BioC 3.4: CHECK report for mQTL.NMR on moscato1

Package: mQTL.NMR

Version: 1.7.0

Command: rm -rf mQTL.NMR.buildbin-libdir mQTL.NMR.Rcheck && mkdir mQTL.NMR.buildbin-libdir mQTL.NMR.Rcheck && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=mQTL.NMR.buildbin-libdir mQTL.NMR_1.7.0.tar.gz >mQTL.NMR.Rcheck\00install.out 2>&1 && cp mQTL.NMR.Rcheck\00install.out mQTL.NMR-install.out && D:\biocbld\bbs-3.4-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_1.7.0.tar.gz

StartedAt: 2016-09-20 12:35:51 -0700 (Tue, 20 Sep 2016)

EndedAt: 2016-09-20 12:42:39 -0700 (Tue, 20 Sep 2016)

EllapsedTime: 408.1 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 && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=mQTL.NMR.buildbin-libdir mQTL.NMR_1.7.0.tar.gz >mQTL.NMR.Rcheck\00install.out 2>&1 && cp mQTL.NMR.Rcheck\00install.out mQTL.NMR-install.out  && D:\biocbld\bbs-3.4-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_1.7.0.tar.gz
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* using log directory 'D:/biocbld/bbs-3.4-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 '1.7.0'
* 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 47.56   0.11   48.02
pre_mQTL         47.13   0.03   47.28
align_mQTL       39.95   0.05   40.00
format_mGWA       0.92   0.00    9.68
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                  user system elapsed
mQTL.NMR-package 52.96   0.08   53.32
pre_mQTL         49.47   0.01   49.48
align_mQTL       45.04   0.05   45.08
process_mGWA      5.35   0.02    5.38
* 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
  'D:/biocbld/bbs-3.4-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_1.7.0.zip
* DONE (mQTL.NMR)

name	user	system	elapsed
SRV	1.45	0.00	1.45
SRV.plot	2.59	0.00	2.61
SRV_lod.plot	0.1	0.0	0.1
Top_SRV.plot	2.46	0.02	2.48
alignSp	0.95	0.01	0.96
align_mQTL	39.95	0.05	40.00
attachSegments	0.72	0.00	0.72
circle_mQTL	0.12	0.00	0.51
configureRSPA	0	0	0
format_mGWA	0.92	0.00	9.68
format_mQTL	1.25	0.02	1.27
load_datafiles	0.02	0.00	0.01
load_demo_data	0	0	0
mQTL.NMR-package	47.56	0.11	48.02
matchSegments	0.76	0.00	0.77
normalise	0.22	0.00	0.21
normalise_mQTL	3.89	0.01	5.00
peakPeaks	0.39	0.02	0.40
post_mQTL	0.28	0.08	0.69
ppersp	0.09	0.01	0.10
pplot	0.03	0.04	0.07
pre_mQTL	47.13	0.03	47.28
process_mGWA	4.34	0.00	4.34
process_mQTL	0.95	0.01	0.97
segmentateSp	0.84	0.00	0.84
selectRefSp	1.17	0.00	1.17
setupRSPA	0	0	0
sgolay	0.02	0.00	0.01
sgolayDeriv	0.20	0.00	0.21
simple.plot	2.50	0.02	2.51
summary_mQTL	0.01	0.00	0.01

name	user	system	elapsed
SRV	1.78	0.01	1.79
SRV.plot	2.22	0.03	2.26
SRV_lod.plot	0.12	0.00	0.13
Top_SRV.plot	1.95	0.02	1.96
alignSp	1.08	0.00	1.09
align_mQTL	45.04	0.05	45.08
attachSegments	0.78	0.00	0.78
circle_mQTL	0.17	0.00	0.28
configureRSPA	0	0	0
format_mGWA	0.67	0.03	0.77
format_mQTL	1.13	0.03	1.15
load_datafiles	0	0	0
load_demo_data	0	0	0
mQTL.NMR-package	52.96	0.08	53.32
matchSegments	0.97	0.00	0.97
normalise	0.41	0.00	0.40
normalise_mQTL	3.18	0.03	3.59
peakPeaks	0.4	0.0	0.4
post_mQTL	0.20	0.06	0.83
ppersp	0.07	0.05	0.16
pplot	0.03	0.03	0.06
pre_mQTL	49.47	0.01	49.48
process_mGWA	5.35	0.02	5.38
process_mQTL	0.89	0.00	0.89
segmentateSp	0.71	0.00	0.72
selectRefSp	1.46	0.00	1.45
setupRSPA	0	0	0
sgolay	0.01	0.00	0.02
sgolayDeriv	0.25	0.00	0.25
simple.plot	1.86	0.00	2.13
summary_mQTL	0.01	0.00	0.02