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BioC 3.4: CHECK report for RTopper on moscato1

This page was generated on 2016-09-21 03:43:51 -0700 (Wed, 21 Sep 2016).

Package 1064/1257HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
RTopper 1.19.0
Luigi Marchionni
Snapshot Date: 2016-09-19 19:15:14 -0700 (Mon, 19 Sep 2016)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/RTopper
Last Changed Rev: 117081 / Revision: 121152
Last Changed Date: 2016-05-03 14:30:44 -0700 (Tue, 03 May 2016)
zin1 Linux (Ubuntu 16.04 LTS) / x86_64  NotNeeded  OK  OK UNNEEDED, same version exists in internal repository
moscato1 Windows Server 2008 R2 Standard (64-bit) / 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: 1.19.0
Command: rm -rf RTopper.buildbin-libdir RTopper.Rcheck && mkdir RTopper.buildbin-libdir RTopper.Rcheck && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=RTopper.buildbin-libdir RTopper_1.19.0.tar.gz >RTopper.Rcheck\00install.out 2>&1 && cp RTopper.Rcheck\00install.out RTopper-install.out && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD check --library=RTopper.buildbin-libdir --install="check:RTopper-install.out" --force-multiarch --no-vignettes --timings RTopper_1.19.0.tar.gz
StartedAt: 2016-09-20 16:00:23 -0700 (Tue, 20 Sep 2016)
EndedAt: 2016-09-20 16:02:36 -0700 (Tue, 20 Sep 2016)
EllapsedTime: 132.7 seconds
RetCode: 0
Status:  OK  
CheckDir: RTopper.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf RTopper.buildbin-libdir RTopper.Rcheck && mkdir RTopper.buildbin-libdir RTopper.Rcheck && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=RTopper.buildbin-libdir RTopper_1.19.0.tar.gz >RTopper.Rcheck\00install.out 2>&1 && cp RTopper.Rcheck\00install.out RTopper-install.out  && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD check --library=RTopper.buildbin-libdir --install="check:RTopper-install.out" --force-multiarch --no-vignettes --timings RTopper_1.19.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'D:/biocbld/bbs-3.4-bioc/meat/RTopper.Rcheck'
* using R version 3.3.1 (2016-06-21)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'RTopper/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'RTopper' version '1.19.0'
* 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 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
               user system elapsed
computeDrStat 14.46      0   14.46
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
               user system elapsed
computeDrStat 16.08   0.01    16.1
* 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
  'D:/biocbld/bbs-3.4-bioc/meat/RTopper.Rcheck/00check.log'
for details.


RTopper.Rcheck/00install.out:


install for i386

* 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

install for x64

* installing *source* package 'RTopper' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'RTopper' as RTopper_1.19.0.zip
* DONE (RTopper)

RTopper.Rcheck/examples_i386/RTopper-Ex.timings:

nameusersystemelapsed
adjustPvalGSE0.030.000.03
combineGSE0.020.000.02
computeDrStat14.46 0.0014.46
convertToDr3.860.003.85
dat0.120.000.12
fgsList0.020.000.02
gseResultsSep0.010.000.02
intScores0.000.010.01
pheno0.130.000.13
runBatchGSE0.060.020.07
sepScores0.020.000.02

RTopper.Rcheck/examples_x64/RTopper-Ex.timings:

nameusersystemelapsed
adjustPvalGSE0.030.000.03
combineGSE0.020.000.02
computeDrStat16.08 0.0116.10
convertToDr4.760.004.76
dat0.110.000.11
fgsList0.010.000.01
gseResultsSep0.020.000.02
intScores0.010.000.01
pheno0.110.000.11
runBatchGSE0.100.000.09
sepScores0.010.000.02