Back to Multiple platform build/check report for BioC 3.14
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This page was generated on 2022-04-13 12:07:33 -0400 (Wed, 13 Apr 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.1.3 (2022-03-10) -- "One Push-Up" 4324
tokay2Windows Server 2012 R2 Standardx644.1.3 (2022-03-10) -- "One Push-Up" 4077
machv2macOS 10.14.6 Mojavex86_644.1.3 (2022-03-10) -- "One Push-Up" 4137
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

CHECK results for wateRmelon on tokay2


To the developers/maintainers of the wateRmelon package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/wateRmelon.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 2059/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
wateRmelon 2.0.0  (landing page)
Leo C Schalkwyk
Snapshot Date: 2022-04-12 01:55:07 -0400 (Tue, 12 Apr 2022)
git_url: https://git.bioconductor.org/packages/wateRmelon
git_branch: RELEASE_3_14
git_last_commit: f6a331b
git_last_commit_date: 2021-10-26 12:05:45 -0400 (Tue, 26 Oct 2021)
nebbiolo2Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: wateRmelon
Version: 2.0.0
Command: C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:wateRmelon.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings wateRmelon_2.0.0.tar.gz
StartedAt: 2022-04-13 04:45:05 -0400 (Wed, 13 Apr 2022)
EndedAt: 2022-04-13 04:54:07 -0400 (Wed, 13 Apr 2022)
EllapsedTime: 541.8 seconds
RetCode: 0
Status:   OK  
CheckDir: wateRmelon.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:wateRmelon.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings wateRmelon_2.0.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.14-bioc/meat/wateRmelon.Rcheck'
* using R version 4.1.3 (2022-03-10)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'wateRmelon/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'wateRmelon' version '2.0.0'
* 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 ...
** running examples for arch 'i386' ... OK
Examples with CPU (user + system) or elapsed time > 5s
        user system elapsed
sextest 8.44   0.17    8.61
seabi   7.55   0.03    7.58
metrics 5.53   0.87    6.40
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
        user system elapsed
sextest 9.01   0.11    9.12
seabi   7.77   0.03    7.80
metrics 6.59   0.25    6.85
* 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
  'C:/Users/biocbuild/bbs-3.14-bioc/meat/wateRmelon.Rcheck/00check.log'
for details.

Installation output

wateRmelon.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.14/bioc/src/contrib/wateRmelon_2.0.0.tar.gz && rm -rf wateRmelon.buildbin-libdir && mkdir wateRmelon.buildbin-libdir && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=wateRmelon.buildbin-libdir wateRmelon_2.0.0.tar.gz && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL wateRmelon_2.0.0.zip && rm wateRmelon_2.0.0.tar.gz wateRmelon_2.0.0.zip
###
##############################################################################
##############################################################################


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  2 3026k    2 86187    0     0   258k      0  0:00:11 --:--:--  0:00:11  258k
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100 3026k  100 3026k    0     0  1290k      0  0:00:02  0:00:02 --:--:-- 1290k

install for i386

* 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
  converting help for package 'wateRmelon'
    finding HTML links ... done
    BMIQ                                    html  
    Beta2M                                  html  
    adaptRefQuantiles                       html  
    adjustedDasen                           html  
    adjustedFunnorm                         html  
    agep                                    html  
    as.methylumi-methods                    html  
    beadc                                   html  
    beadcount                               html  
    bscon                                   html  
    colnames-methods                        html  
    combo                                   html  
    dasen-MethyLumiSet                      html  
    dasen-MethySet                          html  
    dasen-exprmethy450                      html  
    dasen                                   html  
    db1                                     html  
    dmrse-methods                           html  
    dmrse                                   html  
    dot-getManifestString                   html  
    estimateCellCounts.wmln                 html  
    estimateSex                             html  
    genki-methods                           html  
    genki                                   html  
    genkme                                  html  
    got                                     html  
    iDMR                                    html  
    melon                                   html  
    metrics                                 html  
    outlyx-methods                          html  
    outlyx                                  html  
    pfilter                                 html  
    pwod-methods                            html  
    pwod                                    html  
    qual                                    html  
    readEPIC                                html  
    seabi-methods                           html  
    seabi                                   html  
    seabird                                 html  
    sextest                                 html  
    wateRmelon-package                      html  
    wm_internal                             html  
** 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

install for x64

* installing *source* package 'wateRmelon' ...
** testing if installed package can be loaded
No methods found in package 'RSQLite' for request: 'dbListFields' when loading 'lumi'
* MD5 sums
packaged installation of 'wateRmelon' as wateRmelon_2.0.0.zip
* DONE (wateRmelon)
* installing to library 'C:/Users/biocbuild/bbs-3.14-bioc/R/library'
package 'wateRmelon' successfully unpacked and MD5 sums checked

Tests output

Example timings

wateRmelon.Rcheck/examples_i386/wateRmelon-Ex.timings

nameusersystemelapsed
BMIQ000
adjustedDasen3.190.333.51
adjustedFunnorm000
agep0.300.130.43
bscon0.170.030.20
combo0.450.010.47
dasen2.940.113.05
dmrse2.330.172.50
estimateSex2.340.102.43
genki2.610.222.83
iDMR0.000.010.02
melon0.240.020.25
metrics5.530.876.40
outlyx0.510.190.71
pfilter0.320.000.31
pwod0.530.030.56
qual3.760.274.03
readEPIC000
seabi7.550.037.58
sextest8.440.178.61

wateRmelon.Rcheck/examples_x64/wateRmelon-Ex.timings

nameusersystemelapsed
BMIQ000
adjustedDasen3.420.203.62
adjustedFunnorm000
agep0.230.050.28
bscon0.130.010.14
combo0.400.020.42
dasen2.640.122.77
dmrse1.720.081.79
estimateSex1.30.11.4
genki2.190.112.29
iDMR000
melon0.230.000.23
metrics6.590.256.85
outlyx0.640.020.65
pfilter0.220.030.25
pwod0.430.030.46
qual1.730.141.87
readEPIC000
seabi7.770.037.80
sextest9.010.119.12