSdataSet : panel.cor: no visible global function definition
for 'par'
methstats,BSdataSet : panel.cor: no visible global function definition
for 'cor.test'
methstats,BSdataSet : panel.cor: no visible global function definition
for 'text'
methstats,BSdataSet : panel.smooth: no visible global function
definition for 'points'
methstats,BSdataSet : panel.smooth: no visible global function
definition for 'lines'
methstats,BSdataSet : panel.hist: no visible global function definition
for 'par'
methstats,BSdataSet : panel.hist: no visible global function definition
for 'hist'
methstats,BSdataSet : panel.hist: no visible global function definition
for 'rect'
methstats,BSdataSet: no visible global function definition for 'pairs'
methstats,BSdataSet: no visible global function definition for 'dist'
methstats,BSdataSet: no visible global function definition for 'hclust'
methstats,BSdataSet: no visible global function definition for
'dev.new'
methstats,BSdataSet: no visible global function definition for 'plot'
show,BSdata: no visible global function definition for 'organism'
show,BSdataSet: no visible global function definition for 'organism'
Undefined global functions or variables:
axis binom.test box cor.test dev.new dist hclust hist kruskal.test
lines mtext organism p.adjust pairs par pchisq plot points rainbow
rect segmentPMDs smooth.spline stopCluster text wilcox.test
write.table
Consider adding
importFrom("grDevices", "dev.new", "rainbow")
importFrom("graphics", "axis", "box", "hist", "lines", "mtext",
"pairs", "par", "plot", "points", "rect", "text")
importFrom("stats", "binom.test", "cor.test", "dist", "hclust",
"kruskal.test", "p.adjust", "pchisq", "smooth.spline",
"wilcox.test")
importFrom("utils", "write.table")
to your NAMESPACE file.
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... WARNING
Undocumented S4 methods:
generic '[' and siglist 'BSdataSet,ANY,ANY,ANY'
generic '[' and siglist 'GElist,ANY,ANY,ANY'
All user-level objects in a package (including S4 classes and methods)
should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking compiled code ... OK
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... ERROR
Running examples in ‘methylPipe-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: plotMeth
> ### Title: Plot DNA methylation together with other omics, or annotation
> ### data for a genomic region
> ### Aliases: plotMeth
>
> ### ** Examples
>
> require(TxDb.Hsapiens.UCSC.hg18.knownGene)
Loading required package: TxDb.Hsapiens.UCSC.hg18.knownGene
Loading required package: GenomicFeatures
Loading required package: AnnotationDbi
> txdb <- TxDb.Hsapiens.UCSC.hg18.knownGene
> require(BSgenome.Hsapiens.UCSC.hg18)
Loading required package: BSgenome.Hsapiens.UCSC.hg18
Loading required package: BSgenome
Loading required package: rtracklayer
> gecH1_file <- system.file('extdata', 'gec.H1.Rdata', package='methylPipe')
> load(gecH1_file)
> gecIMR_file <- system.file('extdata', 'gec.IMR90.Rdata', package='methylPipe')
> load(gecIMR_file)
> gel <- GElist(gecH1=gec.H1, gecIMR90=gec.IMR90)
> uncov_GR <- GRanges(Rle('chr20'), IRanges(c(14350,69251,84185), c(18349,73250,88184)))
> H1data <- system.file('extdata', 'H1_chr20_CG_10k_tabix_out.txt.gz', package='methylPipe')
> H1.db <- BSdata(file=H1data, uncov=uncov_GR, org=Hsapiens)
> IMR90data <- system.file('extdata', 'IMR90_chr20_CG_10k_tabix_out.txt.gz', package='methylPipe')
> IMR90.db <- BSdata(file=IMR90data, uncov=uncov_GR, org=Hsapiens)
> H1.IMR90.set <- list(H1=H1.db, IMR90=IMR90.db)
> plotMeth(gel, colors=c("red","blue"), datatype=c("mC","mC"), yLim=c(.025, .025), brmeth=H1.IMR90.set, mcContext="CG", transcriptDB=txdb, chr="chr20", start=14350 , end=474481, org=Hsapiens)
Error in `genome<-`(`*tmp*`, value = "hg18") :
Failed to set session genome to 'hg18'
Calls: plotMeth ... .doCache -> eval -> eval -> eval -> genome<- -> genome<-
Execution halted
* 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: 1 ERROR, 1 WARNING, 1 NOTE
See
‘/home/biocbuild/bbs-3.3-bioc/meat/methylPipe.Rcheck/00check.log’
for details.