BioC 3.2: CHECK report for mQTL.NMR on oaxaca

Package: mQTL.NMR

Version: 1.3.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings mQTL.NMR_1.3.0.tar.gz

StartedAt: 2015-08-24 01:59:56 -0700 (Mon, 24 Aug 2015)

EndedAt: 2015-08-24 02:05:50 -0700 (Mon, 24 Aug 2015)

EllapsedTime: 353.6 seconds

RetCode: 0

Status:  OK

CheckDir: mQTL.NMR.Rcheck

Warnings: 0

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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_1.3.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.2-bioc/meat/mQTL.NMR.Rcheck’
* using R version 3.2.2 (2015-08-14)
* using platform: x86_64-apple-darwin13.4.0 (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 ‘1.3.0’
* 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 ... [3s/4s] 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 ... [200s/308s] OK
Examples with CPU or elapsed time > 5s
                   user system elapsed
mQTL.NMR-package 61.235  0.373 122.479
pre_mQTL         54.618  0.394  71.169
align_mQTL       51.078  0.358  77.560
process_mGWA      5.942  0.033   6.089
* 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.

* 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)

name	user	system	elapsed
SRV	2.212	0.044	2.262
SRV.plot	2.826	0.050	3.000
SRV_lod.plot	0.118	0.002	0.122
Top_SRV.plot	2.473	0.026	3.797
alignSp	1.399	0.014	2.792
align_mQTL	51.078	0.358	77.560
attachSegments	1.118	0.010	1.133
circle_mQTL	0.163	0.001	0.187
configureRSPA	0.006	0.001	0.007
format_mGWA	0.751	0.014	0.890
format_mQTL	1.376	0.026	1.745
load_datafiles	0.005	0.001	0.006
load_demo_data	0.000	0.000	0.001
mQTL.NMR-package	61.235	0.373	122.479
matchSegments	1.262	0.023	1.814
normalise	0.364	0.003	0.471
normalise_mQTL	3.229	0.061	3.415
peakPeaks	0.742	0.006	0.750
post_mQTL	0.409	0.028	0.454
ppersp	0.031	0.007	0.039
pplot	0.020	0.006	0.026
pre_mQTL	54.618	0.394	71.169
process_mGWA	5.942	0.033	6.089
process_mQTL	0.774	0.011	0.841
segmentateSp	1.146	0.014	1.187
selectRefSp	1.400	0.004	1.413
setupRSPA	0.006	0.001	0.007
sgolay	0.001	0.000	0.002
sgolayDeriv	0.246	0.007	0.254
simple.plot	2.336	0.029	2.455
summary_mQTL	0.017	0.001	0.018