methylumi 2.5.8
Sean Davis
| Snapshot Date: 2013-01-15 17:01:14 -0800 (Tue, 15 Jan 2013) | | URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/methylumi | | Last Changed Rev: 71618 / Revision: 72575 | | Last Changed Date: 2012-12-03 13:43:13 -0800 (Mon, 03 Dec 2012) |
| george2 | Linux (Ubuntu 12.04.1 LTS) / x86_64 | OK | WARNINGS | |
| lamb2 | Linux (openSUSE 11.4) / x86_64 | OK | [ WARNINGS ] | |
| moscato2 | Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 | OK | WARNINGS | OK |
| petty | Mac OS X Leopard (10.5.8) / i386 | OK | WARNINGS | OK |
* using log directory ‘/loc/home/biocbuild/bbs-2.12-bioc/meat/methylumi.Rcheck’
* using R Under development (unstable) (2012-12-17 r61365)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘methylumi/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘methylumi’ version ‘2.5.8’
* 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 ‘methylumi’ can be installed ... OK
* checking installed package size ... NOTE
installed size is 5.2Mb
sub-directories of 1Mb or more:
data 2.7Mb
extdata 1.7Mb
* 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
getBarcodes: warning in list.files(path = path, patt = "idat"): partial
argument match of 'patt' to 'pattern'
methylumIDAT: warning in gsub("_(Red|Grn)", "", barcodes, ignore =
TRUE): partial argument match of 'ignore' to 'ignore.case'
methylumIDAT: warning in gsub(".idat", "", barcodes, ignore = TRUE):
partial argument match of 'ignore' to 'ignore.case'
methylumIDAT2: warning in gsub("_(Red|Grn)", "", barcodes, ignore =
TRUE): partial argument match of 'ignore' to 'ignore.case'
methylumIDAT2: warning in gsub(".idat", "", barcodes, ignore = TRUE):
partial argument match of 'ignore' to 'ignore.case'
normexp.signal: warning in pnorm(0, mean = mu.sf, sd = sigma,
lower.tail = FALSE, log = TRUE): partial argument match of 'log' to
'log.p'
compare.chips: no visible binding for global variable
‘IlluminaHumanMethylation450kCOLOR_CHANNEL’
compare.chips: no visible binding for global variable
‘IlluminaHumanMethylation27kCOLOR_CHANNEL’
compare.chips: no visible binding for global variable ‘chip’
cy3: no visible global function definition for ‘addColorChannelInfo’
cy5: no visible global function definition for ‘addColorChannelInfo’
gamma.get.xcs: no visible global function definition for
‘gamma.integral’
gamma.get.xs : <anonymous>: no visible global function definition for
‘gamma.mle’
gamma.get.xs : <anonymous>: no visible global function definition for
‘gamma.integral’
gamma.signal: no visible global function definition for
‘gamma.integral’
gammaM.get.xs : <anonymous>: no visible global function definition for
‘gamma.mode’
gammaM.get.xs : <anonymous>: no visible global function definition for
‘gamma.mle’
normalize27kAnd450k: no visible binding for global variable
‘history.submitted’
normalizeViaSQN: no visible global function definition for
‘assayDataElements’
normalizeViaSQN: no visible binding for global variable ‘CpGs’
normalizeViaSQN: no visible binding for global variable ‘ctrl.id’
normalizeViaSQN: no visible binding for global variable ‘withins’
normalizeViaSQN: no visible binding for global variable
‘normprobes.Cy3’
normalizeViaSQN: no visible binding for global variable
‘normprobes.Cy5’
plotNegOob: no visible binding for global variable ‘intensity’
plotNegOob: no visible binding for global variable ‘channel.probes’
plotNegOob: no visible binding for global variable ‘..density..’
qc.probe.plot: no visible binding for global variable ‘grouping’
qc.probe.plot: no visible binding for global variable ‘variable’
qc.probe.plot: no visible binding for global variable ‘value’
plotNAs,methylData: no visible binding for global variable ‘index’
plotNAs,methylData: no visible binding for global variable ‘dropouts’
plotProbeNAs,methylData: no visible binding for global variable ‘mu’
plotProbeNAs,methylData: no visible binding for global variable ‘drops’
* checking Rd files ... NOTE
prepare_Rd: estimateM.Rd:34-36: Dropping empty section \seealso
prepare_Rd: estimateM.Rd:37-39: Dropping empty section \examples
prepare_Rd: methylumIDAT.Rd:52-54: Dropping empty section \seealso
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... WARNING
Undocumented S4 methods:
generic 'betas' and siglist 'GenomicMethylSet'
generic 'betas' and siglist 'MethylSet'
generic 'betas' and siglist 'SummarizedExperiment'
generic 'methylated' and siglist 'MethylSet'
generic 'unmethylated' and siglist 'MethylSet'
All user-level objects in a package (including S4 classes and methods)
should have documentation entries.
See the 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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking examples ... 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 vignettes ... SKIPPED
* checking PDF version of manual ... OK
WARNING: There was 1 warning.
NOTE: There were 3 notes.
See
‘/loc/home/biocbuild/bbs-2.12-bioc/meat/methylumi.Rcheck/00check.log’
for details.
* installing *source* package ‘methylumi’ ...
** R
** data
** inst
** preparing package for lazy loading
Warning: replacing previous import ‘image’ when loading ‘graphics’
in method for ‘total.intensity’ with signature ‘object="MethyLumiSet"’: no definition for class “MethyLumiSet”
in method for ‘total.intensity’ with signature ‘object="MethyLumiM"’: no definition for class “MethyLumiM”
in method for ‘intensitiesByChannel’ with signature ‘object="MethyLumiSet"’: no definition for class “MethyLumiSet”
in method for ‘intensitiesByChannel’ with signature ‘object="MethyLumiM"’: no definition for class “MethyLumiM”
in method for ‘Cy3.SD’ with signature ‘object="MethyLumiSet"’: no definition for class “MethyLumiSet”
in method for ‘Cy3.N’ with signature ‘object="MethyLumiSet"’: no definition for class “MethyLumiSet”
in method for ‘Cy5.SD’ with signature ‘object="MethyLumiSet"’: no definition for class “MethyLumiSet”
in method for ‘Cy5.N’ with signature ‘object="MethyLumiSet"’: no definition for class “MethyLumiSet”
in method for ‘negctls’ with signature ‘object="MethyLumiSet",channel="character"’: no definition for class “MethyLumiSet”
in method for ‘negctls’ with signature ‘object="MethyLumiSet",channel="missing"’: no definition for class “MethyLumiSet”
in method for ‘negctls’ with signature ‘object="MethyLumiM",channel="character"’: no definition for class “MethyLumiM”
in method for ‘negctls’ with signature ‘object="MethyLumiM",channel="missing"’: no definition for class “MethyLumiM”
in method for ‘negctls.SD’ with signature ‘object="MethyLumiSet",channel="character"’: no definition for class “MethyLumiSet”
in method for ‘negctls.SD’ with signature ‘object="MethyLumiM",channel="character"’: no definition for class “MethyLumiM”
in method for ‘negctls.stderr’ with signature ‘object="MethyLumiSet",channel="character"’: no definition for class “MethyLumiSet”
in method for ‘negctls.stderr’ with signature ‘object="MethyLumiSet",channel="missing"’: no definition for class “MethyLumiSet”
in method for ‘negnorm’ with signature ‘object="MethyLumiSet",channel="character"’: no definition for class “MethyLumiSet”
in method for ‘negnorm’ with signature ‘object="MethyLumiM",channel="character"’: no definition for class “MethyLumiM”
in method for ‘negnorm’ with signature ‘object="MethyLumiSet",channel="missing"’: no definition for class “MethyLumiSet”
in method for ‘negnorm’ with signature ‘object="MethyLumiM",channel="missing"’: no definition for class “MethyLumiM”
in method for ‘normctls’ with signature ‘object="MethyLumiSet"’: no definition for class “MethyLumiSet”
in method for ‘normctls’ with signature ‘object="MethyLumiM"’: no definition for class “MethyLumiM”
Warning: replacing previous import ‘initialize’ when loading ‘rtracklayer’
Warning: replacing previous import ‘show’ when loading ‘rtracklayer’
** help
*** installing help indices
** building package indices
** installing vignettes
‘methylumi.Rnw’
** testing if installed package can be loaded
Warning: replacing previous import ‘image’ when loading ‘graphics’
* DONE (methylumi)