BioC 3.5: CHECK report for mQTL.NMR on tokay2

Package: mQTL.NMR

Version: 1.10.0

Command: rm -rf mQTL.NMR.buildbin-libdir mQTL.NMR.Rcheck && mkdir mQTL.NMR.buildbin-libdir mQTL.NMR.Rcheck && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=mQTL.NMR.buildbin-libdir mQTL.NMR_1.10.0.tar.gz >mQTL.NMR.Rcheck\00install.out 2>&1 && cp mQTL.NMR.Rcheck\00install.out mQTL.NMR-install.out && C:\Users\biocbuild\bbs-3.5-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_1.10.0.tar.gz

StartedAt: 2017-08-16 01:25:20 -0400 (Wed, 16 Aug 2017)

EndedAt: 2017-08-16 01:31:09 -0400 (Wed, 16 Aug 2017)

EllapsedTime: 349.0 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 && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=mQTL.NMR.buildbin-libdir mQTL.NMR_1.10.0.tar.gz >mQTL.NMR.Rcheck\00install.out 2>&1 && cp mQTL.NMR.Rcheck\00install.out mQTL.NMR-install.out  &&  C:\Users\biocbuild\bbs-3.5-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_1.10.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.5-bioc/meat/mQTL.NMR.Rcheck'
* using R version 3.4.1 (2017-06-30)
* 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 '1.10.0'
* 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 41.11   0.19   41.36
pre_mQTL         33.82   0.14   33.96
align_mQTL       27.09   0.13   27.24
process_mGWA      7.21   0.02    7.22
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                  user system elapsed
pre_mQTL         43.10   0.10   43.19
mQTL.NMR-package 38.97   0.17   39.29
align_mQTL       33.79   0.04   33.84
process_mGWA      7.78   0.01    9.53
* 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
  'C:/Users/biocbuild/bbs-3.5-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_1.10.0.zip
* DONE (mQTL.NMR)

name	user	system	elapsed
SRV	1.40	0.04	1.46
SRV.plot	2.66	0.08	2.75
SRV_lod.plot	0.67	0.00	0.67
Top_SRV.plot	2.11	0.02	2.13
alignSp	1.28	0.01	1.30
align_mQTL	27.09	0.13	27.24
attachSegments	0.55	0.00	0.55
circle_mQTL	0.14	0.00	0.14
configureRSPA	0	0	0
format_mGWA	0.66	0.00	0.72
format_mQTL	1.12	0.01	1.14
load_datafiles	0	0	0
load_demo_data	0	0	0
mQTL.NMR-package	41.11	0.19	41.36
matchSegments	0.58	0.00	0.58
normalise	0.24	0.00	0.23
normalise_mQTL	3.40	0.00	3.41
peakPeaks	0.42	0.00	0.43
post_mQTL	0.22	0.05	0.26
ppersp	0.03	0.01	0.05
pplot	0.03	0.00	0.03
pre_mQTL	33.82	0.14	33.96
process_mGWA	7.21	0.02	7.22
process_mQTL	1.83	0.02	1.85
segmentateSp	0.57	0.00	0.58
selectRefSp	0.66	0.00	0.65
setupRSPA	0	0	0
sgolay	0	0	0
sgolayDeriv	0.08	0.00	0.08
simple.plot	2.05	0.03	2.07
summary_mQTL	0.00	0.02	0.02

name	user	system	elapsed
SRV	1.86	0.03	1.90
SRV.plot	2.39	0.04	2.43
SRV_lod.plot	0.66	0.00	0.66
Top_SRV.plot	1.75	0.02	1.77
alignSp	1.31	0.02	1.32
align_mQTL	33.79	0.04	33.84
attachSegments	0.57	0.02	0.60
circle_mQTL	0.23	0.01	0.28
configureRSPA	0	0	0
format_mGWA	0.70	0.04	0.77
format_mQTL	1.27	0.00	1.26
load_datafiles	0.01	0.00	0.02
load_demo_data	0	0	0
mQTL.NMR-package	38.97	0.17	39.29
matchSegments	0.66	0.01	0.68
normalise	0.26	0.00	0.26
normalise_mQTL	2.71	0.05	2.75
peakPeaks	0.34	0.00	0.34
post_mQTL	0.20	0.05	0.25
ppersp	0.05	0.01	0.07
pplot	0.03	0.00	0.03
pre_mQTL	43.10	0.10	43.19
process_mGWA	7.78	0.01	9.53
process_mQTL	1.76	0.00	1.76
segmentateSp	0.5	0.0	0.5
selectRefSp	0.88	0.00	0.88
setupRSPA	0.00	0.02	0.01
sgolay	0	0	0
sgolayDeriv	0.09	0.00	0.10
simple.plot	1.33	0.00	1.33
summary_mQTL	0.02	0.00	0.01