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BioC 3.4: CHECK report for CexoR on moscato1

This page was generated on 2016-09-21 03:45:17 -0700 (Wed, 21 Sep 2016).

Package 170/1257HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
CexoR 1.11.0
Pedro Madrigal
Snapshot Date: 2016-09-19 19:15:14 -0700 (Mon, 19 Sep 2016)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/CexoR
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: CexoR
Version: 1.11.0
Command: rm -rf CexoR.buildbin-libdir CexoR.Rcheck && mkdir CexoR.buildbin-libdir CexoR.Rcheck && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=CexoR.buildbin-libdir CexoR_1.11.0.tar.gz >CexoR.Rcheck\00install.out 2>&1 && cp CexoR.Rcheck\00install.out CexoR-install.out && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD check --library=CexoR.buildbin-libdir --install="check:CexoR-install.out" --force-multiarch --no-vignettes --timings CexoR_1.11.0.tar.gz
StartedAt: 2016-09-20 05:21:07 -0700 (Tue, 20 Sep 2016)
EndedAt: 2016-09-20 05:28:10 -0700 (Tue, 20 Sep 2016)
EllapsedTime: 422.8 seconds
RetCode: 0
Status:  OK  
CheckDir: CexoR.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf CexoR.buildbin-libdir CexoR.Rcheck && mkdir CexoR.buildbin-libdir CexoR.Rcheck && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=CexoR.buildbin-libdir CexoR_1.11.0.tar.gz >CexoR.Rcheck\00install.out 2>&1 && cp CexoR.Rcheck\00install.out CexoR-install.out  && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD check --library=CexoR.buildbin-libdir --install="check:CexoR-install.out" --force-multiarch --no-vignettes --timings CexoR_1.11.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'D:/biocbld/bbs-3.4-bioc/meat/CexoR.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 'CexoR/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'CexoR' version '1.11.0'
* 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 'CexoR' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... NOTE
License components with restrictions not permitted:
  GPL-2 + file LICENSE
* 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
* 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
cexor: no visible global function definition for 'subsetByOverlaps'
cexor : Stouffer.test: no visible global function definition for
  'qnorm'
cexor : Stouffer.test: no visible global function definition for
  'pnorm'
cexor : Fisher.test: no visible global function definition for 'pchisq'
plotcexor: no visible global function definition for 'colorRampPalette'
plotcexor: no visible global function definition for 'par'
plotcexor: no visible global function definition for 'plot'
plotcexor: no visible global function definition for 'points'
plotcexor: no visible global function definition for 'abline'
plotcexor: no visible global function definition for 'legend'
pskellam: no visible global function definition for 'pchisq'
pskellam.sp: no visible global function definition for 'pnorm'
pskellam.sp: no visible global function definition for 'dnorm'
Undefined global functions or variables:
  abline colorRampPalette dnorm legend par pchisq plot pnorm points
  qnorm subsetByOverlaps
Consider adding
  importFrom("grDevices", "colorRampPalette")
  importFrom("graphics", "abline", "legend", "par", "plot", "points")
  importFrom("stats", "dnorm", "pchisq", "pnorm", "qnorm")
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 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
cexor         15.90   0.10   15.99
plotcexor     15.74   0.03   15.77
CexoR-package 15.52   0.06   15.60
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
               user system elapsed
cexor         18.27   0.07   18.33
CexoR-package 18.21   0.12   18.46
plotcexor     18.14   0.04   18.19
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'runTests.R'
 OK
** running tests for arch 'x64' ...
  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
  'D:/biocbld/bbs-3.4-bioc/meat/CexoR.Rcheck/00check.log'
for details.


CexoR.Rcheck/00install.out:


install for i386

* installing *source* package 'CexoR' ...
** R
** 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 'CexoR' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'CexoR' as CexoR_1.11.0.zip
* DONE (CexoR)

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

nameusersystemelapsed
CexoR-package15.52 0.0615.60
cexor15.90 0.1015.99
plotcexor15.74 0.0315.77

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

nameusersystemelapsed
CexoR-package18.21 0.1218.46
cexor18.27 0.0718.33
plotcexor18.14 0.0418.19