BioC 3.3: CHECK report for mQTL.NMR on moscato2

Package: mQTL.NMR

Version: 1.6.0

Command: rm -rf mQTL.NMR.buildbin-libdir mQTL.NMR.Rcheck && mkdir mQTL.NMR.buildbin-libdir mQTL.NMR.Rcheck && E:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=mQTL.NMR.buildbin-libdir mQTL.NMR_1.6.0.tar.gz >mQTL.NMR.Rcheck\00install.out 2>&1 && cp mQTL.NMR.Rcheck\00install.out mQTL.NMR-install.out && E:\biocbld\bbs-3.3-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_1.6.0.tar.gz

StartedAt: 2016-10-13 06:32:29 -0700 (Thu, 13 Oct 2016)

EndedAt: 2016-10-13 06:41:34 -0700 (Thu, 13 Oct 2016)

EllapsedTime: 545.1 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-3.3-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=mQTL.NMR.buildbin-libdir mQTL.NMR_1.6.0.tar.gz >mQTL.NMR.Rcheck\00install.out 2>&1 && cp mQTL.NMR.Rcheck\00install.out mQTL.NMR-install.out  && E:\biocbld\bbs-3.3-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_1.6.0.tar.gz
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* using log directory 'E:/biocbld/bbs-3.3-bioc/meat/mQTL.NMR.Rcheck'
* using R version 3.3.1 (2016-06-21)
* 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 '1.6.0'
* 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 ... NOTE
circle_mQTL: no visible global function definition for 'rainbow'
post_mQTL: no visible global function definition for 'dev.new'
post_mQTL: no visible global function definition for 'png'
post_mQTL: no visible global function definition for 'dev.off'
ppersp: no visible global function definition for 'colorRampPalette'
Undefined global functions or variables:
  colorRampPalette dev.new dev.off png rainbow
Consider adding
  importFrom("grDevices", "colorRampPalette", "dev.new", "dev.off",
             "png", "rainbow")
to your NAMESPACE file.
* 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' ... OK
Examples with CPU or elapsed time > 5s
                  user system elapsed
mQTL.NMR-package 67.88   0.19   69.11
pre_mQTL         63.00   0.07   63.09
align_mQTL       57.77   0.07   57.83
process_mGWA      6.14   0.00    6.17
normalise_mQTL    5.43   0.06    5.50
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                  user system elapsed
mQTL.NMR-package 72.74   0.16   73.41
pre_mQTL         60.43   0.06   60.60
align_mQTL       57.39   0.08   59.14
process_mGWA      7.94   0.02    8.04
* 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: 2 NOTEs
See
  'E:/biocbld/bbs-3.3-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_1.6.0.zip
* DONE (mQTL.NMR)

name	user	system	elapsed
SRV	2.78	0.03	2.81
SRV.plot	4.04	0.02	4.07
SRV_lod.plot	0.15	0.00	0.16
Top_SRV.plot	3.14	0.01	3.48
alignSp	1.56	0.00	1.56
align_mQTL	57.77	0.07	57.83
attachSegments	0.97	0.00	0.97
circle_mQTL	0.16	0.00	0.17
configureRSPA	0	0	0
format_mGWA	1.17	0.00	1.32
format_mQTL	1.98	0.00	2.07
load_datafiles	0	0	0
load_demo_data	0	0	0
mQTL.NMR-package	67.88	0.19	69.11
matchSegments	1.00	0.02	1.01
normalise	0.39	0.00	0.39
normalise_mQTL	5.43	0.06	5.50
peakPeaks	0.63	0.01	0.65
post_mQTL	0.25	0.07	0.33
ppersp	0.08	0.01	0.09
pplot	0.03	0.02	0.05
pre_mQTL	63.00	0.07	63.09
process_mGWA	6.14	0.00	6.17
process_mQTL	1.15	0.02	1.17
segmentateSp	0.91	0.00	0.90
selectRefSp	1.78	0.02	1.80
setupRSPA	0	0	0
sgolay	0.02	0.00	0.02
sgolayDeriv	0.37	0.00	0.37
simple.plot	3.01	0.00	3.01
summary_mQTL	0.02	0.00	0.01

name	user	system	elapsed
SRV	2.87	0.00	2.87
SRV.plot	4.14	0.00	4.14
SRV_lod.plot	0.23	0.00	0.23
Top_SRV.plot	2.14	0.02	2.15
alignSp	1.25	0.00	1.25
align_mQTL	57.39	0.08	59.14
attachSegments	1.24	0.00	1.23
circle_mQTL	0.25	0.00	0.95
configureRSPA	0.00	0.01	0.02
format_mGWA	1.01	0.00	1.20
format_mQTL	1.37	0.00	1.37
load_datafiles	0.02	0.00	0.02
load_demo_data	0	0	0
mQTL.NMR-package	72.74	0.16	73.41
matchSegments	1.12	0.00	1.13
normalise	0.43	0.00	0.42
normalise_mQTL	4.16	0.00	4.22
peakPeaks	0.58	0.00	0.58
post_mQTL	0.28	0.08	0.52
ppersp	0.06	0.04	0.89
pplot	0.05	0.02	0.06
pre_mQTL	60.43	0.06	60.60
process_mGWA	7.94	0.02	8.04
process_mQTL	1.38	0.01	1.39
segmentateSp	1.12	0.00	1.12
selectRefSp	2.23	0.00	2.23
setupRSPA	0.02	0.00	0.01
sgolay	0	0	0
sgolayDeriv	0.40	0.00	0.41
simple.plot	2.64	0.05	2.68
summary_mQTL	0.00	0.01	0.02