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CHECK report for mQTL.NMR on veracruz1

This page was generated on 2018-04-12 13:38:58 -0400 (Thu, 12 Apr 2018).

Package 896/1472HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
mQTL.NMR 1.12.0
Lyamine Hedjazi
Snapshot Date: 2018-04-11 16:45:18 -0400 (Wed, 11 Apr 2018)
URL: https://git.bioconductor.org/packages/mQTL.NMR
Branch: RELEASE_3_6
Last Commit: cd36672
Last Changed Date: 2017-10-30 12:40:19 -0400 (Mon, 30 Oct 2017)
malbec1 Linux (Ubuntu 16.04.1 LTS) / x86_64  NotNeeded  OK  OK UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository
veracruz1 OS X 10.11.6 El Capitan / x86_64  NotNeeded  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: mQTL.NMR
Version: 1.12.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings mQTL.NMR_1.12.0.tar.gz
StartedAt: 2018-04-12 06:45:52 -0400 (Thu, 12 Apr 2018)
EndedAt: 2018-04-12 06:48:43 -0400 (Thu, 12 Apr 2018)
EllapsedTime: 170.5 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 --no-vignettes --timings mQTL.NMR_1.12.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.6-bioc/meat/mQTL.NMR.Rcheck’
* using R version 3.4.4 (2018-03-15)
* 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 ‘1.12.0’
* 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 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
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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                   user system elapsed
mQTL.NMR-package 37.183  0.260  38.483
pre_mQTL         34.307  0.222  35.634
align_mQTL       32.080  0.182  32.832
process_mGWA      6.147  0.032   6.369
* 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-3.6-bioc/meat/mQTL.NMR.Rcheck/00check.log’
for details.



Installation output

mQTL.NMR.Rcheck/00install.out

* installing *source* package ‘mQTL.NMR’ ...
** R
** inst
** preparing 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
SRV1.6540.0341.713
SRV.plot1.7970.0401.856
SRV_lod.plot0.1070.0020.115
Top_SRV.plot1.7160.0201.761
alignSp1.2730.0101.300
align_mQTL32.080 0.18232.832
attachSegments0.7710.0070.795
circle_mQTL0.1670.0010.171
configureRSPA0.0050.0010.006
format_mGWA0.5720.0140.612
format_mQTL0.9110.0130.957
load_datafiles0.0050.0000.005
load_demo_data0.0010.0010.001
mQTL.NMR-package37.183 0.26038.483
matchSegments0.7930.0080.826
normalise0.3590.0040.372
normalise_mQTL2.2770.0462.434
peakPeaks0.4170.0030.434
post_mQTL0.3990.0240.440
ppersp0.0260.0070.035
pplot0.0180.0060.024
pre_mQTL34.307 0.22235.634
process_mGWA6.1470.0326.369
process_mQTL0.6020.0140.652
segmentateSp0.6300.0110.660
selectRefSp1.1160.0051.137
setupRSPA0.0050.0010.006
sgolay0.0020.0000.001
sgolayDeriv0.1170.0010.118
simple.plot1.4780.0211.577
summary_mQTL0.0140.0010.016