methylumi 2.16.0
Sean Davis
| Snapshot Date: 2016-04-22 16:20:12 -0700 (Fri, 22 Apr 2016) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_2/madman/Rpacks/methylumi | | Last Changed Rev: 109589 / Revision: 116712 | | Last Changed Date: 2015-10-13 12:36:05 -0700 (Tue, 13 Oct 2015) |
| zin1 | Linux (Ubuntu 14.04.2 LTS) / x86_64 | OK | OK | WARNINGS | |  |
| moscato1 | Windows Server 2008 R2 Standard (64-bit) / x64 | OK | OK | WARNINGS | OK | |
| oaxaca | Mac OS X Mavericks (10.9.5) / x86_64 | OK | OK | [ WARNINGS ] | 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 methylumi_2.16.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.2-bioc/meat/methylumi.Rcheck’
* using R version 3.2.4 (2016-03-10)
* using platform: x86_64-apple-darwin13.4.0 (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 ‘2.16.0’
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Depends: includes the non-default packages:
‘Biobase’ ‘scales’ ‘reshape2’ ‘ggplot2’ ‘matrixStats’
‘FDb.InfiniumMethylation.hg19’ ‘minfi’
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 ‘methylumi’ can be installed ... [32s/32s] WARNING
Found the following significant warnings:
Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Users/biocbuild/bbs-3.2-bioc/meat/methylumi.Rcheck/00install.out’ for details.
* checking installed package size ... NOTE
installed size is 9.7Mb
sub-directories of 1Mb or more:
data 6.8Mb
extdata 1.7Mb
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Packages listed in more than one of Depends, Imports, Suggests, Enhances:
‘Biobase’ ‘minfi’ ‘lattice’ ‘matrixStats’
A package should be listed in only one of these fields.
* 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' calls to packages already attached by Depends:
‘FDb.InfiniumMethylation.hg19’ ‘ggplot2’ ‘matrixStats’ ‘minfi’
‘reshape2’ ‘scales’
Please remove these calls from your code.
'library' or 'require' calls in package code:
‘Biostrings’ ‘MASS’ ‘lumi’ ‘parallel’ ‘rtracklayer’
Please use :: or requireNamespace() instead.
See section 'Suggested packages' in the 'Writing R Extensions' manual.
Namespace in Imports field not imported from: ‘graphics’
All declared Imports should be used.
Packages in Depends field not imported from:
‘FDb.InfiniumMethylation.hg19’ ‘ggplot2’ ‘matrixStats’ ‘methods’
‘reshape2’ ‘scales’
These packages need to be imported from (in the NAMESPACE file)
for when this namespace is loaded but not attached.
':::' call which should be '::': ‘lumi:::produceMethylationGEOSubmissionFile’
See the note in ?`:::` about the use of this operator.
Unexported objects imported by ':::' calls:
‘Biobase:::unsafeSetSlot’ ‘genefilter:::.findCentralMap’
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
getBarcodes: warning in list.files(path = path, patt = "idat"): partial
argument match of 'patt' to 'pattern'
normexp.signal: warning in pnorm(0, mean = mu.sf, sd = sigma,
lower.tail = FALSE, log = TRUE): partial argument match of 'log' to
'log.p'
.mclapply: no visible global function definition for ‘mclapply’
SEtoGRset: no visible global function definition for ‘GenomicRatioSet’
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’
getMethylationBeadMappers : <anonymous>: no visible binding for global
variable ‘hm27.controls’
getMethylationBeadMappers : <anonymous>: no visible binding for global
variable ‘hm450.controls’
getMethylationBeadMappers : <anonymous>: no visible binding for global
variable ‘hm27.ordering’
getMethylationBeadMappers : <anonymous>: no visible binding for global
variable ‘hm450.ordering’
getPlatform: no visible global function definition for ‘features’
getPlatform: no visible binding for global variable
‘FDb.InfiniumMethylation.hg19’
getPlatform: no visible global function definition for ‘DNAStringSet’
illumina.get.xs: no visible global function definition for
‘colQuantiles’
median.get.xs: no visible global function definition for ‘colMedians’
methylumi.bgcorr: no visible binding for global variable
‘IlluminaHumanMethylation27kCOLORCHANNEL’
methylumi.bgcorr: no visible binding for global variable
‘IlluminaHumanMethylation450kCOLORCHANNEL’
methylumi.diagnostics: no visible binding for global variable
‘IlluminaHumanMethylation27kCOLORCHANNEL’
methylumi.diagnostics: no visible binding for global variable
‘IlluminaHumanMethylation450kCOLORCHANNEL’
methylumi.diagnostics: no visible global function definition for
‘plot.density’
methylumiCSV: no visible global function definition for
‘DFsToNChannelSet’
methylumiToMinfi: no visible global function definition for
‘RGChannelSet’
normexp.get.xs: no visible global function definition for ‘huber’
normexp.get.xs: no visible global function definition for ‘colSds’
plotNegOob : <anonymous>: no visible global function definition for
‘melt’
plotNegOob: no visible global function definition for ‘ggplot’
plotNegOob: no visible global function definition for ‘aes’
plotNegOob: no visible binding for global variable ‘intensity’
plotNegOob: no visible binding for global variable ‘channel.probes’
plotNegOob: no visible global function definition for ‘geom_histogram’
plotNegOob: no visible binding for global variable ‘..density..’
plotNegOob: no visible global function definition for
‘position_identity’
plotNegOob: no visible global function definition for ‘facet_grid’
plotNegOob: no visible global function definition for
‘scale_x_continuous’
plotNegOob: no visible global function definition for
‘scale_y_continuous’
plotNegOob: no visible global function definition for
‘scale_fill_manual’
plotNegOob: no visible global function definition for ‘opts’
plotNegOob: no visible global function definition for ‘theme_bw’
qc.probe.plot: no visible global function definition for ‘log_trans’
qc.probe.plot: no visible global function definition for ‘melt’
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’
qc.probe.plot: no visible global function definition for ‘coord_flip’
qc.probe.plot: no visible global function definition for
‘scale_x_continuous’
qc.probe.plot: no visible global function definition for
‘scale_y_discrete’
qc.probe.plot: no visible global function definition for ‘facet_grid’
qc.probe.plot: no visible global function definition for
‘scale_colour_manual’
qc.probe.plot: no visible global function definition for
‘scale_shape_manual’
qc.probe.plot: no visible global function definition for ‘theme_bw’
coerce,MethyLumiM-MethylSet: no visible global function definition for
‘MethylSet’
coerce,MethyLumiSet-MethylSet: no visible global function definition
for ‘MethylSet’
coerce,RangedSummarizedExperiment-GenomicMethylSet: no visible global
function definition for ‘GenomicMethylSet’
combine27k450k,MethyLumiSet-MethyLumiSet : .local: no visible global
function definition for ‘subsetCommonProbes’
getProbesByChannel,methylData : .local : <anonymous>: no visible
binding for global variable ‘allele’
initialize,MethyLumiQC : .local: ... may be used in an incorrect
context: ‘assayDataNew(...)’
intensities.IB,MethyLumiSet-character: no visible binding for global
variable ‘IlluminaHumanMethylation27kCOLORCHANNEL’
intensities.IB,MethyLumiSet-character: no visible binding for global
variable ‘IlluminaHumanMethylation450kCOLORCHANNEL’
intensities.M,MethyLumiSet-character: no visible binding for global
variable ‘IlluminaHumanMethylation27kCOLORCHANNEL’
intensities.M,MethyLumiSet-character: no visible binding for global
variable ‘IlluminaHumanMethylation450kCOLORCHANNEL’
intensities.OOB.allelic,MethyLumiSet-character-character: no visible
binding for global variable ‘IlluminaHumanMethylation27kCOLORCHANNEL’
intensities.OOB.allelic,MethyLumiSet-character-character: no visible
binding for global variable
‘IlluminaHumanMethylation450kCOLORCHANNEL’
intensities.OOB,MethyLumiSet-character: no visible binding for global
variable ‘IlluminaHumanMethylation27kCOLORCHANNEL’
intensities.OOB,MethyLumiSet-character: no visible binding for global
variable ‘IlluminaHumanMethylation450kCOLORCHANNEL’
intensities.U,MethyLumiSet-character: no visible binding for global
variable ‘IlluminaHumanMethylation27kCOLORCHANNEL’
intensities.U,MethyLumiSet-character: no visible binding for global
variable ‘IlluminaHumanMethylation450kCOLORCHANNEL’
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’
pval.detect<-,methylData-numeric: no visible global function definition
for ‘rowMins’
* checking Rd files ... NOTE
prepare_Rd: estimateM.Rd:34-36: Dropping empty section \seealso
prepare_Rd: estimateM.Rd:37-39: Dropping empty section \examples
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... WARNING
Undocumented code objects:
‘IDATsToMatrices’ ‘IDATtoMatrix’ ‘tcgaPipeline’
Undocumented data sets:
‘mset’
Undocumented S4 methods:
generic '[' and siglist 'MethyLumiM,ANY,ANY,ANY'
generic '[' and siglist 'MethyLumiSet,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 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 ... [19s/19s] 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: 2 WARNINGs, 6 NOTEs
See
‘/Users/biocbuild/bbs-3.2-bioc/meat/methylumi.Rcheck/00check.log’
for details.
* installing *source* package ‘methylumi’ ...
** R
** data
** inst
** preparing package for lazy loading
Warning in rgl.init(initValue, onlyNULL) :
RGL: GLX extension missing on server
Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Warning in rgl.init(initValue, onlyNULL) :
RGL: GLX extension missing on server
Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
* DONE (methylumi)