BioC 3.2: CHECK report for mQTL.NMR on moscato1

Package: mQTL.NMR

Version: 1.3.0

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_1.3.0.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_1.3.0.tar.gz

StartedAt: 2015-08-20 07:37:19 -0700 (Thu, 20 Aug 2015)

EndedAt: 2015-08-20 07:45:36 -0700 (Thu, 20 Aug 2015)

EllapsedTime: 497.4 seconds

RetCode: 0

Status:  OK

CheckDir: mQTL.NMR.Rcheck

Warnings: 0

##############################################################################
##############################################################################
###
### Running 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_1.3.0.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_1.3.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'D:/biocbld/bbs-3.2-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 '1.3.0'
* 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 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' ... [210s] OK
Examples with CPU or elapsed time > 5s
                  user system elapsed
mQTL.NMR-package 62.70   0.15   63.02
pre_mQTL         55.77   0.05   55.83
align_mQTL       53.21   0.03   53.25
process_mGWA      5.97   0.02    6.58
normalise_mQTL    5.50   0.00    5.50
** running examples for arch 'x64' ... [225s] OK
Examples with CPU or elapsed time > 5s
                  user system elapsed
mQTL.NMR-package 64.79   0.13   65.80
pre_mQTL         60.77   0.00   60.76
align_mQTL       58.13   0.03   58.39
process_mGWA      7.30   0.02    8.54
* 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_1.3.0.zip
* DONE (mQTL.NMR)

name	user	system	elapsed
SRV	1.63	0.00	1.68
SRV.plot	3.23	0.00	3.25
SRV_lod.plot	0.14	0.00	0.14
Top_SRV.plot	3.39	0.01	3.40
alignSp	1.22	0.00	1.22
align_mQTL	53.21	0.03	53.25
attachSegments	1.12	0.03	1.16
circle_mQTL	0.19	0.04	0.50
configureRSPA	0	0	0
format_mGWA	1.18	0.03	1.84
format_mQTL	1.74	0.00	1.73
load_datafiles	0.01	0.00	0.02
load_demo_data	0	0	0
mQTL.NMR-package	62.70	0.15	63.02
matchSegments	0.97	0.00	0.97
normalise	0.28	0.00	0.28
normalise_mQTL	5.5	0.0	5.5
peakPeaks	0.69	0.00	0.69
post_mQTL	0.25	0.10	0.36
ppersp	0.08	0.01	0.09
pplot	0.02	0.03	0.05
pre_mQTL	55.77	0.05	55.83
process_mGWA	5.97	0.02	6.58
process_mQTL	1.13	0.00	1.13
segmentateSp	1.06	0.00	1.06
selectRefSp	1.62	0.00	1.62
setupRSPA	0.02	0.00	0.01
sgolay	0	0	0
sgolayDeriv	0.36	0.00	0.36
simple.plot	2.98	0.00	2.98
summary_mQTL	0.01	0.00	0.01

name	user	system	elapsed
SRV	2.23	0.00	2.23
SRV.plot	2.95	0.02	3.48
SRV_lod.plot	0.12	0.00	0.60
Top_SRV.plot	2.76	0.01	2.86
alignSp	1.05	0.00	1.05
align_mQTL	58.13	0.03	58.39
attachSegments	0.92	0.00	0.92
circle_mQTL	0.20	0.00	0.21
configureRSPA	0.00	0.02	0.01
format_mGWA	0.84	0.01	3.18
format_mQTL	1.47	0.02	1.49
load_datafiles	0.00	0.01	0.01
load_demo_data	0	0	0
mQTL.NMR-package	64.79	0.13	65.80
matchSegments	1.18	0.00	1.19
normalise	0.34	0.00	0.34
normalise_mQTL	4.65	0.04	4.70
peakPeaks	0.47	0.02	0.48
post_mQTL	0.20	0.08	0.31
ppersp	0.05	0.01	0.07
pplot	0.04	0.00	0.04
pre_mQTL	60.77	0.00	60.76
process_mGWA	7.30	0.02	8.54
process_mQTL	1.03	0.01	1.04
segmentateSp	0.98	0.00	0.99
selectRefSp	1.89	0.00	1.88
setupRSPA	0.01	0.00	0.02
sgolay	0	0	0
sgolayDeriv	0.33	0.00	0.33
simple.plot	2.50	0.00	2.49
summary_mQTL	0.01	0.00	0.02