Lukas Chavez
| Snapshot Date: 2019-04-15 17:01:12 -0400 (Mon, 15 Apr 2019) |
| URL: https://git.bioconductor.org/packages/MEDIPS |
| Branch: RELEASE_3_8 |
| Last Commit: f92a513 |
| Last Changed Date: 2018-10-30 11:41:46 -0400 (Tue, 30 Oct 2018) |
| Back to Multiple platform build/check report for BioC 3.8 |
|
This page was generated on 2019-04-16 11:49:01 -0400 (Tue, 16 Apr 2019).
| Package 905/1649 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| MEDIPS 1.34.0 Lukas Chavez
| malbec1 | Linux (Ubuntu 16.04.6 LTS) / x86_64 | OK | OK | [ OK ] | | ||||||
| merida1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | |
| Package: MEDIPS |
| Version: 1.34.0 |
| Command: /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD check --install=check:MEDIPS.install-out.txt --library=/home/biocbuild/bbs-3.8-bioc/R/library --no-vignettes --timings MEDIPS_1.34.0.tar.gz |
| StartedAt: 2019-04-16 01:13:20 -0400 (Tue, 16 Apr 2019) |
| EndedAt: 2019-04-16 01:18:46 -0400 (Tue, 16 Apr 2019) |
| EllapsedTime: 325.9 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: MEDIPS.Rcheck |
| Warnings: 0 |
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### Running command:
###
### /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD check --install=check:MEDIPS.install-out.txt --library=/home/biocbuild/bbs-3.8-bioc/R/library --no-vignettes --timings MEDIPS_1.34.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.8-bioc/meat/MEDIPS.Rcheck’
* using R version 3.5.3 (2019-03-11)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘MEDIPS/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘MEDIPS’ version ‘1.34.0’
* 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 for sufficient/correct file permissions ... 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 ‘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 ‘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’
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
‘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:
countMatches dev.off elementMetadata elementMetadata<- findOverlaps
hist new p.adjust pdf pie points pt qpois runLength runValue sd
seqlengths seqlevels seqnames strand<-
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 or elapsed time > 5s
user system elapsed
MEDIPS.meth 45.164 0.084 45.307
MEDIPS.addCNV 21.976 0.268 22.306
MEDIPS.plotSaturation 7.556 0.016 7.587
MEDIPS.saturation 6.868 0.000 6.869
* 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
‘/home/biocbuild/bbs-3.8-bioc/meat/MEDIPS.Rcheck/00check.log’
for details.
MEDIPS.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD INSTALL MEDIPS ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.8-bioc/R/library’ * installing *source* package ‘MEDIPS’ ... ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded * DONE (MEDIPS)
MEDIPS.Rcheck/MEDIPS-Ex.timings
| name | user | system | elapsed | |
| COUPLINGset-class | 0.000 | 0.000 | 0.001 | |
| MEDIPS.CpGenrich | 0.048 | 0.000 | 0.075 | |
| MEDIPS.addCNV | 21.976 | 0.268 | 22.306 | |
| MEDIPS.correlation | 1.460 | 0.012 | 1.496 | |
| MEDIPS.couplingVector | 3.128 | 0.004 | 3.131 | |
| MEDIPS.createROIset | 1.224 | 0.012 | 1.259 | |
| MEDIPS.createSet | 1.280 | 0.000 | 1.282 | |
| MEDIPS.exportWIG | 2.372 | 0.008 | 2.386 | |
| MEDIPS.getAnnotation | 0 | 0 | 0 | |
| MEDIPS.mergeFrames | 0.008 | 0.000 | 0.006 | |
| MEDIPS.mergeSets | 0.824 | 0.000 | 0.849 | |
| MEDIPS.meth | 45.164 | 0.084 | 45.307 | |
| MEDIPS.plotCalibrationPlot | 4.036 | 0.024 | 4.062 | |
| MEDIPS.plotSaturation | 7.556 | 0.016 | 7.587 | |
| MEDIPS.plotSeqCoverage | 3.104 | 0.028 | 3.134 | |
| MEDIPS.saturation | 6.868 | 0.000 | 6.869 | |
| MEDIPS.selectROIs | 1.888 | 0.036 | 1.924 | |
| MEDIPS.selectSig | 4.092 | 0.044 | 4.140 | |
| MEDIPS.seqCoverage | 3.136 | 0.036 | 3.174 | |
| MEDIPS.setAnnotation | 3.732 | 0.020 | 3.755 | |
| MEDIPSroiSet-class | 0 | 0 | 0 | |
| MEDIPSset-class | 0 | 0 | 0 | |