Leo C Schalkwyk
| Snapshot Date: 2022-03-17 13:55:23 -0400 (Thu, 17 Mar 2022) |
| git_url: https://git.bioconductor.org/packages/wateRmelon |
| git_branch: master |
| git_last_commit: dd5a310 |
| git_last_commit_date: 2021-10-26 12:05:45 -0400 (Tue, 26 Oct 2021) |
| Back to Multiple platform build/check report for BioC 3.15 |
|
This page was generated on 2022-03-18 11:08:58 -0400 (Fri, 18 Mar 2022).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 20.04.4 LTS) | x86_64 | R Under development (unstable) (2022-02-17 r81757) -- "Unsuffered Consequences" | 4334 |
| riesling1 | Windows Server 2019 Standard | x64 | R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences" | 4097 |
| palomino3 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2022-02-17 r81757 ucrt) -- "Unsuffered Consequences" | 4083 |
| merida1 | macOS 10.14.6 Mojave | x86_64 | R Under development (unstable) (2022-03-02 r81842) -- "Unsuffered Consequences" | 4134 |
| 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 | ||||
|
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? here for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 2066/2090 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| wateRmelon 2.1.0 (landing page) Leo C Schalkwyk
| nebbiolo1 | Linux (Ubuntu 20.04.4 LTS) / x86_64 | OK | OK | OK | | ||||||||
| riesling1 | Windows Server 2019 Standard / x64 | OK | OK | OK | OK | |||||||||
| palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| merida1 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | | ||||||||
| Package: wateRmelon |
| Version: 2.1.0 |
| Command: D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:wateRmelon.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings wateRmelon_2.1.0.tar.gz |
| StartedAt: 2022-03-17 20:36:03 -0400 (Thu, 17 Mar 2022) |
| EndedAt: 2022-03-17 20:40:45 -0400 (Thu, 17 Mar 2022) |
| EllapsedTime: 281.1 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: wateRmelon.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:wateRmelon.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings wateRmelon_2.1.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory 'D:/biocbuild/bbs-3.15-bioc/meat/wateRmelon.Rcheck'
* using R Under development (unstable) (2021-11-21 r81221)
* 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 '2.1.0'
* 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 5.63 0.15 5.78
* 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
'D:/biocbuild/bbs-3.15-bioc/meat/wateRmelon.Rcheck/00check.log'
for details.
wateRmelon.Rcheck/00install.out
##############################################################################
##############################################################################
###
### Running command:
###
### D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL wateRmelon
###
##############################################################################
##############################################################################
* installing to library 'D:/biocbuild/bbs-3.15-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
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
* DONE (wateRmelon)
Making 'packages.html' ... done
wateRmelon.Rcheck/wateRmelon-Ex.timings
| name | user | system | elapsed | |
| BMIQ | 0 | 0 | 0 | |
| adjustedDasen | 2.02 | 0.12 | 2.14 | |
| adjustedFunnorm | 0 | 0 | 0 | |
| agep | 0.14 | 0.05 | 0.18 | |
| bscon | 0.09 | 0.01 | 0.11 | |
| combo | 0.27 | 0.00 | 0.27 | |
| dasen | 1.71 | 0.14 | 1.86 | |
| dmrse | 1.07 | 0.11 | 1.17 | |
| estimateSex | 0.93 | 0.03 | 0.97 | |
| genki | 1.11 | 0.16 | 1.26 | |
| iDMR | 0 | 0 | 0 | |
| melon | 0.11 | 0.02 | 0.13 | |
| metrics | 3.39 | 0.28 | 3.67 | |
| outlyx | 0.38 | 0.01 | 0.39 | |
| pfilter | 0.15 | 0.00 | 0.16 | |
| pwod | 0.24 | 0.00 | 0.23 | |
| qual | 1.14 | 0.07 | 1.20 | |
| readEPIC | 0 | 0 | 0 | |
| seabi | 4.56 | 0.03 | 4.60 | |
| sextest | 5.63 | 0.15 | 5.78 | |