Lukas Burger
| Snapshot Date: 2022-03-17 13:55:23 -0400 (Thu, 17 Mar 2022) |
| git_url: https://git.bioconductor.org/packages/MethylSeekR |
| git_branch: master |
| git_last_commit: 6945a28 |
| git_last_commit_date: 2021-10-26 12:06:34 -0400 (Tue, 26 Oct 2021) |
| Back to Multiple platform build/check report for BioC 3.15 |
|
This page was generated on 2022-03-18 11:08:00 -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 MethylSeekR package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/MethylSeekR.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 1132/2090 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| MethylSeekR 1.35.0 (landing page) Lukas Burger
| nebbiolo1 | Linux (Ubuntu 20.04.4 LTS) / x86_64 | OK | ERROR | skipped | |||||||||
| 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 | ERROR | OK | |||||||||
| Package: MethylSeekR |
| Version: 1.35.0 |
| Command: D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:MethylSeekR.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings MethylSeekR_1.35.0.tar.gz |
| StartedAt: 2022-03-17 19:33:23 -0400 (Thu, 17 Mar 2022) |
| EndedAt: 2022-03-17 19:38:49 -0400 (Thu, 17 Mar 2022) |
| EllapsedTime: 326.7 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: MethylSeekR.Rcheck |
| Warnings: 0 |
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### Running command:
###
### D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:MethylSeekR.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings MethylSeekR_1.35.0.tar.gz
###
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* using log directory 'D:/biocbuild/bbs-3.15-bioc/meat/MethylSeekR.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 'MethylSeekR/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'MethylSeekR' version '1.35.0'
* checking package namespace information ... OK
* checking package dependencies ... OK
* 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 'MethylSeekR' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Description field: should contain one or more complete sentences.
Package listed in more than one of Depends, Imports, Suggests, Enhances:
'parallel'
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
Namespace in Imports field not imported from: 'geneplotter'
All declared Imports should be used.
Package in Depends field not imported from: 'rtracklayer'
These packages need to be imported from (in the NAMESPACE file)
for when this namespace is loaded but not attached.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
PMDviterbiSegmentation : <anonymous>: no visible global function
definition for 'values'
PMDviterbiSegmentation : <anonymous>: no visible global function
definition for 'predict'
PMDviterbiSegmentation : <anonymous>: no visible global function
definition for 'Rle'
PMDviterbiSegmentation : <anonymous>: no visible global function
definition for 'runValue'
calculateAlphaDistr : <anonymous>: no visible global function
definition for 'Rle'
calculateFDRs: no visible global function definition for 'values'
calculateFDRs: no visible global function definition for 'queryHits'
calculateFDRs: no visible global function definition for 'values<-'
calculateFDRs : <anonymous>: no visible global function definition for
'Rle'
calculateFDRs : <anonymous>: no visible global function definition for
'values'
calculateFDRs : <anonymous>: no visible global function definition for
'runValue'
createGRangesObjectPMDSegmentation : <anonymous>: no visible global
function definition for 'Rle'
createGRangesObjectPMDSegmentation : <anonymous>: no visible global
function definition for 'nrun'
createGRangesObjectPMDSegmentation : <anonymous>: no visible global
function definition for 'runValue'
plotAlphaDistributionOneChr: no visible global function definition for
'values'
plotFinalSegmentation: no visible global function definition for
'values'
plotFinalSegmentation: no visible global function definition for 'Rle'
plotPMDSegmentation: no visible global function definition for 'values'
readMethylome: no visible global function definition for 'values'
removeSNPs: no visible global function definition for 'queryHits'
savePMDSegments: no visible global function definition for 'values'
saveUMRLMRSegments: no visible global function definition for 'values'
segmentUMRsLMRs: no visible global function definition for 'values'
segmentUMRsLMRs : <anonymous>: no visible global function definition
for 'Rle'
segmentUMRsLMRs : <anonymous>: no visible global function definition
for 'values'
segmentUMRsLMRs : <anonymous>: no visible global function definition
for 'runValue'
segmentUMRsLMRs: no visible global function definition for 'queryHits'
segmentUMRsLMRs: no visible global function definition for
'subjectHits'
segmentUMRsLMRs: no visible global function definition for 'Rle'
segmentUMRsLMRs: no visible global function definition for 'values<-'
segmentUMRsLMRs: no visible global function definition for 'DataFrame'
segmentUMRsLMRs: no visible global function definition for
'colorRampPalette'
trainPMDHMM: no visible global function definition for 'values'
Undefined global functions or variables:
DataFrame Rle colorRampPalette nrun predict queryHits runValue
subjectHits values values<-
Consider adding
importFrom("grDevices", "colorRampPalette")
importFrom("stats", "predict")
to your NAMESPACE file.
* 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 files in 'vignettes' ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
MethylSeekR-package 44.35 7.28 57.81
plotPMDSegmentation 24.20 4.85 29.22
segmentPMDs 22.41 4.50 26.91
savePMDSegments 21.09 4.14 25.24
calculateFDRs 7.75 1.98 14.82
plotAlphaDistributionOneChr 5.04 0.83 5.86
* 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: 3 NOTEs
See
'D:/biocbuild/bbs-3.15-bioc/meat/MethylSeekR.Rcheck/00check.log'
for details.
MethylSeekR.Rcheck/00install.out
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###
### Running command:
###
### D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL MethylSeekR
###
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* installing to library 'D:/biocbuild/bbs-3.15-bioc/R/library'
* installing *source* package 'MethylSeekR' ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'MethylSeekR'
finding HTML links ... done
MethylSeekR-package html
calculateFDRs html
plotAlphaDistributionOneChr html
plotFinalSegmentation html
plotPMDSegmentation html
readMethylome html
readSNPTable html
removeSNPs html
savePMDSegments html
saveUMRLMRSegments html
segmentPMDs html
segmentUMRsLMRs html
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (MethylSeekR)
Making 'packages.html' ...Warning in packageDescription(i, lib.loc = lib, fields = "Title", encoding = "UTF-8") :
DESCRIPTION file of package 'OUTRIDER' is missing or broken
done
MethylSeekR.Rcheck/MethylSeekR-Ex.timings
| name | user | system | elapsed | |
| MethylSeekR-package | 44.35 | 7.28 | 57.81 | |
| calculateFDRs | 7.75 | 1.98 | 14.82 | |
| plotAlphaDistributionOneChr | 5.04 | 0.83 | 5.86 | |
| plotFinalSegmentation | 1.48 | 0.31 | 1.79 | |
| plotPMDSegmentation | 24.20 | 4.85 | 29.22 | |
| readMethylome | 0.28 | 0.03 | 0.31 | |
| readSNPTable | 0.08 | 0.01 | 0.10 | |
| removeSNPs | 0.30 | 0.11 | 0.40 | |
| savePMDSegments | 21.09 | 4.14 | 25.24 | |
| saveUMRLMRSegments | 0.75 | 0.38 | 1.12 | |
| segmentPMDs | 22.41 | 4.50 | 26.91 | |
| segmentUMRsLMRs | 1.17 | 0.17 | 1.34 | |