Lukas Chavez
| Snapshot Date: 2018-10-15 16:45:08 -0400 (Mon, 15 Oct 2018) |
| URL: https://git.bioconductor.org/packages/MEDIPS |
| Branch: RELEASE_3_7 |
| Last Commit: 1af6ad6 |
| Last Changed Date: 2018-04-30 10:35:15 -0400 (Mon, 30 Apr 2018) |
| Back to Multiple platform build/check report for BioC 3.7 |
|
This page was generated on 2018-10-17 08:23:18 -0400 (Wed, 17 Oct 2018).
| Package 856/1561 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| MEDIPS 1.32.0 Lukas Chavez
| malbec2 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | OK | OK | [ OK ] | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | | ||||||
| merida2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | |
| Package: MEDIPS |
| Version: 1.32.0 |
| Command: /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD check --install=check:MEDIPS.install-out.txt --library=/home/biocbuild/bbs-3.7-bioc/R/library --no-vignettes --timings MEDIPS_1.32.0.tar.gz |
| StartedAt: 2018-10-16 01:45:55 -0400 (Tue, 16 Oct 2018) |
| EndedAt: 2018-10-16 01:50:08 -0400 (Tue, 16 Oct 2018) |
| EllapsedTime: 252.2 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: MEDIPS.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD check --install=check:MEDIPS.install-out.txt --library=/home/biocbuild/bbs-3.7-bioc/R/library --no-vignettes --timings MEDIPS_1.32.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.7-bioc/meat/MEDIPS.Rcheck’
* using R version 3.5.1 Patched (2018-07-12 r74967)
* 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 ‘1.32.0’
* 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 34.420 0.040 34.491
MEDIPS.addCNV 24.052 0.236 24.349
MEDIPS.plotSaturation 5.636 0.008 5.649
MEDIPS.saturation 5.360 0.004 5.368
* 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-3.7-bioc/meat/MEDIPS.Rcheck/00check.log’
for details.
MEDIPS.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD INSTALL MEDIPS ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.7-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 | 0.002 | |
| MEDIPS.CpGenrich | 0.092 | 0.004 | 0.121 | |
| MEDIPS.addCNV | 24.052 | 0.236 | 24.349 | |
| MEDIPS.correlation | 1.316 | 0.020 | 1.365 | |
| MEDIPS.couplingVector | 2.572 | 0.004 | 2.580 | |
| MEDIPS.createROIset | 0.956 | 0.000 | 0.967 | |
| MEDIPS.createSet | 0.980 | 0.004 | 0.987 | |
| MEDIPS.exportWIG | 1.748 | 0.000 | 1.750 | |
| MEDIPS.getAnnotation | 0.004 | 0.000 | 0.000 | |
| MEDIPS.mergeFrames | 0.004 | 0.000 | 0.004 | |
| MEDIPS.mergeSets | 0.580 | 0.000 | 0.595 | |
| MEDIPS.meth | 34.420 | 0.040 | 34.491 | |
| MEDIPS.plotCalibrationPlot | 2.812 | 0.040 | 2.855 | |
| MEDIPS.plotSaturation | 5.636 | 0.008 | 5.649 | |
| MEDIPS.plotSeqCoverage | 2.404 | 0.048 | 2.455 | |
| MEDIPS.saturation | 5.360 | 0.004 | 5.368 | |
| MEDIPS.selectROIs | 1.456 | 0.016 | 1.472 | |
| MEDIPS.selectSig | 2.744 | 0.028 | 2.774 | |
| MEDIPS.seqCoverage | 2.392 | 0.036 | 2.429 | |
| MEDIPS.setAnnotation | 2.740 | 0.040 | 2.779 | |
| MEDIPSroiSet-class | 0.004 | 0.000 | 0.001 | |
| MEDIPSset-class | 0.000 | 0.000 | 0.001 | |