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BioC 3.4: CHECK report for mQTL.NMR on zin1

This page was generated on 2016-09-21 03:39:07 -0700 (Wed, 21 Sep 2016).

Package 780/1257HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
mQTL.NMR 1.7.0
Lyamine Hedjazi
Snapshot Date: 2016-09-19 19:15:14 -0700 (Mon, 19 Sep 2016)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/mQTL.NMR
Last Changed Rev: 117081 / Revision: 121152
Last Changed Date: 2016-05-03 14:30:44 -0700 (Tue, 03 May 2016)
zin1 Linux (Ubuntu 16.04 LTS) / x86_64  NotNeeded  OK [ OK ]UNNEEDED, same version exists in internal repository
moscato1 Windows Server 2008 R2 Standard (64-bit) / x64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository
morelia Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: mQTL.NMR
Version: 1.7.0
Command: /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings mQTL.NMR_1.7.0.tar.gz
StartedAt: 2016-09-20 09:36:47 -0700 (Tue, 20 Sep 2016)
EndedAt: 2016-09-20 09:39:03 -0700 (Tue, 20 Sep 2016)
EllapsedTime: 136.0 seconds
RetCode: 0
Status:  OK 
CheckDir: mQTL.NMR.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings mQTL.NMR_1.7.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.4-bioc/meat/mQTL.NMR.Rcheck’
* using R version 3.3.1 (2016-06-21)
* using platform: x86_64-pc-linux-gnu (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 ‘1.7.0’
* 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 34.004  0.056  34.150
pre_mQTL         30.368  0.012  30.644
align_mQTL       29.852  0.032  29.885
* 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
  ‘/home/biocbuild/bbs-3.4-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
SRV1.1120.0121.126
SRV.plot1.3240.0121.338
SRV_lod.plot0.0880.0000.088
Top_SRV.plot1.1880.0161.203
alignSp0.6800.0000.678
align_mQTL29.852 0.03229.885
attachSegments0.5360.0040.539
circle_mQTL0.1200.0000.119
configureRSPA0.0040.0000.004
format_mGWA0.4280.0040.444
format_mQTL0.6680.0000.670
load_datafiles0.0040.0000.004
load_demo_data0.0000.0000.001
mQTL.NMR-package34.004 0.05634.150
matchSegments0.5240.0040.526
normalise0.1960.0000.192
normalise_mQTL1.5920.0121.625
peakPeaks0.2440.0040.248
post_mQTL0.1920.0000.191
ppersp0.0240.0000.027
pplot0.0120.0000.014
pre_mQTL30.368 0.01230.644
process_mGWA4.1320.0044.138
process_mQTL1.1440.0001.142
segmentateSp0.4680.0000.468
selectRefSp0.9560.0000.955
setupRSPA0.0040.0000.005
sgolay000
sgolayDeriv0.2160.0000.219
simple.plot0.9520.0040.959
summary_mQTL0.0080.0000.011