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BioC 3.4: CHECK report for RTopper on malbec1

This page was generated on 2017-04-15 16:10:38 -0400 (Sat, 15 Apr 2017).

Package 1093/1296HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
RTopper 1.20.0
Luigi Marchionni
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/RTopper
Last Changed Rev: 122710 / Revision: 128728
Last Changed Date: 2016-10-17 14:45:06 -0400 (Mon, 17 Oct 2016)
malbec1 Linux (Ubuntu 16.04.1 LTS) / x86_64  NotNeeded  OK [ OK ]UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository
morelia Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: RTopper
Version: 1.20.0
Command: /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings RTopper_1.20.0.tar.gz
StartedAt: 2017-04-15 01:06:29 -0400 (Sat, 15 Apr 2017)
EndedAt: 2017-04-15 01:07:36 -0400 (Sat, 15 Apr 2017)
EllapsedTime: 66.5 seconds
RetCode: 0
Status:  OK 
CheckDir: RTopper.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings RTopper_1.20.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.4-bioc/meat/RTopper.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 ‘RTopper/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘RTopper’ version ‘1.20.0’
* 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 ‘RTopper’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Package listed in more than one of Depends, Imports, Suggests, Enhances:
  ‘limma’
A package should be listed in only one of these fields.
* checking top-level files ... NOTE
File
  LICENSE
is not mentioned in the DESCRIPTION file.
* 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
computeScore: no visible global function definition for ‘glm’
computeScore: no visible global function definition for ‘binomial’
computeScore: no visible global function definition for ‘AIC’
convertToDr: no visible binding for global variable ‘data’
myMean : medianM: no visible binding for global variable ‘median’
Undefined global functions or variables:
  AIC binomial data glm median
Consider adding
  importFrom("stats", "AIC", "binomial", "glm", "median")
  importFrom("utils", "data")
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
computeDrStat 11.332  0.012  11.353
* 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: 3 NOTEs
See
  ‘/home/biocbuild/bbs-3.4-bioc/meat/RTopper.Rcheck/00check.log’
for details.


RTopper.Rcheck/00install.out:

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

RTopper.Rcheck/RTopper-Ex.timings:

nameusersystemelapsed
adjustPvalGSE0.020.000.02
combineGSE0.0080.0000.006
computeDrStat11.332 0.01211.353
convertToDr2.9360.0082.946
dat0.1000.0000.098
fgsList0.0080.0000.008
gseResultsSep0.0120.0000.010
intScores0.0040.0000.003
pheno0.0960.0000.098
runBatchGSE0.0600.0000.058
sepScores0.0080.0000.006