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BioC 3.4: CHECK report for mQTL.NMR on malbec1

This page was generated on 2017-04-15 16:12:14 -0400 (Sat, 15 Apr 2017).

Package 803/1296HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
mQTL.NMR 1.8.0
Lyamine Hedjazi
Snapshot Date: 2017-04-14 17:17:13 -0400 (Fri, 14 Apr 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_4/madman/Rpacks/mQTL.NMR
Last Changed Rev: 122710 / Revision: 128728
Last Changed Date: 2016-10-17 14:45:06 -0400 (Mon, 17 Oct 2016)
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
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: 1.8.0
Command: /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings mQTL.NMR_1.8.0.tar.gz
StartedAt: 2017-04-14 23:59:42 -0400 (Fri, 14 Apr 2017)
EndedAt: 2017-04-15 00:02:05 -0400 (Sat, 15 Apr 2017)
EllapsedTime: 143.1 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_1.8.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.4-bioc/meat/mQTL.NMR.Rcheck’
* using R version 3.3.3 (2017-03-06)
* 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 ‘1.8.0’
* 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 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 33.988  0.052  34.084
pre_mQTL         33.196  0.024  33.253
align_mQTL       28.424  0.040  28.490
process_mGWA      5.336  0.008   5.351
* 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
SRV1.2920.0121.308
SRV.plot1.5480.0081.556
SRV_lod.plot0.0840.0040.090
Top_SRV.plot1.2360.0041.241
alignSp0.6720.0080.679
align_mQTL28.424 0.04028.490
attachSegments0.7080.0120.720
circle_mQTL0.1240.0040.128
configureRSPA0.0040.0000.005
format_mGWA0.4240.0040.427
format_mQTL0.70.00.7
load_datafiles0.0040.0000.003
load_demo_data0.0000.0040.001
mQTL.NMR-package33.988 0.05234.084
matchSegments0.6440.0040.653
normalise0.1840.0000.186
normalise_mQTL1.9080.0041.917
peakPeaks0.2280.0080.240
post_mQTL0.1720.0000.175
ppersp0.0240.0000.027
pplot0.0160.0000.013
pre_mQTL33.196 0.02433.253
process_mGWA5.3360.0085.351
process_mQTL0.5640.0000.563
segmentateSp0.4840.0000.486
selectRefSp0.7320.0000.732
setupRSPA0.0040.0040.008
sgolay0.0040.0000.001
sgolayDeriv0.1640.0000.164
simple.plot1.2120.0121.224
summary_mQTL0.0200.0000.019