Leo C Schalkwyk
| Snapshot Date: 2025-01-10 13:40 -0500 (Fri, 10 Jan 2025) |
| git_url: https://git.bioconductor.org/packages/wateRmelon |
| git_branch: devel |
| git_last_commit: d54e843 |
| git_last_commit_date: 2024-11-27 06:20:28 -0500 (Wed, 27 Nov 2024) |
| Back to Multiple platform build/check report for BioC 3.21: simplified long |
|
This page was generated on 2025-01-11 11:47 -0500 (Sat, 11 Jan 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | R Under development (unstable) (2024-10-21 r87258) -- "Unsuffered Consequences" | 4760 |
| palomino7 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2024-10-26 r87273 ucrt) -- "Unsuffered Consequences" | 4479 |
| lconway | macOS 12.7.1 Monterey | x86_64 | R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" | 4443 |
| kjohnson3 | macOS 13.7.1 Ventura | arm64 | R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" | 4398 |
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | R Under development (unstable) (2024-11-24 r87369) -- "Unsuffered Consequences" | 4391 |
| 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 | ||||
| Package 2249/2277 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| wateRmelon 2.13.0 (landing page) Leo C Schalkwyk
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||||
| palomino7 | Windows Server 2022 Datacenter / x64 | OK | OK | WARNINGS | OK | | ||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | WARNINGS | OK | | ||||||||
| kjohnson3 | macOS 13.7.1 Ventura / arm64 | OK | OK | WARNINGS | OK | | ||||||||
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | WARNINGS | ||||||||||
|
To the developers/maintainers of the wateRmelon package: - 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 Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. - See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host. |
| Package: wateRmelon |
| Version: 2.13.0 |
| Command: /home/biocbuild/R/R/bin/R CMD check --install=check:wateRmelon.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings wateRmelon_2.13.0.tar.gz |
| StartedAt: 2025-01-11 12:28:39 -0000 (Sat, 11 Jan 2025) |
| EndedAt: 2025-01-11 12:38:34 -0000 (Sat, 11 Jan 2025) |
| EllapsedTime: 595.7 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: wateRmelon.Rcheck |
| Warnings: 9 |
##############################################################################
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### Running command:
###
### /home/biocbuild/R/R/bin/R CMD check --install=check:wateRmelon.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings wateRmelon_2.13.0.tar.gz
###
##############################################################################
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* using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/wateRmelon.Rcheck’
* using R Under development (unstable) (2024-11-24 r87369)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0
GNU Fortran (GCC) 14.2.0
* running under: openEuler 24.03 (LTS)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘wateRmelon/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘wateRmelon’ version ‘2.13.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... INFO
Depends: includes the non-default packages:
'Biobase', 'limma', 'matrixStats', 'methylumi', 'lumi', 'ROC',
'IlluminaHumanMethylation450kanno.ilmn12.hg19', 'illuminaio'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘wateRmelon’ can be installed ... WARNING
Found the following significant warnings:
Warning: program compiled against libxml 212 using older 211
See ‘/home/biocbuild/bbs-3.21-bioc/meat/wateRmelon.Rcheck/00install.out’ for details.
* 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 code 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 ... NOTE
Warning: program compiled against libxml 212 using older 211
A namespace must be able to be loaded with just the base namespace
loaded: otherwise if the namespace gets loaded by a saved object, the
session will be unable to start.
Probably some imports need to be declared in the NAMESPACE file.
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking dependencies in R code ... WARNING
Warning: program compiled against libxml 212 using older 211
'::' or ':::' import not declared from: ‘R.utils’
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 ... WARNING
Warning: program compiled against libxml 212 using older 211
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
* checking replacement functions ... WARNING
Warning: program compiled against libxml 212 using older 211
The argument of a replacement function which corresponds to the right
hand side must be named ‘value’.
* checking foreign function calls ... NOTE
Warning: program compiled against libxml 212 using older 211
See chapter ‘System and foreign language interfaces’ in the ‘Writing R
Extensions’ manual.
* checking R code for possible problems ... NOTE
Warning: program compiled against libxml 212 using older 211
readPepo: warning in dir(idatdir, patt = "idat"): partial argument
match of 'patt' to 'pattern'
.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
‘pvals<-’
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’
canno: no visible global function definition for
‘IlluminaMethylationManifest’
combo : <anonymous>: no visible global function definition for ‘QCdata’
combo: no visible global function definition for ‘QCdata<-’
detectP: no visible global function definition for ‘QCdata’
detectP: no visible global function definition for ‘methylated’
detectP: no visible global function definition for ‘unmethylated’
detectP: no visible global function definition for ‘colMedians’
detectP: no visible global function definition for ‘colMads’
detectP: no visible global function definition for ‘pnorm’
dfort: no visible binding for global variable
‘IlluminaHumanMethylation450kanno.ilmn12.hg19’
epicv2clean.gds.class: no visible global function definition for
‘chainsaw’
estimateSex: no visible global function definition for ‘head’
estimateSex: no visible binding for global variable ‘sex_coef’
estimateSex: no visible global function definition for ‘colSds’
genall: no visible global function definition for ‘head’
generateManifest: no visible binding for global variable ‘.manifest’
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 '<<-'
assignment to ‘epicV2.ordering’
getMethylationBeadMappers2 : <anonymous>: no visible binding for global
variable ‘epicV2.ordering’
getMethylationBeadMappers2 : <anonymous>: no visible binding for global
variable ‘.manifest’
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’
getMethylationBeadMappers2 : <anonymous>: no visible binding for global
variable ‘epicV2.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’
read.manifest: no visible global function definition for ‘DNAStringSet’
read.manifest: no visible global function definition for
‘oligonucleotideFrequency’
read.manifest: no visible global function definition for
‘letterFrequency’
readEPIC: no visible binding for global variable ‘n.sd’
readPepo: no visible binding for '<<-' assignment to ‘.manifest’
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 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,MethylSet: no visible global function definition for ‘head’
dmrse,RGChannelSet: no visible global function definition for ‘getBeta’
dmrse,RGChannelSet: no visible global function definition for ‘head’
dmrse_col,MethylSet: no visible global function definition for
‘getBeta’
dmrse_col,MethylSet: no visible global function definition for ‘head’
dmrse_col,RGChannelSet: no visible global function definition for
‘getBeta’
dmrse_col,RGChannelSet: no visible global function definition for
‘head’
dmrse_row,MethylSet: no visible global function definition for
‘getBeta’
dmrse_row,MethylSet: no visible global function definition for ‘head’
dmrse_row,RGChannelSet: no visible global function definition for
‘getBeta’
dmrse_row,RGChannelSet: no visible global function definition for
‘head’
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’
smokp,MethylSet: 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:
.manifest .mclapply DNAStringSet
IlluminaHumanMethylation450kanno.ilmn12.hg19
IlluminaMethylationManifest MethylSet PATH_RES QCdata QCdata<-
RGChannelSetExtended addSex assay<- assays betas betas<- chainsaw
colCummaxs colData colMads colMeans2 colMedians colQuantiles colSds
detectionP epic.controls epic.ordering epicV2.controls
epicV2.ordering getAnnotation getAnnotationObject getBeta getCN
getControlAddress getGreen getManifest getManifestInfo getMeth
getNBeads getOOB getProbeInfo getProbeType getRed getSex getSnpBeta
getUnmeth head hm27.controls hm27.ordering hm450.controls
hm450.ordering intensitiesByChannel letterFrequency mapToGenome
mclapply metadata methylated methylated<- methylumiR n.sd
oligonucleotideFrequency pnorm preprocessNoob preprocessRaw
preprocessSWAN probeAnnotationsCategory projectName pvals pvals<-
rowMeans2 seqnames sex_coef subsetByLoci unmethylated unmethylated<-
warn
Consider adding
importFrom("stats", "pnorm")
importFrom("utils", "head")
to your NAMESPACE file.
* checking Rd files ... NOTE
checkRd: (-1) combo.Rd:24: Lost braces; missing escapes or markup?
24 | and \code{phenoData} are joined on \code{sampleName} . \code{featureData} and {annotation} are taken from
| ^
* checking Rd metadata ... WARNING
Rd files with duplicated alias 'NChannelSetToMethyLumiSet2':
‘NChannelSetToMethyLumiSet2.Rd’ ‘wm_internal.Rd’
Rd files with duplicated alias 'fot':
‘dot-getManifestString.Rd’ ‘got.Rd’
Rd files with duplicated alias 'got':
‘dot-getManifestString.Rd’ ‘got.Rd’
* checking Rd cross-references ... OK
* checking for missing documentation entries ... WARNING
Warning: program compiled against libxml 212 using older 211
Undocumented code objects:
‘detectP’
Undocumented data sets:
‘ageCoefs’ ‘epicV2.controls’ ‘sex_coef’
Undocumented S4 methods:
generic 'adjustedDasen' and siglist 'MethyLumiSet'
generic 'adjustedDasen' and siglist 'MethylSet'
generic 'adjustedDasen' and siglist 'RGChannelSet'
All user-level objects in a package (including S4 classes and methods)
should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* checking for code/documentation mismatches ... WARNING
Warning: program compiled against libxml 212 using older 211
Codoc mismatches from Rd file 'readEPIC.Rd':
readEPIC
Code: function(idatPath, barcodes = NULL, pdat = NULL, parallel = F,
n = T, oob = F, force = F, two = TRUE, ...)
Docs: function(idatPath, barcodes = NULL, pdat = NULL, parallel = F,
n = T, oob = F, force = F, ...)
Argument names in code not in docs:
two
Mismatches in argument names:
Position: 8 Code: two Docs: ...
Warning: program compiled against libxml 212 using older 211
Warning: program compiled against libxml 212 using older 211
* checking Rd \usage sections ... WARNING
Undocumented arguments in Rd file 'canno.Rd'
‘name’
Undocumented arguments in Rd file 'dot-createAnnotation.Rd'
‘object’
Documented arguments not in \usage in Rd file 'dot-getManifestString.Rd':
‘x’ ‘obj’ ‘fd’ ‘rn’
Undocumented arguments in Rd file 'epicv2clean.default.Rd'
‘x’
Undocumented arguments in Rd file 'readPepo.Rd'
‘oob’
Documented arguments not in \usage in Rd file 'readPepo.Rd':
‘keep’
Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Warning: program compiled against libxml 212 using older 211
The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* checking Rd contents ... NOTE
Argument items with no description in Rd file 'read.manifest.Rd':
‘file’
Argument items with no description in Rd file 'wm_internal.Rd':
‘mats’ ‘chans’ ‘parallel’ ‘protocol.data’ ‘IDAT’ ‘force’
* checking for unstated dependencies in examples ... OK
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... WARNING
Warning: program compiled against libxml 212 using older 211
* 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
adjustedDasen 24.686 0.948 26.393
sextest 11.249 0.077 11.357
seabi 9.557 0.069 9.647
metrics 6.255 0.092 6.363
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: 9 WARNINGs, 6 NOTEs
See
‘/home/biocbuild/bbs-3.21-bioc/meat/wateRmelon.Rcheck/00check.log’
for details.
wateRmelon.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R/bin/R CMD INSTALL wateRmelon ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library’ * installing *source* package ‘wateRmelon’ ... ** using staged installation ** R ** data ** inst ** byte-compile and prepare package for lazy loading Warning: program compiled against libxml 212 using older 211 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 ‘smokp’ 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 Warning: program compiled against libxml 212 using older 211 No methods found in package ‘RSQLite’ for request: ‘dbListFields’ when loading ‘lumi’ ** testing if installed package can be loaded from final location Warning: program compiled against libxml 212 using older 211 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)
wateRmelon.Rcheck/wateRmelon-Ex.timings
| name | user | system | elapsed | |
| BMIQ | 0 | 0 | 0 | |
| adjustedDasen | 24.686 | 0.948 | 26.393 | |
| adjustedFunnorm | 0 | 0 | 0 | |
| agep | 0.261 | 0.008 | 0.274 | |
| bscon | 0.14 | 0.00 | 0.14 | |
| combo | 0.450 | 0.035 | 0.492 | |
| dasen | 1.997 | 0.093 | 2.202 | |
| dmrse | 1.992 | 0.051 | 2.136 | |
| estimateSex | 2.358 | 0.040 | 2.496 | |
| genki | 2.459 | 0.069 | 2.707 | |
| iDMR | 0.002 | 0.000 | 0.006 | |
| melon | 0.178 | 0.000 | 0.179 | |
| metrics | 6.255 | 0.092 | 6.363 | |
| outlyx | 1.070 | 0.008 | 1.081 | |
| pfilter | 0.240 | 0.008 | 0.249 | |
| pwod | 0.450 | 0.008 | 0.459 | |
| qual | 1.998 | 0.075 | 2.242 | |
| readEPIC | 0 | 0 | 0 | |
| seabi | 9.557 | 0.069 | 9.647 | |
| sextest | 11.249 | 0.077 | 11.357 | |
| smokp | 0.145 | 0.004 | 0.149 | |