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: 2017-10-18 01:31:41 -0400 (Wed, 18 Oct 2017)

EndedAt: 2017-10-18 01:36:50 -0400 (Wed, 18 Oct 2017)

EllapsedTime: 308.7 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 3.4.2 Patched (2017-10-07 r73498)
* 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 34.67   0.23   34.97
pre_mQTL         31.14   0.05   31.19
align_mQTL       26.63   0.11   26.73
process_mGWA      6.06   0.00    6.06
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                  user system elapsed
mQTL.NMR-package 37.51   0.21   37.77
align_mQTL       34.50   0.06   34.58
pre_mQTL         31.35   0.06   31.42
process_mGWA      6.75   0.02    6.77
* 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	1.35	0.01	1.36
SRV.plot	2.03	0.00	2.04
SRV_lod.plot	0.43	0.02	0.44
Top_SRV.plot	1.95	0.01	1.97
alignSp	1.11	0.02	1.12
align_mQTL	26.63	0.11	26.73
attachSegments	0.56	0.00	0.56
circle_mQTL	0.13	0.00	0.13
configureRSPA	0.01	0.00	0.02
format_mGWA	1.02	0.03	1.15
format_mQTL	1.7	0.0	1.7
load_datafiles	0.00	0.02	0.02
load_demo_data	0	0	0
mQTL.NMR-package	34.67	0.23	34.97
matchSegments	0.53	0.02	0.55
normalise	0.22	0.00	0.21
normalise_mQTL	2.69	0.00	2.69
peakPeaks	0.28	0.00	0.28
post_mQTL	0.16	0.06	0.22
ppersp	0.04	0.00	0.05
pplot	0.02	0.01	0.03
pre_mQTL	31.14	0.05	31.19
process_mGWA	6.06	0.00	6.06
process_mQTL	1.75	0.00	1.75
segmentateSp	0.59	0.02	0.61
selectRefSp	0.71	0.00	0.70
setupRSPA	0	0	0
sgolay	0	0	0
sgolayDeriv	0.08	0.00	0.08
simple.plot	2.20	0.00	2.21
summary_mQTL	0.02	0.00	0.01

name	user	system	elapsed
SRV	1.43	0.03	1.47
SRV.plot	1.64	0.01	1.66
SRV_lod.plot	0.52	0.00	0.51
Top_SRV.plot	1.64	0.02	1.67
alignSp	1.17	0.00	1.18
align_mQTL	34.50	0.06	34.58
attachSegments	0.58	0.02	0.59
circle_mQTL	0.24	0.01	0.30
configureRSPA	0.01	0.00	0.01
format_mGWA	0.91	0.00	1.03
format_mQTL	1.23	0.01	1.25
load_datafiles	0	0	0
load_demo_data	0	0	0
mQTL.NMR-package	37.51	0.21	37.77
matchSegments	0.82	0.00	0.81
normalise	0.29	0.00	0.30
normalise_mQTL	2.94	0.08	3.01
peakPeaks	0.53	0.00	0.54
post_mQTL	0.30	0.09	0.39
ppersp	0.08	0.00	0.07
pplot	0.01	0.03	0.05
pre_mQTL	31.35	0.06	31.42
process_mGWA	6.75	0.02	6.77
process_mQTL	1.90	0.00	1.91
segmentateSp	0.55	0.00	0.54
selectRefSp	0.94	0.00	0.94
setupRSPA	0	0	0
sgolay	0.01	0.00	0.02
sgolayDeriv	0.10	0.00	0.09
simple.plot	1.84	0.00	1.84
summary_mQTL	0.01	0.00	0.02