Back to Multiple platform build/check report for BioC 3.6 |
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This page was generated on 2018-04-12 13:09:16 -0400 (Thu, 12 Apr 2018).
Package 807/1472 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
MEDIPS 1.30.0 Lukas Chavez
| malbec1 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | NotNeeded | OK | [ OK ] | ![]() | ||||||
tokay1 | Windows Server 2012 R2 Standard / x64 | NotNeeded | OK | OK | OK | ![]() | ||||||
veracruz1 | OS X 10.11.6 El Capitan / x86_64 | NotNeeded | OK | OK | OK | ![]() |
Package: MEDIPS |
Version: 1.30.0 |
Command: /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings MEDIPS_1.30.0.tar.gz |
StartedAt: 2018-04-12 00:51:18 -0400 (Thu, 12 Apr 2018) |
EndedAt: 2018-04-12 00:55:49 -0400 (Thu, 12 Apr 2018) |
EllapsedTime: 271.2 seconds |
RetCode: 0 |
Status: OK |
CheckDir: MEDIPS.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings MEDIPS_1.30.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.6-bioc/meat/MEDIPS.Rcheck’ * using R version 3.4.4 (2018-03-15) * 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 ‘1.30.0’ * 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 loading without being on the library search path ... 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 installed files from ‘inst/doc’ ... OK * checking files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU or elapsed time > 5s user system elapsed MEDIPS.meth 36.928 0.036 37.048 MEDIPS.addCNV 26.232 0.208 26.507 MEDIPS.saturation 5.984 0.008 5.998 MEDIPS.plotSaturation 5.496 0.020 5.516 * 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-3.6-bioc/meat/MEDIPS.Rcheck/00check.log’ for details.
MEDIPS.Rcheck/00install.out
* installing *source* package ‘MEDIPS’ ... ** R ** inst ** preparing 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 | 0.080 | 0.000 | 0.096 | |
MEDIPS.addCNV | 26.232 | 0.208 | 26.507 | |
MEDIPS.correlation | 1.060 | 0.016 | 1.339 | |
MEDIPS.couplingVector | 2.192 | 0.012 | 2.293 | |
MEDIPS.createROIset | 0.804 | 0.004 | 0.832 | |
MEDIPS.createSet | 0.828 | 0.004 | 0.833 | |
MEDIPS.exportWIG | 1.952 | 0.004 | 1.958 | |
MEDIPS.getAnnotation | 0.000 | 0.000 | 0.001 | |
MEDIPS.mergeFrames | 0.004 | 0.000 | 0.004 | |
MEDIPS.mergeSets | 0.476 | 0.000 | 0.501 | |
MEDIPS.meth | 36.928 | 0.036 | 37.048 | |
MEDIPS.plotCalibrationPlot | 2.528 | 0.028 | 2.558 | |
MEDIPS.plotSaturation | 5.496 | 0.020 | 5.516 | |
MEDIPS.plotSeqCoverage | 2.232 | 0.056 | 2.290 | |
MEDIPS.saturation | 5.984 | 0.008 | 5.998 | |
MEDIPS.selectROIs | 3.152 | 0.024 | 3.182 | |
MEDIPS.selectSig | 3.308 | 0.040 | 3.353 | |
MEDIPS.seqCoverage | 2.092 | 0.044 | 2.136 | |
MEDIPS.setAnnotation | 2.492 | 0.024 | 2.516 | |
MEDIPSroiSet-class | 0.000 | 0.000 | 0.001 | |
MEDIPSset-class | 0.000 | 0.004 | 0.001 | |