Back to the "Multiple platform build/check report" A  B  C  D  E  F  G  H  I  J  K  L  M  N  O  P  Q [R] S  T  U  V  W  X  Y  Z 

BioC 3.4: CHECK report for regioneR on malbec1

This page was generated on 2017-04-15 16:12:52 -0400 (Sat, 15 Apr 2017).

Package 1032/1296HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
regioneR 1.6.2
Bernat Gel
Snapshot Date: 2017-04-14 17:17:13 -0400 (Fri, 14 Apr 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_4/madman/Rpacks/regioneR
Last Changed Rev: 126242 / Revision: 128728
Last Changed Date: 2017-01-26 11:13:44 -0500 (Thu, 26 Jan 2017)
malbec1 Linux (Ubuntu 16.04.1 LTS) / x86_64  OK  OK [ OK ]UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
morelia Mac OS X Mavericks (10.9.5) / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: regioneR
Version: 1.6.2
Command: /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings regioneR_1.6.2.tar.gz
StartedAt: 2017-04-15 00:49:48 -0400 (Sat, 15 Apr 2017)
EndedAt: 2017-04-15 00:54:36 -0400 (Sat, 15 Apr 2017)
EllapsedTime: 288.2 seconds
RetCode: 0
Status:  OK 
CheckDir: regioneR.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings regioneR_1.6.2.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.4-bioc/meat/regioneR.Rcheck’
* using R version 3.3.3 (2017-03-06)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘regioneR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘regioneR’ version ‘1.6.2’
* 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 ‘regioneR’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Packages listed in more than one of Depends, Imports, Suggests, Enhances:
  ‘memoise’ ‘GenomicRanges’ ‘BSgenome’ ‘rtracklayer’ ‘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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
commonRegions: no visible global function definition for ‘hasArg’
createFunctionsList: no visible global function definition for ‘hasArg’
extendRegions: no visible global function definition for ‘hasArg’
joinRegions: no visible global function definition for ‘hasArg’
localZScore: no visible global function definition for ‘hasArg’
meanDistance: no visible global function definition for ‘hasArg’
meanInRegions: no visible global function definition for ‘hasArg’
mergeRegions: no visible global function definition for ‘hasArg’
numOverlaps: no visible global function definition for ‘hasArg’
overlapGraphicalSummary: no visible global function definition for
  ‘hasArg’
overlapPermTest: no visible global function definition for ‘hasArg’
overlapRegions: no visible global function definition for ‘hasArg’
overlapRegions: no visible global function definition for ‘queryHits’
overlapRegions: no visible global function definition for ‘subjectHits’
permTest: no visible global function definition for ‘hasArg’
plot.localZScoreResultsList: no visible global function definition for
  ‘is’
plot.permTestResultsList: no visible global function definition for
  ‘is’
plotRegions: no visible global function definition for ‘hasArg’
randomizeRegions: no visible global function definition for ‘hasArg’
removeOverlapping: no visible global function definition for
  ‘queryHits’
removeOverlapping: no visible global function definition for
  ‘subjectHits’
resampleRegions: no visible global function definition for ‘hasArg’
splitRegions: no visible global function definition for ‘hasArg’
subtractRegions: no visible global function definition for ‘hasArg’
toDataframe: no visible global function definition for ‘hasArg’
toDataframe: no visible global function definition for ‘is’
toGRanges: no visible global function definition for ‘hasArg’
toGRanges: no visible global function definition for ‘is’
toGRanges : <anonymous>: no visible global function definition for
  ‘read.delim’
toGRanges : <anonymous> : <anonymous>: no visible global function
  definition for ‘read.csv’
uniqueRegions: no visible global function definition for ‘hasArg’
Undefined global functions or variables:
  hasArg is queryHits read.csv read.delim subjectHits
Consider adding
  importFrom("methods", "hasArg", "is")
  importFrom("utils", "read.csv", "read.delim")
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
circularRandomizeRegions 22.544  1.120  23.828
filterChromosomes        19.708  1.644  21.391
maskFromBSGenome         17.236  2.064  19.317
getMask                  17.608  1.416  19.080
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* 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: 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.4-bioc/meat/regioneR.Rcheck/00check.log’
for details.


regioneR.Rcheck/00install.out:

* installing *source* package ‘regioneR’ ...
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (regioneR)

regioneR.Rcheck/regioneR-Ex.timings:

nameusersystemelapsed
characterToBSGenome0.5720.0400.630
circularRandomizeRegions22.544 1.12023.828
commonRegions0.1640.0000.163
createFunctionsList1.1320.0481.181
createRandomRegions0.0920.0000.091
emptyCacheRegioneR0.0000.0000.001
extendRegions0.0880.0040.092
filterChromosomes19.708 1.64421.391
getChromosomesByOrganism000
getGenome0.0280.0000.026
getGenomeAndMask0.0360.0000.036
getMask17.608 1.41619.080
joinRegions0.1000.0000.096
listChrTypes0.0120.0000.011
localZScore3.0200.1604.119
maskFromBSGenome17.236 2.06419.317
meanDistance0.0600.0000.059
meanInRegions0.0960.0040.098
mergeRegions0.0680.0000.067
numOverlaps0.1160.0000.118
overlapGraphicalSummary0.0840.0000.085
overlapPermTest0.6240.0000.623
overlapRegions0.0360.0000.036
permTest0.9360.0000.936
plot.localZScoreResults1.3320.0001.334
plot.localZScoreResultsList2.8560.0042.866
plot.permTestResults1.8240.0001.827
plot.permTestResultsList1.8160.0001.815
plotRegions0.0520.0000.051
print.permTestResults1.3680.0001.368
randomizeRegions0.2440.0000.244
recomputePermTest0.6480.0000.648
resampleRegions0.0360.0000.035
splitRegions0.0840.0000.082
subtractRegions0.1160.0000.115
toDataframe0.0120.0000.011
toGRanges0.0160.0000.014
uniqueRegions0.2160.0000.219