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CHECK report for qvalue on malbec1

This page was generated on 2020-04-15 12:04:09 -0400 (Wed, 15 Apr 2020).

Package 1356/1823HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
qvalue 2.18.0
John D. Storey , Andrew J. Bass
Snapshot Date: 2020-04-14 16:46:13 -0400 (Tue, 14 Apr 2020)
URL: https://git.bioconductor.org/packages/qvalue
Branch: RELEASE_3_10
Last Commit: 605a5bb
Last Changed Date: 2019-10-29 13:07:27 -0400 (Tue, 29 Oct 2019)
malbec1 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK [ OK ]UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  OK  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: 2.18.0
Command: /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD check --install=check:qvalue.install-out.txt --library=/home/biocbuild/bbs-3.10-bioc/R/library --no-vignettes --timings qvalue_2.18.0.tar.gz
StartedAt: 2020-04-15 00:11:00 -0400 (Wed, 15 Apr 2020)
EndedAt: 2020-04-15 00:11:38 -0400 (Wed, 15 Apr 2020)
EllapsedTime: 37.2 seconds
RetCode: 0
Status:  OK 
CheckDir: qvalue.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD check --install=check:qvalue.install-out.txt --library=/home/biocbuild/bbs-3.10-bioc/R/library --no-vignettes --timings qvalue_2.18.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.10-bioc/meat/qvalue.Rcheck’
* using R version 3.6.3 (2020-02-29)
* using platform: x86_64-pc-linux-gnu (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 ‘2.18.0’
* 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 ‘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 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
  ‘/home/biocbuild/bbs-3.10-bioc/meat/qvalue.Rcheck/00check.log’
for details.



Installation output

qvalue.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD INSTALL qvalue
###
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* installing to library ‘/home/biocbuild/bbs-3.10-bioc/R/library’
* installing *source* package ‘qvalue’ ...
** using staged installation
** 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 from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (qvalue)

Tests output


Example timings

qvalue.Rcheck/qvalue-Ex.timings

nameusersystemelapsed
empPvals0.0680.0080.077
hedenfalk1.3280.0321.368
hist.qvalue0.6240.0040.630
lfdr0.5760.0080.581
pi0est1.2120.0001.217
plot.qvalue0.9880.0081.005
qvalue1.4520.0081.468
summary.qvalue0.040.000.04
write.qvalue0.0760.0000.077