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### Running command:
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### /home/biocbuild/bbs-3.1-bioc/R/bin/R CMD check --no-vignettes --timings wateRmelon_1.8.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.1-bioc/meat/wateRmelon.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 ‘wateRmelon/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘wateRmelon’ version ‘1.8.0’
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Package which this enhances but not available for checking: ‘IMA’
Depends: includes the non-default packages:
‘limma’ ‘matrixStats’ ‘methylumi’ ‘lumi’ ‘ROC’
‘IlluminaHumanMethylation450kanno.ilmn12.hg19’
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 ‘wateRmelon’ can be installed ... [22s/22s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Package listed in more than one of Depends, Imports, Suggests, Enhances:
‘methylumi’
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 ... WARNING
Invalid citation information in ‘inst/CITATION’:
Error in parse(file = cfile): /home/biocbuild/bbs-3.1-bioc/meat/wateRmelon.Rcheck/00_pkg_src/wateRmelon/inst/CITATION:4:1: unexpected '/'
3: doi = "10.1186/1471-2164-14-293",
4: /
^
* 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' call to ‘methylumi’ which was already attached by Depends.
Please remove these calls from your code.
'library' or 'require' calls in package code:
‘IMA’ ‘minfi’
Please use :: or requireNamespace() instead.
See section 'Suggested packages' in the 'Writing R Extensions' manual.
Packages in Depends field not imported from:
‘IlluminaHumanMethylation450kanno.ilmn12.hg19’ ‘ROC’ ‘limma’ ‘lumi’
‘matrixStats’ ‘methods’ ‘methylumi’
These packages need to be imported from (in the NAMESPACE file)
for when this namespace is loaded but not attached.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
beadcount: no visible global function definition for ‘assayDataElement’
beadcount: no visible global function definition for ‘getProbeInfo’
beadcount: no visible global function definition for ‘getManifestInfo’
beadcount: no visible global function definition for ‘sampleNames’
bgIntensitySwan.methylumi: no visible global function definition for
‘colMedians’
combo: no visible binding for global variable ‘assayData’
combo: no visible binding for global variable ‘pData’
combo: no visible binding for global variable ‘protocolData’
combo: no visible binding for global variable ‘experimentData’
combo : <anonymous>: no visible global function definition for
‘assayData’
combo : <anonymous>: no visible global function definition for ‘QCdata’
combo: no visible global function definition for ‘assayData<-’
combo: no visible global function definition for ‘pData<-’
combo: no visible global function definition for ‘protocolData<-’
combo: no visible global function definition for ‘experimentData<-’
combo: no visible global function definition for ‘QCdata<-’
combo: no visible global function definition for ‘fData<-’
combo: no visible global function definition for ‘fData’
combo: no visible global function definition for ‘annotation<-’
combo: no visible global function definition for ‘annotation’
db1: no visible global function definition for ‘normalizeQuantiles’
detectionPval.filter: no visible global function definition for
‘assayDataElement’
dfort: no visible binding for global variable
‘IlluminaHumanMethylation450kanno.ilmn12.hg19’
filterXY: no visible global function definition for ‘fData’
filterXY: no visible global function definition for ‘featureNames’
genall: no visible global function definition for ‘featureNames’
genall: no visible global function definition for ‘betas’
getMethylumiBeta: no visible global function definition for
‘featureNames’
getMethylumiBeta: no visible global function definition for
‘unmethylated’
getMethylumiBeta: no visible global function definition for
‘methylated’
getSamples: no visible global function definition for ‘sampleNames’
got: no visible global function definition for ‘getProbeInfo’
loadMethylumi2: no visible global function definition for
‘addControlData2methyLumiM’
lumiMethyR2: no visible global function definition for ‘methylumiR’
lumiMethyR2: no visible global function definition for ‘sampleNames’
lumiMethyR2: no visible global function definition for
‘assayDataElement<-’
lumiMethyR2: no visible global function definition for
‘assayDataElement’
lumiMethyR2: no visible global function definition for
‘addAnnotationInfo’
lumiMethyR2: no visible global function definition for ‘controlData<-’
nbBeadsFilter: no visible global function definition for
‘assayDataElement’
nbBeadsFilter: no visible global function definition for
‘assayDataElement<-’
pipelineIlluminaMethylation.batch: possible error in
preprocessIlluminaMethylation(path2data = path2data, path2controlData
= path2controlData, projectName = projectName, nbBeads.threshold =
nbBeads.threshold, detectionPval.threshold = detectionPval.threshold,
detectionPval.perc.threshold = detectionPval.perc.threshold,
sample2keep = path2sampleList, probeSNP_LIST, XY.filtering =
XY.filtering, colorBias.corr = colorBias.corr, bg.adjust = bg.adjust,
PATH = PATH_RES): unused arguments (path2data = path2data,
path2controlData = path2controlData, projectName = projectName)
pipelineIlluminaMethylation.batch: no visible binding for global
variable ‘PATH_RES’
pipelineIlluminaMethylation.batch: no visible global function
definition for ‘assayDataElement’
pipelineIlluminaMethylation.batch: no visible global function
definition for ‘fData’
pipelineIlluminaMethylation.batch: no visible binding for global
variable ‘probeAnnotationsCategory’
preprocessIlluminaMethylation: no visible binding for global variable
‘projectName’
preprocessIlluminaMethylation: no visible global function definition
for ‘sampleNames’
preprocessIlluminaMethylation: no visible global function definition
for ‘featureNames’
preprocessIlluminaMethylation: no visible global function definition
for ‘lumiMethyB’
seabird: no visible global function definition for ‘pAUC’
seabird: no visible global function definition for ‘rocdemo.sca’
BMIQ,MethyLumiSet : .local : <anonymous>: no visible global function
definition for ‘warn’
BMIQ,MethyLumiSet : .local: no visible global function definition for
‘betas<-’
as.methylumi,MethyLumiSet : .local: no visible global function
definition for ‘methylated’
as.methylumi,MethyLumiSet : .local: no visible global function
definition for ‘unmethylated’
as.methylumi,MethyLumiSet : .local: no visible global function
definition for ‘betas’
as.methylumi,MethyLumiSet : .local: no visible global function
definition for ‘pvals’
as.methylumi,MethyLumiSet : .local: no visible global function
definition for ‘QCdata’
as.methylumi,MethylSet : .local: no visible global function definition
for ‘getMeth’
as.methylumi,MethylSet : .local: no visible global function definition
for ‘getUnmeth’
as.methylumi,MethylSet : .local: no visible global function definition
for ‘getBeta’
betaqn,MethyLumiSet: no visible global function definition for
‘betas<-’
betaqn,MethyLumiSet: no visible global function definition for ‘betas’
betaqn,MethylSet: no visible global function definition for ‘getBeta’
betaqn,RGChannelSet: no visible global function definition for
‘getBeta’
colnames,MethyLumiSet: no visible global function definition for
‘methylated’
danen,MethyLumiSet: no visible global function definition for
‘methylated’
danen,MethyLumiSet: no visible global function definition for
‘unmethylated’
danen,MethyLumiSet: no visible global function definition for ‘betas<-’
danen,MethyLumiSet: no visible global function definition for
‘methylated<-’
danen,MethyLumiSet: no visible global function definition for
‘unmethylated<-’
danen,MethylSet: no visible global function definition for ‘getMeth’
danen,MethylSet: no visible global function definition for ‘getUnmeth’
danen,RGChannelSet: no visible global function definition for
‘preprocessRaw’
danes,MethyLumiSet: no visible global function definition for
‘methylated’
danes,MethyLumiSet: no visible global function definition for
‘unmethylated’
danes,MethyLumiSet: no visible global function definition for ‘betas<-’
danes,MethyLumiSet: no visible global function definition for
‘methylated<-’
danes,MethyLumiSet: no visible global function definition for
‘unmethylated<-’
danes,MethylSet : .local: no visible global function definition for
‘getMeth’
danes,MethylSet : .local: no visible global function definition for
‘getUnmeth’
danes,RGChannelSet : .local: no visible global function definition for
‘preprocessRaw’
danet,MethyLumiSet: no visible global function definition for
‘methylated’
danet,MethyLumiSet: no visible global function definition for
‘unmethylated’
danet,MethyLumiSet: no visible global function definition for ‘betas<-’
danet,MethyLumiSet: no visible global function definition for
‘methylated<-’
danet,MethyLumiSet: no visible global function definition for
‘unmethylated<-’
danet,MethylSet : .local: no visible global function definition for
‘getMeth’
danet,MethylSet : .local: no visible global function definition for
‘getUnmeth’
danet,RGChannelSet : .local: no visible global function definition for
‘preprocessRaw’
dasen,MethyLumiSet : .local: no visible global function definition for
‘methylated’
dasen,MethyLumiSet : .local: no visible global function definition for
‘unmethylated’
dasen,MethyLumiSet : .local: no visible global function definition for
‘betas<-’
dasen,MethyLumiSet : .local: no visible global function definition for
‘methylated<-’
dasen,MethyLumiSet : .local: no visible global function definition for
‘unmethylated<-’
dasen,MethylSet : .local: no visible global function definition for
‘getMeth’
dasen,MethylSet : .local: no visible global function definition for
‘getUnmeth’
dasen,RGChannelSet : .local: no visible global function definition for
‘preprocessRaw’
daten1,MethyLumiSet: no visible global function definition for
‘methylated’
daten1,MethyLumiSet: no visible global function definition for
‘unmethylated’
daten1,MethyLumiSet: no visible global function definition for
‘betas<-’
daten1,MethyLumiSet: no visible global function definition for
‘methylated<-’
daten1,MethyLumiSet: no visible global function definition for
‘unmethylated<-’
daten1,MethylSet: no visible global function definition for ‘getMeth’
daten1,MethylSet: no visible global function definition for ‘getUnmeth’
daten1,RGChannelSet: no visible global function definition for
‘preprocessRaw’
daten2,MethyLumiSet: no visible global function definition for
‘methylated’
daten2,MethyLumiSet: no visible global function definition for
‘unmethylated’
daten2,MethyLumiSet: no visible global function definition for
‘betas<-’
daten2,MethyLumiSet: no visible global function definition for
‘methylated<-’
daten2,MethyLumiSet: no visible global function definition for
‘unmethylated<-’
daten2,MethylSet: no visible global function definition for ‘getMeth’
daten2,MethylSet: no visible global function definition for ‘getUnmeth’
daten2,RGChannelSet : .local: no visible global function definition for
‘preprocessRaw’
dmrse,MethylSet: no visible global function definition for ‘getBeta’
dmrse,RGChannelSet: no visible global function definition for ‘getBeta’
dmrse_col,MethylSet: no visible global function definition for
‘getBeta’
dmrse_col,RGChannelSet: no visible global function definition for
‘getBeta’
dmrse_row,MethylSet: no visible global function definition for
‘getBeta’
dmrse_row,RGChannelSet: no visible global function definition for
‘getBeta’
fuks,MethyLumiSet : .local: no visible global function definition for
‘betas<-’
fuks,MethyLumiSet : .local: no visible global function definition for
‘betas’
fuks,MethylSet : .local: no visible global function definition for
‘getBeta’
fuks,RGChannelSet : .local: no visible global function definition for
‘preprocessRaw’
fuks,RGChannelSet : .local: no visible global function definition for
‘getBeta’
genki,MethyLumiSet : .local: no visible global function definition for
‘betas’
genki,MethylSet : .local: no visible global function definition for
‘getBeta’
genki,RGChannelSet : .local: no visible global function definition for
‘getBeta’
nanes,MethyLumiSet : .local: no visible global function definition for
‘methylated’
nanes,MethyLumiSet : .local: no visible global function definition for
‘unmethylated’
nanes,MethyLumiSet : .local: no visible global function definition for
‘betas<-’
nanes,MethyLumiSet : .local: no visible global function definition for
‘methylated<-’
nanes,MethyLumiSet : .local: no visible global function definition for
‘unmethylated<-’
nanes,MethylSet : .local: no visible global function definition for
‘getMeth’
nanes,MethylSet : .local: no visible global function definition for
‘getUnmeth’
nanes,RGChannelSet : .local: no visible global function definition for
‘preprocessRaw’
nanet,MethyLumiSet : .local: no visible global function definition for
‘methylated’
nanet,MethyLumiSet : .local: no visible global function definition for
‘unmethylated’
nanet,MethyLumiSet : .local: no visible global function definition for
‘betas<-’
nanet,MethyLumiSet : .local: no visible global function definition for
‘methylated<-’
nanet,MethyLumiSet : .local: no visible global function definition for
‘unmethylated<-’
nanet,MethylSet : .local: no visible global function definition for
‘getMeth’
nanet,MethylSet : .local: no visible global function definition for
‘getUnmeth’
nanet,RGChannelSet : .local: no visible global function definition for
‘preprocessRaw’
nasen,MethyLumiSet : .local: no visible global function definition for
‘methylated’
nasen,MethyLumiSet : .local: no visible global function definition for
‘unmethylated’
nasen,MethyLumiSet : .local: no visible global function definition for
‘betas<-’
nasen,MethyLumiSet : .local: no visible global function definition for
‘methylated<-’
nasen,MethyLumiSet : .local: no visible global function definition for
‘unmethylated<-’
nasen,MethylSet : .local: no visible global function definition for
‘getMeth’
nasen,MethylSet : .local: no visible global function definition for
‘getUnmeth’
nasen,RGChannelSet : .local: no visible global function definition for
‘preprocessRaw’
naten,MethyLumiSet : .local: no visible global function definition for
‘methylated’
naten,MethyLumiSet : .local: no visible global function definition for
‘unmethylated’
naten,MethyLumiSet : .local: no visible global function definition for
‘betas<-’
naten,MethyLumiSet : .local: no visible global function definition for
‘methylated<-’
naten,MethyLumiSet : .local: no visible global function definition for
‘unmethylated<-’
naten,MethylSet : .local: no visible global function definition for
‘getMeth’
naten,MethylSet : .local: no visible global function definition for
‘getUnmeth’
naten,RGChannelSet : .local: no visible global function definition for
‘preprocessRaw’
pfilter,MethyLumiSet : .local: no visible global function definition
for ‘betas’
pfilter,MethyLumiSet : .local: no visible global function definition
for ‘methylated’
pfilter,MethyLumiSet : .local: no visible global function definition
for ‘unmethylated’
pfilter,MethyLumiSet : .local: no visible global function definition
for ‘pvals’
pfilter,RGChannelSetExtended : .local: no visible binding for global
variable ‘RGChannelSetExtended’
pfilter,RGChannelSetExtended : .local: no visible global function
definition for ‘detectionP’
seabi,MethyLumiSet: no visible global function definition for ‘betas’
seabi,MethylSet: no visible global function definition for ‘getBeta’
seabi,RGChannelSet: no visible global function definition for ‘getBeta’
seabi,exprmethy450: no visible binding for global variable ‘object’
swan,MethyLumiSet : .local: no visible global function definition for
‘methylated’
swan,MethyLumiSet : .local: no visible global function definition for
‘unmethylated’
swan,MethyLumiSet : .local: no visible global function definition for
‘intensitiesByChannel’
swan,MethyLumiSet : .local: no visible global function definition for
‘QCdata’
swan,MethyLumiSet : .local: no visible global function definition for
‘getBeta’
swan,MethyLumiSet : .local: no visible global function definition for
‘getMeth’
swan,MethyLumiSet : .local: no visible global function definition for
‘getUnmeth’
swan,MethyLumiSet : .local: no visible global function definition for
‘fData<-’
swan,MethyLumiSet : .local: no visible global function definition for
‘fData’
swan,MethyLumiSet : .local: no visible global function definition for
‘betas’
swan,RGChannelSet : .local: no visible global function definition for
‘preprocessSWAN’
tost,MethyLumiSet : .local: no visible global function definition for
‘methylated’
tost,MethyLumiSet : .local: no visible global function definition for
‘betas<-’
tost,MethyLumiSet : .local: no visible global function definition for
‘unmethylated’
tost,MethyLumiSet : .local: no visible global function definition for
‘featureNames’
tost,MethyLumiSet : .local: no visible global function definition for
‘pvals’
tost,RGChannelSet : .local: no visible global function definition for
‘detectionP’
tost,RGChannelSet : .local: no visible global function definition for
‘preprocessRaw’
tost,RGChannelSet : .local: no visible global function definition for
‘getMeth’
tost,RGChannelSet : .local: no visible global function definition for
‘getUnmeth’
tost,RGChannelSet : .local: no visible global function definition for
‘featureNames’
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... WARNING
Undocumented code objects:
‘anSNP’ ‘aoget’ ‘dfort’ ‘genall’ ‘genme’ ‘genus’ ‘goodSNP’ ‘qual’
All user-level objects in a package should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* checking for code/documentation mismatches ... WARNING
Functions or methods with usage in documentation object 'got' but not in code:
pop
Codoc mismatches from documentation object 'dasen':
danes
Code: function(mn, un, onetwo, fudge = 100, ret2 = FALSE, ...)
Docs: function(mn, un, onetwo, fudge = 100, ...)
Argument names in code not in docs:
ret2
Mismatches in argument names:
Position: 5 Code: ret2 Docs: ...
* 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 ... [50s/50s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
sextest 11.454 0.011 11.477
seabi 9.351 0.004 9.407
metrics 6.673 0.036 6.705
* 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: 3 WARNINGs, 4 NOTEs
See
‘/home/biocbuild/bbs-3.1-bioc/meat/wateRmelon.Rcheck/00check.log’
for details.
