Back to Build/check report for BioC 3.17
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This page was generated on 2023-01-02 09:00:56 -0500 (Mon, 02 Jan 2023).

HostnameOSArch (*)R versionInstalled pkgs
palomino5Windows Server 2022 Datacenterx64R Under development (unstable) (2022-12-25 r83502 ucrt) -- "Unsuffered Consequences" 4165
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CHECK results for wateRmelon on palomino5


To the developers/maintainers of the wateRmelon package:
Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 2133/2158HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
wateRmelon 2.5.0  (landing page)
Leo C Schalkwyk
Snapshot Date: 2022-12-28 11:00:06 -0500 (Wed, 28 Dec 2022)
git_url: https://git.bioconductor.org/packages/wateRmelon
git_branch: master
git_last_commit: 7cac6c6
git_last_commit_date: 2022-11-01 11:07:41 -0500 (Tue, 01 Nov 2022)
palomino5Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  

Summary

Package: wateRmelon
Version: 2.5.0
Command: F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:wateRmelon.install-out.txt --library=F:\biocbuild\bbs-3.17-bioc\R\library --no-vignettes --timings wateRmelon_2.5.0.tar.gz
StartedAt: 2022-12-29 04:32:35 -0500 (Thu, 29 Dec 2022)
EndedAt: 2022-12-29 04:37:50 -0500 (Thu, 29 Dec 2022)
EllapsedTime: 315.3 seconds
RetCode: 0
Status:   OK  
CheckDir: wateRmelon.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:wateRmelon.install-out.txt --library=F:\biocbuild\bbs-3.17-bioc\R\library --no-vignettes --timings wateRmelon_2.5.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'F:/biocbuild/bbs-3.17-bioc-rtools43/meat/wateRmelon.Rcheck'
* using R Under development (unstable) (2022-12-25 r83502 ucrt)
* using platform: x86_64-w64-mingw32 (64-bit)
* R was compiled by
    gcc.exe (GCC) 10.4.0
    GNU Fortran (GCC) 10.4.0
* running under: Windows Server x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'wateRmelon/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'wateRmelon' version '2.5.0'
* 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 whether package 'wateRmelon' can be installed ... 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:
  '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
Packages in Depends field not imported from:
  'IlluminaHumanMethylation450kanno.ilmn12.hg19' '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:::.annoGet' 'minfi:::.availableAnnotation'
  'minfi:::.isRGOrStop'
  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
.adjusted_normalizeFunnorm450k : unbiased_normalizeQuantiles: no
  visible global function definition for 'colQuantiles'
.adjusted_normalizeFunnorm450k: no visible global function definition
  for 'getMeth'
.adjusted_normalizeFunnorm450k: no visible global function definition
  for 'getUnmeth'
.adjusted_normalizeFunnorm450k: no visible global function definition
  for 'assay<-'
.buildControlMatrix450k: no visible global function definition for
  'colMeans2'
.extractFromRGSet450k: no visible global function definition for
  'getProbeInfo'
.extractFromRGSet450k: no visible global function definition for
  'getRed'
.extractFromRGSet450k: no visible global function definition for
  'getGreen'
.extractFromRGSet450k: no visible global function definition for
  'getOOB'
.extractFromRGSet450k: no visible global function definition for
  'colQuantiles'
.getFunnormIndices: no visible global function definition for
  'getProbeType'
.getFunnormIndices: no visible global function definition for
  'seqnames'
.isMatrixBacked: no visible global function definition for 'assays'
.regularizeQuantiles: no visible global function definition for
  'colCummaxs'
.returnFit: no visible global function definition for 'rowMeans2'
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<-'
adjustedFunnorm: no visible global function definition for
  'preprocessNoob'
adjustedFunnorm: no visible global function definition for
  'mapToGenome'
adjustedFunnorm: no visible global function definition for 'addSex'
adjustedFunnorm: no visible global function definition for 'getSex'
adjustedFunnorm: no visible global function definition for 'getCN'
adjustedFunnorm: no visible global function definition for 'assay<-'
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'
estimateSex: no visible binding for global variable 'sex_coef'
estimateSex: no visible global function definition for 'colSds'
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<-'
p_dfsfit: no visible global function definition for 'mclapply'
pipelineIlluminaMethylation.batch: no visible binding for global
  variable 'PATH_RES'
pipelineIlluminaMethylation.batch: no visible binding for global
  variable 'probeAnnotationsCategory'
preprocessIlluminaMethylation: no visible binding for global variable
  'projectName'
readEPIC: no visible binding for global variable 'n.sd'
sort_order: no visible binding for global variable 'i'
sort_order: no visible binding for global variable 'n_1'
uSexQNengine: no visible global function definition for 'mclapply'
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'
adjustedDasen,MethyLumiSet: no visible global function definition for
  'methylated'
adjustedDasen,MethyLumiSet: no visible global function definition for
  'unmethylated'
adjustedDasen,MethyLumiSet: no visible binding for global variable 'ds'
adjustedDasen,MethyLumiSet: no visible global function definition for
  'betas<-'
adjustedDasen,MethyLumiSet: no visible global function definition for
  'methylated<-'
adjustedDasen,MethyLumiSet: no visible global function definition for
  'unmethylated<-'
adjustedDasen,MethylSet: no visible global function definition for
  'getMeth'
adjustedDasen,MethylSet: no visible global function definition for
  'getUnmeth'
adjustedDasen,MethylSet: no visible global function definition for
  'getAnnotation'
adjustedDasen,MethylSet: no visible global function definition for
  'MethylSet'
adjustedDasen,MethylSet: no visible global function definition for
  'colData'
adjustedDasen,MethylSet: no visible global function definition for
  'metadata'
adjustedDasen,RGChannelSet: no visible global function definition for
  'preprocessRaw'
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'
estimateCellCounts.wateRmelon,MethylSet: no visible global function
  definition for 'getManifest'
estimateCellCounts.wateRmelon,MethylSet: no visible global function
  definition for 'getMeth'
estimateCellCounts.wateRmelon,MethylSet: no visible global function
  definition for 'getUnmeth'
estimateCellCounts.wateRmelon,MethylSet: no visible global function
  definition for 'getBeta'
estimateCellCounts.wateRmelon,RGChannelSet: no visible global function
  definition for 'getManifest'
estimateCellCounts.wateRmelon,RGChannelSet: no visible global function
  definition for 'preprocessRaw'
estimateCellCounts.wateRmelon,RGChannelSet: no visible global function
  definition for 'getMeth'
estimateCellCounts.wateRmelon,RGChannelSet: no visible global function
  definition for 'getUnmeth'
estimateCellCounts.wateRmelon,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'
pfilter,RGChannelSetExtended: no visible global function definition for
  'subsetByLoci'
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'
uSexQN,MethyLumiSet: no visible global function definition for
  'methylated'
uSexQN,MethyLumiSet: no visible global function definition for
  'unmethylated'
uSexQN,MethyLumiSet: no visible global function definition for
  'betas<-'
uSexQN,MethyLumiSet: no visible global function definition for
  'methylated<-'
uSexQN,MethyLumiSet: no visible global function definition for
  'unmethylated<-'
uSexQN,MethylSet: no visible global function definition for 'getMeth'
uSexQN,MethylSet: no visible global function definition for 'getUnmeth'
uSexQN,MethylSet: no visible global function definition for
  'getAnnotation'
uSexQN,MethylSet: no visible global function definition for 'MethylSet'
uSexQN,MethylSet: no visible global function definition for 'colData'
uSexQN,MethylSet: no visible global function definition for 'metadata'
uSexQN,RGChannelSet: no visible global function definition for
  'preprocessRaw'
Undefined global functions or variables:
  .mclapply IlluminaHumanMethylation450kanno.ilmn12.hg19 MethylSet
  PATH_RES QCdata QCdata<- RGChannelSetExtended addSex assay<- assays
  betas betas<- colCummaxs colData colMeans2 colMedians colQuantiles
  colSds detectionP ds epic.controls epic.ordering getAnnotation
  getAnnotationObject getBeta getCN getControlAddress getGreen
  getManifest getManifestInfo getMeth getNBeads getOOB getProbeInfo
  getProbeType getRed getSex getSnpBeta getUnmeth hm27.controls
  hm27.ordering hm450.controls hm450.ordering i intensitiesByChannel
  mapToGenome mclapply metadata methylated methylated<- methylumiR n.sd
  n_1 preprocessNoob preprocessRaw preprocessSWAN
  probeAnnotationsCategory projectName pval.detect<- pvals rowMeans2
  seqnames sex_coef subsetByLoci 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 files in 'vignettes' ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
        user system elapsed
sextest 7.59   0.24    7.83
* 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: 4 NOTEs
See
  'F:/biocbuild/bbs-3.17-bioc-rtools43/meat/wateRmelon.Rcheck/00check.log'
for details.

Installation output

wateRmelon.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD INSTALL wateRmelon
###
##############################################################################
##############################################################################


* installing to library 'F:/biocbuild/bbs-3.17-bioc/R/library'
* installing *source* package 'wateRmelon' ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
No methods found in package 'RSQLite' for request: 'dbListFields' when loading 'lumi'
Creating a generic function from function 'as.methylumi' in package 'wateRmelon'
Creating a generic function from function 'adjustedDasen' in package 'wateRmelon'
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
No methods found in package 'RSQLite' for request: 'dbListFields' when loading 'lumi'
** testing if installed package can be loaded from final location
No methods found in package 'RSQLite' for request: 'dbListFields' when loading 'lumi'
** testing if installed package keeps a record of temporary installation path
* DONE (wateRmelon)

Tests output

Example timings

wateRmelon.Rcheck/wateRmelon-Ex.timings

nameusersystemelapsed
BMIQ000
adjustedDasen3.110.193.29
adjustedFunnorm000
agep0.170.080.25
bscon0.110.000.11
combo0.430.020.45
dasen1.270.061.33
dmrse1.380.011.39
estimateSex1.060.081.14
genki1.480.021.50
iDMR0.000.010.02
melon0.140.020.15
metrics3.610.083.69
outlyx0.440.030.47
pfilter0.160.030.19
pwod0.280.000.28
qual1.280.081.36
readEPIC000
seabi4.780.094.87
sextest7.590.247.83