BioC 3.2: CHECK report for mQTL.NMR on windows1.bioconductor.org

Package: mQTL.NMR

Version: 1.4.0

Command: rm -rf mQTL.NMR.buildbin-libdir mQTL.NMR.Rcheck && mkdir mQTL.NMR.buildbin-libdir mQTL.NMR.Rcheck && C:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=mQTL.NMR.buildbin-libdir mQTL.NMR_1.4.0.tar.gz >mQTL.NMR.Rcheck\00install.out 2>&1 && cp mQTL.NMR.Rcheck\00install.out mQTL.NMR-install.out && C:\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_1.4.0.tar.gz

StartedAt: 2015-10-27 03:49:41 -0400 (Tue, 27 Oct 2015)

EndedAt: 2015-10-27 03:55:49 -0400 (Tue, 27 Oct 2015)

EllapsedTime: 367.9 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:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=mQTL.NMR.buildbin-libdir mQTL.NMR_1.4.0.tar.gz >mQTL.NMR.Rcheck\00install.out 2>&1 && cp mQTL.NMR.Rcheck\00install.out mQTL.NMR-install.out  && C:\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_1.4.0.tar.gz
###
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* using log directory 'C:/biocbld/bbs-3.2-bioc/meat/mQTL.NMR.Rcheck'
* using R version 3.2.2 Patched (2015-08-16 r69094)
* 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 '1.4.0'
* 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' ... [135s] OK
Examples with CPU or elapsed time > 5s
                  user system elapsed
pre_mQTL         44.70   0.14   45.17
mQTL.NMR-package 37.91   0.09   38.24
align_mQTL       30.56   0.11   30.68
** running examples for arch 'x64' ... [185s] OK
Examples with CPU or elapsed time > 5s
                  user system elapsed
mQTL.NMR-package 55.71   0.14   58.00
align_mQTL       51.88   0.17   58.22
pre_mQTL         40.64   0.09   40.73
process_mGWA      5.11   0.03    5.18
* 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
  'C:/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_1.4.0.zip
* DONE (mQTL.NMR)

name	user	system	elapsed
SRV	1.06	0.00	1.06
SRV.plot	1.81	0.03	1.89
SRV_lod.plot	0.08	0.00	0.08
Top_SRV.plot	1.67	0.01	1.68
alignSp	0.72	0.02	0.74
align_mQTL	30.56	0.11	30.68
attachSegments	0.58	0.01	0.59
circle_mQTL	0.09	0.02	0.11
configureRSPA	0.02	0.00	0.02
format_mGWA	0.56	0.02	0.81
format_mQTL	0.94	0.00	0.94
load_datafiles	0.01	0.00	0.01
load_demo_data	0	0	0
mQTL.NMR-package	37.91	0.09	38.24
matchSegments	0.63	0.00	0.62
normalise	0.14	0.00	0.14
normalise_mQTL	2.61	0.00	2.61
peakPeaks	0.36	0.00	0.36
post_mQTL	0.10	0.06	0.22
ppersp	0.04	0.03	0.06
pplot	0.01	0.03	0.05
pre_mQTL	44.70	0.14	45.17
process_mGWA	4.27	0.04	4.31
process_mQTL	0.72	0.00	0.72
segmentateSp	0.58	0.00	0.58
selectRefSp	0.90	0.00	0.91
setupRSPA	0.02	0.00	0.01
sgolay	0	0	0
sgolayDeriv	0.16	0.00	0.16
simple.plot	2.01	0.00	2.02
summary_mQTL	0.01	0.00	0.02

name	user	system	elapsed
SRV	2.22	0.03	2.27
SRV.plot	2.83	0.04	2.93
SRV_lod.plot	0.17	0.00	0.18
Top_SRV.plot	2.67	0.02	3.09
alignSp	1.33	0.05	1.48
align_mQTL	51.88	0.17	58.22
attachSegments	0.75	0.00	0.75
circle_mQTL	0.22	0.00	0.22
configureRSPA	0.01	0.00	0.01
format_mGWA	0.81	0.01	0.85
format_mQTL	1.32	0.04	1.34
load_datafiles	0.01	0.00	0.02
load_demo_data	0	0	0
mQTL.NMR-package	55.71	0.14	58.00
matchSegments	0.64	0.00	0.64
normalise	0.22	0.00	0.21
normalise_mQTL	2.57	0.01	2.60
peakPeaks	0.33	0.02	0.34
post_mQTL	0.17	0.03	0.21
ppersp	0.05	0.01	0.06
pplot	0.00	0.04	0.03
pre_mQTL	40.64	0.09	40.73
process_mGWA	5.11	0.03	5.18
process_mQTL	0.72	0.00	0.71
segmentateSp	0.59	0.00	0.60
selectRefSp	1.21	0.00	1.20
setupRSPA	0.01	0.00	0.02
sgolay	0	0	0
sgolayDeriv	0.22	0.00	0.22
simple.plot	1.5	0.0	1.5
summary_mQTL	0.02	0.00	0.01