BioC 3.2: CHECK report for mQTL.NMR on moscato1

Package: mQTL.NMR

Version: 1.4.0

Command: rm -rf mQTL.NMR.buildbin-libdir mQTL.NMR.Rcheck && mkdir mQTL.NMR.buildbin-libdir mQTL.NMR.Rcheck && D:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=mQTL.NMR.buildbin-libdir mQTL.NMR_1.4.0.tar.gz >mQTL.NMR.Rcheck\00install.out 2>&1 && cp mQTL.NMR.Rcheck\00install.out mQTL.NMR-install.out && D:\biocbld\bbs-3.2-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_1.4.0.tar.gz

StartedAt: 2016-04-23 05:01:09 -0700 (Sat, 23 Apr 2016)

EndedAt: 2016-04-23 05:12:49 -0700 (Sat, 23 Apr 2016)

EllapsedTime: 699.9 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 && D:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=mQTL.NMR.buildbin-libdir mQTL.NMR_1.4.0.tar.gz >mQTL.NMR.Rcheck\00install.out 2>&1 && cp mQTL.NMR.Rcheck\00install.out mQTL.NMR-install.out  && D:\biocbld\bbs-3.2-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_1.4.0.tar.gz
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* using log directory 'D:/biocbld/bbs-3.2-bioc/meat/mQTL.NMR.Rcheck'
* using R version 3.2.4 (2016-03-10)
* 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 '1.4.0'
* 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 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' ... [304s] OK
Examples with CPU or elapsed time > 5s
                  user system elapsed
mQTL.NMR-package 87.42   0.27   88.69
pre_mQTL         82.42   0.08   82.51
align_mQTL       80.42   0.13   80.61
normalise_mQTL    8.41   0.03    8.44
process_mGWA      7.33   0.01    7.44
SRV.plot          4.90   0.11    5.25
** running examples for arch 'x64' ... [300s] OK
Examples with CPU or elapsed time > 5s
                  user system elapsed
mQTL.NMR-package 80.29   0.13   83.73
pre_mQTL         79.90   0.05   83.45
align_mQTL       66.72   0.17   67.91
process_mGWA      8.79   0.02    8.97
normalise_mQTL    4.71   0.06    7.94
format_mGWA       1.01   0.00   14.17
circle_mQTL       0.22   0.00    5.85
* 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
  'D:/biocbld/bbs-3.2-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_1.4.0.zip
* DONE (mQTL.NMR)

name	user	system	elapsed
SRV	3.36	0.05	3.40
SRV.plot	4.90	0.11	5.25
SRV_lod.plot	0.21	0.00	0.27
Top_SRV.plot	4.18	0.03	4.21
alignSp	1.92	0.00	1.92
align_mQTL	80.42	0.13	80.61
attachSegments	1.37	0.01	1.40
circle_mQTL	0.23	0.00	0.23
configureRSPA	0.02	0.00	0.02
format_mGWA	1.39	0.00	2.06
format_mQTL	2.2	0.0	2.2
load_datafiles	0.01	0.00	0.01
load_demo_data	0	0	0
mQTL.NMR-package	87.42	0.27	88.69
matchSegments	1.86	0.00	1.85
normalise	0.5	0.0	0.5
normalise_mQTL	8.41	0.03	8.44
peakPeaks	1.09	0.00	1.09
post_mQTL	0.40	0.11	0.77
ppersp	0.08	0.01	0.09
pplot	0.03	0.02	0.05
pre_mQTL	82.42	0.08	82.51
process_mGWA	7.33	0.01	7.44
process_mQTL	1.64	0.00	1.65
segmentateSp	1.21	0.00	1.22
selectRefSp	1.22	0.00	1.22
setupRSPA	0.02	0.00	0.01
sgolay	0	0	0
sgolayDeriv	0.2	0.0	0.2
simple.plot	2.81	0.05	2.86
summary_mQTL	0.03	0.00	0.03

name	user	system	elapsed
SRV	2.26	0.00	2.26
SRV.plot	3.10	0.00	3.18
SRV_lod.plot	0.19	0.00	0.19
Top_SRV.plot	3.31	0.01	3.32
alignSp	1.95	0.02	1.97
align_mQTL	66.72	0.17	67.91
attachSegments	1.04	0.00	1.04
circle_mQTL	0.22	0.00	5.85
configureRSPA	0.02	0.00	0.02
format_mGWA	1.01	0.00	14.17
format_mQTL	1.20	0.01	1.22
load_datafiles	0.02	0.00	0.01
load_demo_data	0	0	0
mQTL.NMR-package	80.29	0.13	83.73
matchSegments	1.06	0.00	1.06
normalise	0.50	0.00	0.49
normalise_mQTL	4.71	0.06	7.94
peakPeaks	0.65	0.00	0.66
post_mQTL	0.21	0.09	0.90
ppersp	0.06	0.03	0.10
pplot	0.06	0.03	0.09
pre_mQTL	79.90	0.05	83.45
process_mGWA	8.79	0.02	8.97
process_mQTL	1.29	0.00	1.29
segmentateSp	1.33	0.00	1.33
selectRefSp	2.31	0.00	2.31
setupRSPA	0.00	0.01	0.01
sgolay	0	0	0
sgolayDeriv	0.52	0.00	0.51
simple.plot	3.02	0.00	3.03
summary_mQTL	0.02	0.00	0.01