CHECK report for methylPipe on celaya2
This page was generated on 2019-10-16 12:53:48 -0400 (Wed, 16 Oct 2019).
methylPipe 1.18.0 Kamal Kishore
Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019) |
URL: https://git.bioconductor.org/packages/methylPipe |
Branch: RELEASE_3_9 |
Last Commit: 72edb06 |
Last Changed Date: 2019-05-02 11:53:49 -0400 (Thu, 02 May 2019) |
| malbec2 | Linux (Ubuntu 18.04.2 LTS) / x86_64 | OK | OK | WARNINGS | | |
tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | WARNINGS | OK | |
celaya2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | [ WARNINGS ] | OK | |
Summary
Command output
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### Running command:
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### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:methylPipe.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings methylPipe_1.18.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/methylPipe.Rcheck’
* using R version 3.6.1 (2019-07-05)
* using platform: x86_64-apple-darwin15.6.0 (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 ‘1.18.0’
* 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 ... NOTE
Note: information on .o files is not available
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... WARNING
Found the following significant warnings:
Warning: working directory was changed to '/private/tmp/Rtmp5unUEg', resetting
Examples with CPU or elapsed time > 5s
user system elapsed
plotMeth 33.288 2.222 47.826
findDMR 3.443 6.527 50.654
methstats 1.247 0.574 28.242
findPMDs 0.371 0.503 34.826
* 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: 2 WARNINGs, 2 NOTEs
See
‘/Users/biocbuild/bbs-3.9-bioc/meat/methylPipe.Rcheck/00check.log’
for details.
Installation output
methylPipe.Rcheck/00install.out
Tests output
Example timings
methylPipe.Rcheck/methylPipe-Ex.timings