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BioC 3.5: CHECK report for qvalue on tokay2

This page was generated on 2017-10-18 14:18:51 -0400 (Wed, 18 Oct 2017).

Package 1049/1381HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
qvalue 2.8.0
John D. Storey , Andrew J. Bass
Snapshot Date: 2017-10-17 17:00:52 -0400 (Tue, 17 Oct 2017)
URL: https://git.bioconductor.org/packages/qvalue
Branch: RELEASE_3_5
Last Commit: c7bf331
Last Changed Date: 2017-04-24 15:45:44 -0400 (Mon, 24 Apr 2017)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository
veracruz2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: qvalue
Version: 2.8.0
Command: rm -rf qvalue.buildbin-libdir qvalue.Rcheck && mkdir qvalue.buildbin-libdir qvalue.Rcheck && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=qvalue.buildbin-libdir qvalue_2.8.0.tar.gz >qvalue.Rcheck\00install.out 2>&1 && cp qvalue.Rcheck\00install.out qvalue-install.out && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD check --library=qvalue.buildbin-libdir --install="check:qvalue-install.out" --force-multiarch --no-vignettes --timings qvalue_2.8.0.tar.gz
StartedAt: 2017-10-18 02:18:07 -0400 (Wed, 18 Oct 2017)
EndedAt: 2017-10-18 02:19:25 -0400 (Wed, 18 Oct 2017)
EllapsedTime: 77.3 seconds
RetCode: 0
Status:  OK  
CheckDir: qvalue.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf qvalue.buildbin-libdir qvalue.Rcheck && mkdir qvalue.buildbin-libdir qvalue.Rcheck && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=qvalue.buildbin-libdir qvalue_2.8.0.tar.gz >qvalue.Rcheck\00install.out 2>&1 && cp qvalue.Rcheck\00install.out qvalue-install.out  &&  C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD check --library=qvalue.buildbin-libdir --install="check:qvalue-install.out" --force-multiarch --no-vignettes --timings qvalue_2.8.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.5-bioc/meat/qvalue.Rcheck'
* using R version 3.4.2 Patched (2017-10-07 r73498)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'qvalue/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'qvalue' version '2.8.0'
* 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 'qvalue' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... OK
* 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
* 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 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
lfdr: no visible global function definition for 'qnorm'
lfdr: no visible global function definition for 'density'
lfdr: no visible global function definition for 'smooth.spline'
lfdr: no visible global function definition for 'predict'
lfdr: no visible global function definition for 'dnorm'
pi0est: no visible global function definition for 'smooth.spline'
pi0est: no visible global function definition for 'predict'
pi0est: no visible global function definition for 'quantile'
plot.qvalue: no visible global function definition for 'quantile'
write.qvalue: no visible global function definition for 'write.table'
Undefined global functions or variables:
  density dnorm predict qnorm quantile smooth.spline write.table
Consider adding
  importFrom("stats", "density", "dnorm", "predict", "qnorm", "quantile",
             "smooth.spline")
  importFrom("utils", "write.table")
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
** running examples for arch 'x64' ... 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: 1 NOTE
See
  'C:/Users/biocbuild/bbs-3.5-bioc/meat/qvalue.Rcheck/00check.log'
for details.


qvalue.Rcheck/00install.out:


install for i386

* installing *source* package 'qvalue' ...
** 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 'qvalue' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'qvalue' as qvalue_2.8.0.zip
* DONE (qvalue)

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

nameusersystemelapsed
empPvals0.250.010.27
hedenfalk2.530.022.55
hist.qvalue1.100.031.13
lfdr0.610.000.61
pi0est1.140.001.14
plot.qvalue0.670.000.67
qvalue1.090.001.09
summary.qvalue0.110.000.11
write.qvalue0.140.000.14

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

nameusersystemelapsed
empPvals0.280.000.28
hedenfalk2.810.032.85
hist.qvalue1.410.001.40
lfdr0.560.020.58
pi0est1.440.001.44
plot.qvalue0.740.000.73
qvalue1.310.001.32
summary.qvalue0.040.000.04
write.qvalue0.080.020.10