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BioC 3.2: CHECK report for mQTL.NMR on perceval

This page was generated on 2015-10-27 17:36:28 -0400 (Tue, 27 Oct 2015).

Package 674/1104HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
mQTL.NMR 1.4.0
Lyamine Hedjazi
Snapshot Date: 2015-10-26 19:24:07 -0400 (Mon, 26 Oct 2015)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_2/madman/Rpacks/mQTL.NMR
Last Changed Rev: 109589 / Revision: 109947
Last Changed Date: 2015-10-13 15:36:05 -0400 (Tue, 13 Oct 2015)
linux1.bioconductor.org Linux (Ubuntu 14.04.2 LTS) / x86_64  NotNeeded  OK  OK UNNEEDED, same version exists in internal repository
windows1.bioconductor.org Windows Server 2012 R2 Enterprise SP1 (64-bit) / x64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository
perceval Mac OS X Snow Leopard (10.6.8) / x86_64  NotNeeded  OK [ OK ] OK UNNEEDED, same version exists in internal repository
oaxaca 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: 1.4.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings mQTL.NMR_1.4.0.tar.gz
StartedAt: 2015-10-27 10:11:51 -0400 (Tue, 27 Oct 2015)
EndedAt: 2015-10-27 10:18:29 -0400 (Tue, 27 Oct 2015)
EllapsedTime: 397.9 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_1.4.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.2-bioc/meat/mQTL.NMR.Rcheck’
* using R version 3.2.2 Patched (2015-10-08 r69496)
* using platform: x86_64-apple-darwin10.8.0 (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 ‘1.4.0’
* 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 ... [5s/34s] 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 ... OK
* 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 ... [245s/305s] OK
Examples with CPU or elapsed time > 5s
                   user system elapsed
align_mQTL       70.695  0.750  92.703
pre_mQTL         70.184  0.608  91.167
mQTL.NMR-package 67.754  0.972  81.993
process_mGWA      6.792  0.039   6.857
normalise_mQTL    4.951  0.110   7.124
* 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: 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.2-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
SRV2.1370.0552.251
SRV.plot1.9210.0401.961
SRV_lod.plot0.1140.0020.118
Top_SRV.plot1.7810.0341.815
alignSp1.1140.0221.159
align_mQTL70.695 0.75092.703
attachSegments0.9130.0320.945
circle_mQTL0.1640.0020.167
configureRSPA0.0060.0010.007
format_mGWA0.5050.0140.610
format_mQTL1.0580.0331.091
load_datafiles0.0050.0010.005
load_demo_data000
mQTL.NMR-package67.754 0.97281.993
matchSegments2.0000.0432.976
normalise0.4740.0050.671
normalise_mQTL4.9510.1107.124
peakPeaks0.9500.0121.386
post_mQTL0.7670.0621.594
ppersp0.0500.0120.062
pplot0.0300.0120.043
pre_mQTL70.184 0.60891.167
process_mGWA6.7920.0396.857
process_mQTL0.8580.0190.878
segmentateSp1.0150.0241.040
selectRefSp1.3640.0161.380
setupRSPA0.0060.0010.007
sgolay0.0010.0000.001
sgolayDeriv0.2380.0010.238
simple.plot2.5390.0493.252
summary_mQTL0.0440.0020.060