Lukas Chavez
| Snapshot Date: 2022-03-17 13:55:23 -0400 (Thu, 17 Mar 2022) |
| git_url: https://git.bioconductor.org/packages/MEDIPS |
| git_branch: master |
| git_last_commit: 3148708 |
| git_last_commit_date: 2021-10-26 11:57:30 -0400 (Tue, 26 Oct 2021) |
| Back to Multiple platform build/check report for BioC 3.15 |
|
This page was generated on 2022-03-18 11:07:57 -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 MEDIPS package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/MEDIPS.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 1081/2090 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| MEDIPS 1.47.0 (landing page) Lukas Chavez
| 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: MEDIPS |
| Version: 1.47.0 |
| Command: D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:MEDIPS.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings MEDIPS_1.47.0.tar.gz |
| StartedAt: 2022-03-17 19:30:28 -0400 (Thu, 17 Mar 2022) |
| EndedAt: 2022-03-17 19:35:24 -0400 (Thu, 17 Mar 2022) |
| EllapsedTime: 296.1 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: MEDIPS.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:MEDIPS.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings MEDIPS_1.47.0.tar.gz
###
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* using log directory 'D:/biocbuild/bbs-3.15-bioc/meat/MEDIPS.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 'MEDIPS/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'MEDIPS' version '1.47.0'
* 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 'MEDIPS' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... OK
* 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
MEDIPS.CpGenrich: no visible global function definition for 'seqlevels'
MEDIPS.CpGenrich: no visible global function definition for
'seqlengths'
MEDIPS.CpGenrich: no visible global function definition for
'GRangesList'
MEDIPS.CpGenrich : <anonymous>: no visible global function definition
for 'seqnames'
MEDIPS.CpGenrich: no visible global function definition for 'new'
MEDIPS.addCNV: no visible global function definition for 'seqnames'
MEDIPS.correlation: no visible global function definition for 'pdf'
MEDIPS.correlation: no visible global function definition for 'dev.off'
MEDIPS.couplingVector: no visible global function definition for 'new'
MEDIPS.createROIset: no visible global function definition for
'seqnames'
MEDIPS.createROIset: no visible global function definition for
'seqlengths'
MEDIPS.createROIset: no visible global function definition for 'new'
MEDIPS.createSet: no visible global function definition for 'seqnames'
MEDIPS.createSet: no visible global function definition for
'seqlengths'
MEDIPS.createSet: no visible global function definition for 'seqlevels'
MEDIPS.createSet: no visible global function definition for 'new'
MEDIPS.diffMeth: no visible global function definition for 'p.adjust'
MEDIPS.exportWIG: no visible global function definition for 'seqnames'
MEDIPS.mergeSets: no visible global function definition for 'new'
MEDIPS.meth: no visible global function definition for 'seqnames'
MEDIPS.plotCalibrationPlot: no visible global function definition for
'seqnames'
MEDIPS.plotCalibrationPlot: no visible global function definition for
'points'
MEDIPS.plotSeqCoverage: no visible global function definition for 'pie'
MEDIPS.plotSeqCoverage: no visible global function definition for
'hist'
MEDIPS.saturation: no visible global function definition for
'seqlevels'
MEDIPS.saturation: no visible global function definition for
'seqlengths'
MEDIPS.selectROIs: no visible global function definition for
'elementMetadata<-'
MEDIPS.selectROIs: no visible global function definition for
'elementMetadata'
MEDIPS.selectROIs: no visible global function definition for
'findOverlaps'
MEDIPS.selectROIs: no visible global function definition for 'values'
MEDIPS.selectROIs: no visible global function definition for 'seqnames'
MEDIPS.seqCoverage: no visible global function definition for
'seqlevels'
MEDIPS.seqCoverage: no visible global function definition for
'seqlengths'
MEDIPS.setAnnotation: no visible global function definition for
'findOverlaps'
MEDIPS.setAnnotation: no visible global function definition for
'values'
getGRange: no visible global function definition for 'qpois'
getGRange: no visible global function definition for 'seqlengths'
getGRange: no visible global function definition for 'countMatches'
getGRange: no visible global function definition for 'strand<-'
getMObjectFromWIG: no visible global function definition for
'seqlengths'
getMObjectFromWIG: no visible global function definition for 'values'
getMObjectFromWIG: no visible global function definition for
'runLength'
getMObjectFromWIG: no visible global function definition for 'seqnames'
getMObjectFromWIG: no visible global function definition for 'runValue'
getMObjectFromWIG: no visible global function definition for 'new'
getPairedGRange: no visible global function definition for 'sd'
getPairedGRange: no visible global function definition for 'qpois'
getPairedGRange: no visible global function definition for 'seqlengths'
getPairedGRange: no visible global function definition for
'countMatches'
getPairedGRange: no visible global function definition for 'strand<-'
matSd: no visible binding for global variable 'sd'
matTtest: no visible binding for global variable 'sd'
matTtest: no visible global function definition for 'pt'
Undefined global functions or variables:
GRangesList countMatches dev.off elementMetadata elementMetadata<-
findOverlaps hist new p.adjust pdf pie points pt qpois runLength
runValue sd seqlengths seqlevels seqnames strand<- values
Consider adding
importFrom("grDevices", "dev.off", "pdf")
importFrom("graphics", "hist", "pie", "points")
importFrom("methods", "new")
importFrom("stats", "p.adjust", "pt", "qpois", "sd")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* 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
MEDIPS.meth 33.14 3.64 36.83
MEDIPS.addCNV 17.38 0.61 18.23
MEDIPS.plotSaturation 5.15 0.82 5.96
MEDIPS.saturation 4.98 0.88 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: 1 NOTE
See
'D:/biocbuild/bbs-3.15-bioc/meat/MEDIPS.Rcheck/00check.log'
for details.
MEDIPS.Rcheck/00install.out
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###
### Running command:
###
### D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL MEDIPS
###
##############################################################################
##############################################################################
* installing to library 'D:/biocbuild/bbs-3.15-bioc/R/library'
* installing *source* package 'MEDIPS' ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
No methods found in package 'IRanges' for request: 'values' when loading 'MEDIPS'
** help
*** installing help indices
converting help for package 'MEDIPS'
finding HTML links ... done
COUPLINGset-class html
MEDIPS-package html
MEDIPS.CpGenrich html
MEDIPS.addCNV html
MEDIPS.correlation html
MEDIPS.couplingVector html
MEDIPS.createROIset html
MEDIPS.createSet html
MEDIPS.exportWIG html
MEDIPS.getAnnotation html
MEDIPS.mergeFrames html
MEDIPS.mergeSets html
MEDIPS.meth html
MEDIPS.plotCalibrationPlot html
MEDIPS.plotSaturation html
MEDIPS.plotSeqCoverage html
MEDIPS.saturation html
MEDIPS.selectROIs html
MEDIPS.selectSig html
MEDIPS.seqCoverage html
MEDIPS.setAnnotation html
MEDIPSroiSet-class html
MEDIPSset-class html
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
No methods found in package 'IRanges' for request: 'values' when loading 'MEDIPS'
** testing if installed package can be loaded from final location
No methods found in package 'IRanges' for request: 'values' when loading 'MEDIPS'
** testing if installed package keeps a record of temporary installation path
* DONE (MEDIPS)
Making 'packages.html' ...Warning in packageDescription(i, lib.loc = lib, fields = "Title", encoding = "UTF-8") :
DESCRIPTION file of package 'recoup' is missing or broken
done
MEDIPS.Rcheck/MEDIPS-Ex.timings
| name | user | system | elapsed | |
| COUPLINGset-class | 0 | 0 | 0 | |
| MEDIPS.CpGenrich | 0.03 | 0.02 | 0.05 | |
| MEDIPS.addCNV | 17.38 | 0.61 | 18.23 | |
| MEDIPS.correlation | 0.98 | 0.15 | 1.14 | |
| MEDIPS.couplingVector | 2.94 | 0.25 | 3.21 | |
| MEDIPS.createROIset | 0.88 | 0.10 | 0.97 | |
| MEDIPS.createSet | 0.94 | 0.12 | 1.06 | |
| MEDIPS.exportWIG | 1.83 | 0.25 | 2.08 | |
| MEDIPS.getAnnotation | 0 | 0 | 0 | |
| MEDIPS.mergeFrames | 0.01 | 0.00 | 0.02 | |
| MEDIPS.mergeSets | 0.64 | 0.00 | 0.65 | |
| MEDIPS.meth | 33.14 | 3.64 | 36.83 | |
| MEDIPS.plotCalibrationPlot | 2.89 | 0.25 | 3.14 | |
| MEDIPS.plotSaturation | 5.15 | 0.82 | 5.96 | |
| MEDIPS.plotSeqCoverage | 2.87 | 0.26 | 3.14 | |
| MEDIPS.saturation | 4.98 | 0.88 | 5.86 | |
| MEDIPS.selectROIs | 1.04 | 0.12 | 1.15 | |
| MEDIPS.selectSig | 1.76 | 0.20 | 1.97 | |
| MEDIPS.seqCoverage | 2.63 | 0.33 | 2.95 | |
| MEDIPS.setAnnotation | 2.29 | 0.19 | 2.49 | |
| MEDIPSroiSet-class | 0 | 0 | 0 | |
| MEDIPSset-class | 0 | 0 | 0 | |