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CHECK report for qvalue on merida1

This page was generated on 2019-04-16 11:54:05 -0400 (Tue, 16 Apr 2019).

Package 1237/1649HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
qvalue 2.14.1
John D. Storey , Andrew J. Bass
Snapshot Date: 2019-04-15 17:01:12 -0400 (Mon, 15 Apr 2019)
URL: https://git.bioconductor.org/packages/qvalue
Branch: RELEASE_3_8
Last Commit: b694e4b
Last Changed Date: 2019-01-10 09:33:11 -0400 (Thu, 10 Jan 2019)
malbec1 Linux (Ubuntu 16.04.6 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
merida1 OS X 10.11.6 El Capitan / x86_64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: qvalue
Version: 2.14.1
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:qvalue.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings qvalue_2.14.1.tar.gz
StartedAt: 2019-04-16 02:09:59 -0400 (Tue, 16 Apr 2019)
EndedAt: 2019-04-16 02:10:43 -0400 (Tue, 16 Apr 2019)
EllapsedTime: 43.9 seconds
RetCode: 0
Status:  OK 
CheckDir: qvalue.Rcheck
Warnings: 0

Command output

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:qvalue.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings qvalue_2.14.1.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.8-bioc/meat/qvalue.Rcheck’
* using R version 3.5.3 (2019-03-11)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘qvalue/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘qvalue’ version ‘2.14.1’
* 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 ‘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
* 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... 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
  ‘/Users/biocbuild/bbs-3.8-bioc/meat/qvalue.Rcheck/00check.log’
for details.



Installation output

qvalue.Rcheck/00install.out

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL qvalue
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library’
* installing *source* package ‘qvalue’ ...
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (qvalue)

Tests output


Example timings

qvalue.Rcheck/qvalue-Ex.timings

nameusersystemelapsed
empPvals0.0830.0190.104
hedenfalk1.6490.0781.741
hist.qvalue0.7000.0170.725
lfdr0.6380.0150.658
pi0est1.4560.0231.487
plot.qvalue0.7900.0090.802
qvalue1.3460.0121.364
summary.qvalue0.0320.0020.034
write.qvalue0.0560.0050.067