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### Running command:
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### /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:wateRmelon.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings wateRmelon_1.27.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.9-bioc/meat/wateRmelon.Rcheck’
* using R Under development (unstable) (2019-03-18 r76245)
* 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 ‘1.27.0’
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Depends: includes the non-default packages:
'Biobase', 'limma', 'matrixStats', 'methylumi', 'lumi', 'ROC',
'IlluminaHumanMethylation450kanno.ilmn12.hg19', 'illuminaio'
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 ... WARNING
Found the following significant warnings:
Note: possible error in 'preprocessIlluminaMethylation(path2data = path2data, ': unused arguments (path2data = path2data, path2controlData = path2controlData, projectName = projectName)
See ‘/home/biocbuild/bbs-3.9-bioc/meat/wateRmelon.Rcheck/00install.out’ for details.
Information on the location(s) of code generating the ‘Note’s can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to ‘yes’.
* 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:
‘Biobase’
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' call to ‘irlba’ in package code.
Please use :: or requireNamespace() instead.
See section 'Suggested packages' in the 'Writing R Extensions' manual.
Packages in Depends field not imported from:
‘matrixStats’ ‘methylumi’
These packages need to be imported from (in the NAMESPACE file)
for when this namespace is loaded but not attached.
Unexported objects imported by ':::' calls:
‘minfi:::.isRGOrStop’ ‘minfi:::pickCompProbes’
‘minfi:::projectCellType’
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
IDATsToMatrices2: no visible global function definition for ‘.mclapply’
NChannelSetToMethyLumiSet2: no visible global function definition for
‘betas’
NChannelSetToMethyLumiSet2: no visible global function definition for
‘methylated’
NChannelSetToMethyLumiSet2: no visible global function definition for
‘unmethylated’
NChannelSetToMethyLumiSet2: no visible global function definition for
‘pval.detect<-’
beadcount: no visible global function definition for ‘getNBeads’
beadcount: no visible global function definition for ‘getProbeInfo’
beadcount: no visible global function definition for ‘getManifestInfo’
bgIntensitySwan.methylumi: no visible global function definition for
‘colMedians’
bscon_methy: no visible global function definition for
‘intensitiesByChannel’
bscon_methy: no visible global function definition for ‘QCdata’
bscon_minfi : csp.green: no visible global function definition for
‘getRed’
bscon_minfi : csp.green: no visible global function definition for
‘getGreen’
bscon_minfi : csp.green : <anonymous>: no visible global function
definition for ‘getControlAddress’
bscon_minfi : csp.red: no visible global function definition for
‘getRed’
bscon_minfi : csp.red: no visible global function definition for
‘getGreen’
bscon_minfi : csp.red : <anonymous>: no visible global function
definition for ‘getControlAddress’
combo : <anonymous>: no visible global function definition for ‘QCdata’
combo: no visible global function definition for ‘QCdata<-’
dfort: no visible binding for global variable
‘IlluminaHumanMethylation450kanno.ilmn12.hg19’
estimateCellCounts.wmln: no visible global function definition for
‘colData’
estimateCellCounts.wmln: no visible global function definition for
‘methylated’
estimateCellCounts.wmln: no visible global function definition for
‘unmethylated’
estimateCellCounts.wmln: no visible global function definition for
‘betas’
estimateCellCounts.wmln: no visible global function definition for
‘preprocessRaw’
estimateCellCounts.wmln: no visible global function definition for
‘getProbeType’
estimateCellCounts.wmln: no visible global function definition for
‘getMeth’
estimateCellCounts.wmln: no visible global function definition for
‘getUnmeth’
genall: no visible global function definition for ‘betas’
generateManifest: no visible global function definition for
‘getAnnotationObject’
generateManifest: no visible global function definition for
‘getAnnotation’
generateManifest: no visible global function definition for
‘getProbeInfo’
getMethylationBeadMappers2 : <anonymous>: no visible binding for global
variable ‘hm27.ordering’
getMethylationBeadMappers2 : <anonymous>: no visible binding for global
variable ‘hm450.ordering’
getMethylationBeadMappers2 : <anonymous>: no visible binding for '<<-'
assignment to ‘epic.ordering’
getMethylationBeadMappers2 : <anonymous>: no visible binding for global
variable ‘epic.ordering’
getMethylationBeadMappers2 : <anonymous>: no visible binding for global
variable ‘hm27.controls’
getMethylationBeadMappers2 : <anonymous>: no visible binding for global
variable ‘hm450.controls’
getMethylationBeadMappers2 : <anonymous>: no visible binding for global
variable ‘epic.controls’
getMethylumiBeta: no visible global function definition for
‘unmethylated’
getMethylumiBeta: no visible global function definition for
‘methylated’
got: no visible global function definition for ‘getProbeInfo’
lumiMethyR2: no visible global function definition for ‘methylumiR’
oxyscale: no visible global function definition for ‘betas’
oxyscale: no visible global function definition for ‘betas<-’
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 binding for global
variable ‘probeAnnotationsCategory’
predictSex: no visible global function definition for ‘colMedians’
predictSex: no visible global function definition for ‘prcomp_irlba’
preprocessIlluminaMethylation: no visible binding for global variable
‘projectName’
readEPIC: no visible binding for global variable ‘n.sd’
BMIQ,MethyLumiSet : <anonymous>: no visible global function definition
for ‘warn’
BMIQ,MethyLumiSet: no visible global function definition for ‘betas<-’
BMIQ,MethylSet: no visible global function definition for ‘getBeta’
BMIQ,MethylSet : <anonymous>: no visible global function definition for
‘warn’
agep,MethylSet: no visible global function definition for ‘getBeta’
as.methylumi,MethyLumiSet: no visible global function definition for
‘methylated’
as.methylumi,MethyLumiSet: no visible global function definition for
‘unmethylated’
as.methylumi,MethyLumiSet: no visible global function definition for
‘betas’
as.methylumi,MethyLumiSet: no visible global function definition for
‘pvals’
as.methylumi,MethyLumiSet: no visible global function definition for
‘QCdata’
as.methylumi,MethylSet: no visible global function definition for
‘getMeth’
as.methylumi,MethylSet: no visible global function definition for
‘getUnmeth’
as.methylumi,MethylSet: no visible global function definition for
‘getBeta’
as.methylumi,MethylSet: no visible global function definition for
‘getAnnotation’
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,MethylSet: no visible global function definition for ‘MethylSet’
danen,MethylSet: no visible global function definition for ‘colData’
danen,MethylSet: no visible global function definition for ‘metadata’
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: no visible global function definition for ‘getMeth’
danes,MethylSet: no visible global function definition for ‘getUnmeth’
danes,MethylSet: no visible global function definition for ‘MethylSet’
danes,MethylSet: no visible global function definition for ‘colData’
danes,MethylSet: no visible global function definition for ‘metadata’
danes,RGChannelSet: 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: no visible global function definition for ‘getMeth’
danet,MethylSet: no visible global function definition for ‘getUnmeth’
danet,MethylSet: no visible global function definition for ‘MethylSet’
danet,MethylSet: no visible global function definition for ‘colData’
danet,MethylSet: no visible global function definition for ‘metadata’
danet,RGChannelSet: no visible global function definition for
‘preprocessRaw’
dasen,MethyLumiSet: no visible global function definition for
‘methylated’
dasen,MethyLumiSet: no visible global function definition for
‘unmethylated’
dasen,MethyLumiSet: no visible global function definition for ‘betas<-’
dasen,MethyLumiSet: no visible global function definition for
‘methylated<-’
dasen,MethyLumiSet: no visible global function definition for
‘unmethylated<-’
dasen,MethylSet: no visible global function definition for ‘getMeth’
dasen,MethylSet: no visible global function definition for ‘getUnmeth’
dasen,MethylSet: no visible global function definition for ‘MethylSet’
dasen,MethylSet: no visible global function definition for ‘colData’
dasen,MethylSet: no visible global function definition for ‘metadata’
dasen,RGChannelSet: 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,MethylSet: no visible global function definition for ‘MethylSet’
daten1,MethylSet: no visible global function definition for ‘colData’
daten1,MethylSet: no visible global function definition for ‘metadata’
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,MethylSet: no visible global function definition for ‘MethylSet’
daten2,MethylSet: no visible global function definition for ‘colData’
daten2,MethylSet: no visible global function definition for ‘metadata’
daten2,RGChannelSet: 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: no visible global function definition for ‘betas<-’
fuks,MethyLumiSet: no visible global function definition for ‘betas’
fuks,MethylSet: no visible global function definition for ‘getBeta’
fuks,RGChannelSet: no visible global function definition for
‘preprocessRaw’
fuks,RGChannelSet: no visible global function definition for ‘getBeta’
genki,MethyLumiSet: no visible global function definition for ‘betas’
genki,MethylSet: no visible global function definition for ‘getBeta’
genki,RGChannelSet: no visible global function definition for
‘getSnpBeta’
nanes,MethyLumiSet: no visible global function definition for
‘methylated’
nanes,MethyLumiSet: no visible global function definition for
‘unmethylated’
nanes,MethyLumiSet: no visible global function definition for ‘betas<-’
nanes,MethyLumiSet: no visible global function definition for
‘methylated<-’
nanes,MethyLumiSet: no visible global function definition for
‘unmethylated<-’
nanes,MethylSet: no visible global function definition for ‘getMeth’
nanes,MethylSet: no visible global function definition for ‘getUnmeth’
nanes,MethylSet: no visible global function definition for ‘MethylSet’
nanes,MethylSet: no visible global function definition for ‘colData’
nanes,MethylSet: no visible global function definition for ‘metadata’
nanes,RGChannelSet: no visible global function definition for
‘preprocessRaw’
nanet,MethyLumiSet: no visible global function definition for
‘methylated’
nanet,MethyLumiSet: no visible global function definition for
‘unmethylated’
nanet,MethyLumiSet: no visible global function definition for ‘betas<-’
nanet,MethyLumiSet: no visible global function definition for
‘methylated<-’
nanet,MethyLumiSet: no visible global function definition for
‘unmethylated<-’
nanet,MethylSet: no visible global function definition for ‘getMeth’
nanet,MethylSet: no visible global function definition for ‘getUnmeth’
nanet,MethylSet: no visible global function definition for ‘MethylSet’
nanet,MethylSet: no visible global function definition for ‘colData’
nanet,MethylSet: no visible global function definition for ‘metadata’
nanet,RGChannelSet: no visible global function definition for
‘preprocessRaw’
nasen,MethyLumiSet: no visible global function definition for
‘methylated’
nasen,MethyLumiSet: no visible global function definition for
‘unmethylated’
nasen,MethyLumiSet: no visible global function definition for ‘betas<-’
nasen,MethyLumiSet: no visible global function definition for
‘methylated<-’
nasen,MethyLumiSet: no visible global function definition for
‘unmethylated<-’
nasen,MethylSet: no visible global function definition for ‘getMeth’
nasen,MethylSet: no visible global function definition for ‘getUnmeth’
nasen,MethylSet: no visible global function definition for ‘MethylSet’
nasen,MethylSet: no visible global function definition for ‘colData’
nasen,MethylSet: no visible global function definition for ‘metadata’
nasen,RGChannelSet: no visible global function definition for
‘preprocessRaw’
naten,MethyLumiSet: no visible global function definition for
‘methylated’
naten,MethyLumiSet: no visible global function definition for
‘unmethylated’
naten,MethyLumiSet: no visible global function definition for ‘betas<-’
naten,MethyLumiSet: no visible global function definition for
‘methylated<-’
naten,MethyLumiSet: no visible global function definition for
‘unmethylated<-’
naten,MethylSet: no visible global function definition for ‘getMeth’
naten,MethylSet: no visible global function definition for ‘getUnmeth’
naten,MethylSet: no visible global function definition for ‘MethylSet’
naten,MethylSet: no visible global function definition for ‘colData’
naten,MethylSet: no visible global function definition for ‘metadata’
naten,RGChannelSet: no visible global function definition for
‘preprocessRaw’
outlyx,MethyLumiSet: no visible global function definition for ‘betas’
outlyx,MethylSet: no visible global function definition for ‘getBeta’
outlyx,RGChannelSet: no visible global function definition for
‘getBeta’
pfilter,MethyLumiSet: no visible global function definition for ‘betas’
pfilter,MethyLumiSet: no visible global function definition for
‘methylated’
pfilter,MethyLumiSet: no visible global function definition for
‘unmethylated’
pfilter,MethyLumiSet: no visible global function definition for ‘pvals’
pfilter,RGChannelSetExtended: no visible binding for global variable
‘RGChannelSetExtended’
pfilter,RGChannelSetExtended: no visible global function definition for
‘preprocessRaw’
pfilter,RGChannelSetExtended: no visible global function definition for
‘detectionP’
pwod,MethyLumiSet: no visible global function definition for ‘betas’
pwod,MethyLumiSet: no visible global function definition for ‘betas<-’
pwod,MethylSet: no visible global function definition for ‘getBeta’
pwod,RGChannelSet: no visible global function definition for ‘getBeta’
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’
swan,MethyLumiSet: no visible global function definition for
‘methylated’
swan,MethyLumiSet: no visible global function definition for
‘unmethylated’
swan,MethyLumiSet: no visible global function definition for
‘intensitiesByChannel’
swan,MethyLumiSet: no visible global function definition for ‘QCdata’
swan,MethyLumiSet: no visible global function definition for ‘getBeta’
swan,MethyLumiSet: no visible global function definition for ‘getMeth’
swan,MethyLumiSet: no visible global function definition for
‘getUnmeth’
swan,MethyLumiSet: no visible global function definition for ‘betas’
swan,RGChannelSet: no visible global function definition for
‘preprocessSWAN’
tost,MethyLumiSet: no visible global function definition for
‘methylated’
tost,MethyLumiSet: no visible global function definition for ‘betas<-’
tost,MethyLumiSet: no visible global function definition for
‘unmethylated’
tost,MethyLumiSet: no visible global function definition for ‘pvals’
tost,RGChannelSet: no visible global function definition for
‘detectionP’
tost,RGChannelSet: no visible global function definition for
‘preprocessRaw’
tost,RGChannelSet: no visible global function definition for ‘getMeth’
tost,RGChannelSet: no visible global function definition for
‘getUnmeth’
Undefined global functions or variables:
.mclapply IlluminaHumanMethylation450kanno.ilmn12.hg19 MethylSet
PATH_RES QCdata QCdata<- RGChannelSetExtended betas betas<- colData
colMedians detectionP epic.controls epic.ordering getAnnotation
getAnnotationObject getBeta getControlAddress getGreen
getManifestInfo getMeth getNBeads getProbeInfo getProbeType getRed
getSnpBeta getUnmeth hm27.controls hm27.ordering hm450.controls
hm450.ordering intensitiesByChannel metadata methylated methylated<-
methylumiR n.sd prcomp_irlba preprocessRaw preprocessSWAN
probeAnnotationsCategory projectName pval.detect<- pvals unmethylated
unmethylated<- warn
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
sextest 10.099 0.008 10.109
seabi 8.326 0.004 8.331
metrics 5.785 0.072 5.869
* 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 ... WARNING
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
LaTeX errors found:
! LaTeX Error: Something's wrong--perhaps a missing \item.
See the LaTeX manual or LaTeX Companion for explanation.
Type H <return> for immediate help.
...
* checking PDF version of manual without hyperrefs or index ... ERROR
* DONE
Status: 1 ERROR, 2 WARNINGs, 4 NOTEs
See
‘/home/biocbuild/bbs-3.9-bioc/meat/wateRmelon.Rcheck/00check.log’
for details.