BioC 3.1: CHECK report for mQTL.NMR on moscato2

Package: mQTL.NMR

Version: 1.2.0

Command: rm -rf mQTL.NMR.buildbin-libdir mQTL.NMR.Rcheck && mkdir mQTL.NMR.buildbin-libdir mQTL.NMR.Rcheck && E:\biocbld\bbs-3.1-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=mQTL.NMR.buildbin-libdir mQTL.NMR_1.2.0.tar.gz >mQTL.NMR.Rcheck\00install.out 2>&1 && cp mQTL.NMR.Rcheck\00install.out mQTL.NMR-install.out && E:\biocbld\bbs-3.1-bioc\R\bin\R.exe CMD check --library=mQTL.NMR.buildbin-libdir --install="check:mQTL.NMR-install.out" --force-multiarch --no-vignettes --timings mQTL.NMR_1.2.0.tar.gz

StartedAt: 2015-10-09 04:07:27 -0700 (Fri, 09 Oct 2015)

EndedAt: 2015-10-09 04:14:48 -0700 (Fri, 09 Oct 2015)

EllapsedTime: 440.2 seconds

RetCode: 0

Status:  OK

CheckDir: mQTL.NMR.Rcheck

Warnings: 0

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### Running command:
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###   rm -rf mQTL.NMR.buildbin-libdir mQTL.NMR.Rcheck && mkdir mQTL.NMR.buildbin-libdir mQTL.NMR.Rcheck && E:\biocbld\bbs-3.1-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=mQTL.NMR.buildbin-libdir mQTL.NMR_1.2.0.tar.gz >mQTL.NMR.Rcheck\00install.out 2>&1 && cp mQTL.NMR.Rcheck\00install.out mQTL.NMR-install.out  && E:\biocbld\bbs-3.1-bioc\R\bin\R.exe CMD check --library=mQTL.NMR.buildbin-libdir --install="check:mQTL.NMR-install.out" --force-multiarch --no-vignettes --timings mQTL.NMR_1.2.0.tar.gz
###
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* using log directory 'E:/biocbld/bbs-3.1-bioc/meat/mQTL.NMR.Rcheck'
* using R version 3.2.2 (2015-08-14)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'mQTL.NMR/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'mQTL.NMR' version '1.2.0'
* 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 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... [186s] OK
Examples with CPU or elapsed time > 5s
                  user system elapsed
mQTL.NMR-package 56.91   0.17   57.42
pre_mQTL         53.60   0.06   53.76
align_mQTL       43.38   0.05   43.43
process_mGWA      5.34   0.00    5.61
** running examples for arch 'x64' ... [195s] OK
Examples with CPU or elapsed time > 5s
                  user system elapsed
mQTL.NMR-package 58.58   0.14   59.14
pre_mQTL         53.38   0.08   53.51
align_mQTL       48.97   0.09   49.07
process_mGWA      6.06   0.02    6.08
* 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
  'E:/biocbld/bbs-3.1-bioc/meat/mQTL.NMR.Rcheck/00check.log'
for details.

install for i386

* 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

install for x64

* installing *source* package 'mQTL.NMR' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'mQTL.NMR' as mQTL.NMR_1.2.0.zip
* DONE (mQTL.NMR)

name	user	system	elapsed
SRV	1.43	0.01	1.46
SRV.plot	2.81	0.00	2.87
SRV_lod.plot	0.10	0.00	0.09
Top_SRV.plot	2.51	0.02	2.53
alignSp	0.94	0.00	0.94
align_mQTL	43.38	0.05	43.43
attachSegments	0.91	0.00	0.91
circle_mQTL	0.14	0.00	0.14
configureRSPA	0	0	0
format_mGWA	1.00	0.00	1.09
format_mQTL	1.4	0.0	1.4
load_datafiles	0	0	0
load_demo_data	0	0	0
mQTL.NMR-package	56.91	0.17	57.42
matchSegments	0.99	0.01	1.02
normalise	0.36	0.00	0.36
normalise_mQTL	4.48	0.00	4.47
peakPeaks	0.45	0.02	0.47
post_mQTL	0.14	0.11	0.25
ppersp	0.07	0.01	0.08
pplot	0.01	0.02	0.03
pre_mQTL	53.60	0.06	53.76
process_mGWA	5.34	0.00	5.61
process_mQTL	0.98	0.00	0.99
segmentateSp	0.95	0.00	0.95
selectRefSp	1.25	0.00	1.25
setupRSPA	0.02	0.00	0.01
sgolay	0	0	0
sgolayDeriv	0.22	0.00	0.22
simple.plot	2.77	0.00	2.78
summary_mQTL	0.02	0.00	0.01

name	user	system	elapsed
SRV	2.00	0.00	1.99
SRV.plot	2.87	0.03	2.92
SRV_lod.plot	0.13	0.00	0.12
Top_SRV.plot	2.49	0.00	2.50
alignSp	1.00	0.00	0.99
align_mQTL	48.97	0.09	49.07
attachSegments	0.88	0.00	0.89
circle_mQTL	0.14	0.02	0.16
configureRSPA	0	0	0
format_mGWA	0.65	0.01	1.34
format_mQTL	1.53	0.00	1.53
load_datafiles	0.01	0.00	0.01
load_demo_data	0	0	0
mQTL.NMR-package	58.58	0.14	59.14
matchSegments	0.83	0.03	0.86
normalise	0.31	0.00	0.32
normalise_mQTL	4.26	0.05	4.40
peakPeaks	0.41	0.00	0.40
post_mQTL	0.23	0.05	0.41
ppersp	0.08	0.00	0.07
pplot	0.02	0.01	0.04
pre_mQTL	53.38	0.08	53.51
process_mGWA	6.06	0.02	6.08
process_mQTL	1.14	0.00	1.14
segmentateSp	0.95	0.00	0.96
selectRefSp	1.92	0.00	1.91
setupRSPA	0.01	0.00	0.02
sgolay	0	0	0
sgolayDeriv	0.41	0.00	0.41
simple.plot	2.62	0.01	2.63
summary_mQTL	0.02	0.00	0.02