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CHECK report for mQTL.NMR on merida2

This page was generated on 2018-07-17 11:13:23 -0400 (Tue, 17 Jul 2018).

Package 946/1560HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
mQTL.NMR 1.14.0
Lyamine Hedjazi
Snapshot Date: 2018-07-16 16:45:11 -0400 (Mon, 16 Jul 2018)
URL: https://git.bioconductor.org/packages/mQTL.NMR
Branch: RELEASE_3_7
Last Commit: ecb1df3
Last Changed Date: 2018-04-30 10:35:33 -0400 (Mon, 30 Apr 2018)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  ERROR  ERROR  skipped 
tokay2 Windows Server 2012 R2 Standard / x64  ERROR  ERROR  skipped  skipped 
merida2 OS X 10.11.6 El Capitan / x86_64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: mQTL.NMR
Version: 1.14.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:mQTL.NMR.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings mQTL.NMR_1.14.0.tar.gz
StartedAt: 2018-07-17 01:00:16 -0400 (Tue, 17 Jul 2018)
EndedAt: 2018-07-17 01:04:12 -0400 (Tue, 17 Jul 2018)
EllapsedTime: 235.7 seconds
RetCode: 0
Status:  OK 
CheckDir: mQTL.NMR.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:mQTL.NMR.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings mQTL.NMR_1.14.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.7-bioc/meat/mQTL.NMR.Rcheck’
* using R version 3.5.0 (2018-04-23)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘mQTL.NMR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘mQTL.NMR’ version ‘1.14.0’
* 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 ‘mQTL.NMR’ 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 ... NOTE
Found the following CITATION file in a non-standard place:
  inst/CITATION.Rd
Most likely ‘inst/CITATION’ should be used instead.
* 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
circle_mQTL: no visible global function definition for ‘rainbow’
post_mQTL: no visible global function definition for ‘dev.new’
post_mQTL: no visible global function definition for ‘png’
post_mQTL: no visible global function definition for ‘dev.off’
ppersp: no visible global function definition for ‘colorRampPalette’
Undefined global functions or variables:
  colorRampPalette dev.new dev.off png rainbow
Consider adding
  importFrom("grDevices", "colorRampPalette", "dev.new", "dev.off",
             "png", "rainbow")
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 sizes of PDF files under ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                   user system elapsed
mQTL.NMR-package 58.545  0.353  59.255
pre_mQTL         58.548  0.257  59.234
align_mQTL       51.663  0.318  52.320
process_mGWA      7.053  0.026   7.129
* 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
  ‘/Users/biocbuild/bbs-3.7-bioc/meat/mQTL.NMR.Rcheck/00check.log’
for details.



Installation output

mQTL.NMR.Rcheck/00install.out

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL mQTL.NMR
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library’
* installing *source* package ‘mQTL.NMR’ ...
** R
** 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 (mQTL.NMR)

Tests output


Example timings

mQTL.NMR.Rcheck/mQTL.NMR-Ex.timings

nameusersystemelapsed
SRV2.1330.0432.185
SRV.plot1.8360.0451.895
SRV_lod.plot0.1350.0020.143
Top_SRV.plot1.6170.0261.654
alignSp1.0300.0241.058
align_mQTL51.663 0.31852.320
attachSegments0.7140.0100.728
circle_mQTL0.1430.0010.146
configureRSPA0.0080.0010.009
format_mGWA0.5780.0130.603
format_mQTL0.8970.0150.920
load_datafiles0.0050.0010.005
load_demo_data0.0010.0000.001
mQTL.NMR-package58.545 0.35359.255
matchSegments0.8180.0130.837
normalise0.5070.0070.520
normalise_mQTL2.4870.0512.565
peakPeaks0.3300.0040.334
post_mQTL0.4290.0410.484
ppersp0.0320.0070.039
pplot0.0230.0090.031
pre_mQTL58.548 0.25759.234
process_mGWA7.0530.0267.129
process_mQTL0.7430.0180.767
segmentateSp0.7370.0140.755
selectRefSp1.8410.0051.856
setupRSPA0.0080.0010.009
sgolay0.0020.0000.001
sgolayDeriv0.1450.0010.147
simple.plot1.5460.0251.586
summary_mQTL0.0200.0020.022