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BioC 3.5: CHECK report for CAFE on malbec2

This page was generated on 2017-08-16 13:15:34 -0400 (Wed, 16 Aug 2017).

Package 162/1382HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
CAFE 1.12.0
Sander Bollen
Snapshot Date: 2017-08-15 17:17:57 -0400 (Tue, 15 Aug 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_5/madman/Rpacks/CAFE
Last Changed Rev: 129126 / Revision: 131943
Last Changed Date: 2017-04-24 15:25:24 -0400 (Mon, 24 Apr 2017)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  NotNeeded  OK [ OK ]UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository
veracruz2 OS X 10.11.6 El Capitan / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: CAFE
Version: 1.12.0
Command: /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD check --no-vignettes --timings CAFE_1.12.0.tar.gz
StartedAt: 2017-08-15 21:38:34 -0400 (Tue, 15 Aug 2017)
EndedAt: 2017-08-15 21:43:26 -0400 (Tue, 15 Aug 2017)
EllapsedTime: 291.8 seconds
RetCode: 0
Status:  OK 
CheckDir: CAFE.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD check --no-vignettes --timings CAFE_1.12.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.5-bioc/meat/CAFE.Rcheck’
* using R version 3.4.1 (2017-06-30)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘CAFE/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘CAFE’ version ‘1.12.0’
* 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 ‘CAFE’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Description field: should contain one or more complete sentences.
* 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
Armchisqr: no visible global function definition for 'chisq.test'
ArmfisherExact: no visible global function definition for 'fisher.test'
ProcessCels: no visible global function definition for 'download.file'
ProcessCels: no visible global function definition for 'read.table'
ProcessCels: no visible global function definition for 'txtProgressBar'
ProcessCels: no visible global function definition for
  'setTxtProgressBar'
ProcessCels: no visible global function definition for 'na.omit'
allBandsOnChrom: no visible global function definition for
  'fisher.test'
allBandsOnChromChi: no visible global function definition for
  'chisq.test'
armStats: no visible global function definition for 'p.adjust'
bandStats: no visible global function definition for 'p.adjust'
chisqr: no visible global function definition for 'chisq.test'
chromosomeStats: no visible global function definition for 'p.adjust'
discontPlot: no visible global function definition for 'png'
discontPlot: no visible global function definition for 'dev.off'
discontPlot: no visible global function definition for 'data'
facetPlot: no visible global function definition for 'png'
facetPlot: no visible global function definition for 'dev.off'
facetPlot: no visible global function definition for 'na.omit'
fisher.method: no visible global function definition for 'pchisq'
fisherExact: no visible global function definition for 'fisher.test'
makelevels: no visible global function definition for 'na.omit'
rawPlot: no visible global function definition for 'png'
rawPlot: no visible global function definition for 'dev.off'
rawPlot: no visible global function definition for 'data'
slidPlot: no visible global function definition for 'png'
slidPlot: no visible global function definition for 'dev.off'
slidPlot: no visible global function definition for 'data'
Undefined global functions or variables:
  chisq.test data dev.off download.file fisher.test na.omit p.adjust
  pchisq png read.table setTxtProgressBar txtProgressBar
Consider adding
  importFrom("grDevices", "dev.off", "png")
  importFrom("stats", "chisq.test", "fisher.test", "na.omit", "p.adjust",
             "pchisq")
  importFrom("utils", "data", "download.file", "read.table",
             "setTxtProgressBar", "txtProgressBar")
to your NAMESPACE file.
* 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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... 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
facetPlot 5.308   0.22   5.532
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.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-3.5-bioc/meat/CAFE.Rcheck/00check.log’
for details.


CAFE.Rcheck/00install.out:

* installing *source* package ‘CAFE’ ...
** R
** data
** inst
** byte-compile and prepare package for lazy loading
No methods found in "RSQLite" for requests: dbGetQuery
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
No methods found in "RSQLite" for requests: dbGetQuery
* DONE (CAFE)

CAFE.Rcheck/CAFE-Ex.timings:

nameusersystemelapsed
CAFE-package0.0000.0000.001
CAFE0.5560.0320.591
ProcessCels0.0000.0000.001
armStats1.6280.0281.659
bandStats1.1440.0521.198
chromosomeStats0.5640.0360.601
cliSubset000
discontPlot3.4240.1203.557
discontSmooth0.0040.0000.006
facetPlot5.3080.2205.532
fisher.method0.0000.0000.001
guiSubset0.0000.0000.001
rawPlot0.9840.0361.027
slidPlot2.0320.1082.152
slidSmooth0.0040.0000.001