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BioC 3.5: CHECK report for mQTL.NMR on veracruz2

This page was generated on 2017-08-16 13:32:10 -0400 (Wed, 16 Aug 2017).

Package 854/1382HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
mQTL.NMR 1.10.0
Lyamine Hedjazi
Snapshot Date: 2017-08-15 17:17:57 -0400 (Tue, 15 Aug 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_5/madman/Rpacks/mQTL.NMR
Last Changed Rev: 129126 / Revision: 131943
Last Changed Date: 2017-04-24 15:25:24 -0400 (Mon, 24 Apr 2017)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  NotNeeded  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository
veracruz2 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: 1.10.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings mQTL.NMR_1.10.0.tar.gz
StartedAt: 2017-08-16 05:39:00 -0400 (Wed, 16 Aug 2017)
EndedAt: 2017-08-16 05:42:11 -0400 (Wed, 16 Aug 2017)
EllapsedTime: 190.7 seconds
RetCode: 0
Status:  OK 
CheckDir: mQTL.NMR.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings mQTL.NMR_1.10.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/mQTL.NMR.Rcheck’
* using R version 3.4.1 (2017-06-30)
* 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 ‘1.10.0’
* 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 39.763  0.261  43.667
align_mQTL       36.569  0.231  44.132
pre_mQTL         33.399  0.200  34.791
process_mGWA      6.229  0.024   6.493
* 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-3.5-bioc/meat/mQTL.NMR.Rcheck/00check.log’
for details.


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)

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

nameusersystemelapsed
SRV2.0410.0402.632
SRV.plot2.0120.0372.280
SRV_lod.plot0.7490.0030.869
Top_SRV.plot1.9960.0312.616
alignSp1.3620.0131.559
align_mQTL36.569 0.23144.132
attachSegments0.7030.0070.737
circle_mQTL0.1600.0010.167
configureRSPA0.0050.0000.006
format_mGWA0.6600.0110.822
format_mQTL1.0160.0131.324
load_datafiles0.0050.0010.007
load_demo_data0.0000.0000.001
mQTL.NMR-package39.763 0.26143.667
matchSegments0.7270.0090.762
normalise0.3180.0020.323
normalise_mQTL2.4100.0442.554
peakPeaks0.4950.0050.504
post_mQTL0.3670.0260.407
ppersp0.0200.0060.026
pplot0.0170.0060.023
pre_mQTL33.399 0.20034.791
process_mGWA6.2290.0246.493
process_mQTL2.3130.0152.377
segmentateSp0.7140.0120.800
selectRefSp1.0450.0031.073
setupRSPA0.0050.0010.010
sgolay0.0020.0000.001
sgolayDeriv0.1090.0000.118
simple.plot1.5350.0181.601
summary_mQTL0.0110.0000.011