BioC 3.3: CHECK report for mQTL.NMR on windows2.bioconductor.org

Package: mQTL.NMR

Version: 1.5.0

Command: rm -rf mQTL.NMR.buildbin-libdir mQTL.NMR.Rcheck && mkdir mQTL.NMR.buildbin-libdir mQTL.NMR.Rcheck && c:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=mQTL.NMR.buildbin-libdir mQTL.NMR_1.5.0.tar.gz >mQTL.NMR.Rcheck\00install.out 2>&1 && cp mQTL.NMR.Rcheck\00install.out mQTL.NMR-install.out && c:\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_1.5.0.tar.gz

StartedAt: 2015-10-27 04:24:44 -0400 (Tue, 27 Oct 2015)

EndedAt: 2015-10-27 04:30:25 -0400 (Tue, 27 Oct 2015)

EllapsedTime: 341.7 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:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=mQTL.NMR.buildbin-libdir mQTL.NMR_1.5.0.tar.gz >mQTL.NMR.Rcheck\00install.out 2>&1 && cp mQTL.NMR.Rcheck\00install.out mQTL.NMR-install.out  && c:\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_1.5.0.tar.gz
###
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* using log directory 'c:/biocbld/bbs-3.3-bioc/meat/mQTL.NMR.Rcheck'
* using R Under development (unstable) (2015-09-22 r69418)
* 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 '1.5.0'
* 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' ... [147s] OK
Examples with CPU or elapsed time > 5s
                  user system elapsed
align_mQTL       42.86   0.08   43.47
mQTL.NMR-package 39.93   0.14   40.80
pre_mQTL         36.37   0.02   36.39
** running examples for arch 'x64' ... [144s] OK
Examples with CPU or elapsed time > 5s
                  user system elapsed
mQTL.NMR-package 41.59   0.12   41.78
pre_mQTL         40.84   0.07   40.92
align_mQTL       39.04   0.12   39.16
process_mGWA      5.09   0.01    5.12
* 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-3.3-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_1.5.0.zip
* DONE (mQTL.NMR)

name	user	system	elapsed
SRV	1.89	0.00	1.89
SRV.plot	2.96	0.03	3.36
SRV_lod.plot	0.11	0.01	0.12
Top_SRV.plot	2.84	0.04	2.88
alignSp	1.28	0.01	1.30
align_mQTL	42.86	0.08	43.47
attachSegments	0.7	0.0	0.7
circle_mQTL	0.16	0.02	0.17
configureRSPA	0.00	0.01	0.02
format_mGWA	0.68	0.05	0.75
format_mQTL	1.24	0.00	1.23
load_datafiles	0.00	0.01	0.02
load_demo_data	0	0	0
mQTL.NMR-package	39.93	0.14	40.80
matchSegments	0.55	0.02	0.56
normalise	0.16	0.00	0.16
normalise_mQTL	2.81	0.00	2.84
peakPeaks	0.38	0.00	0.37
post_mQTL	0.12	0.06	0.32
ppersp	0.05	0.02	0.47
pplot	0.00	0.04	0.04
pre_mQTL	36.37	0.02	36.39
process_mGWA	3.72	0.00	3.74
process_mQTL	0.89	0.02	0.90
segmentateSp	0.97	0.00	0.97
selectRefSp	0.8	0.0	0.8
setupRSPA	0	0	0
sgolay	0	0	0
sgolayDeriv	0.15	0.00	0.16
simple.plot	1.58	0.01	1.59
summary_mQTL	0.00	0.02	0.02

name	user	system	elapsed
SRV	1.33	0.04	1.36
SRV.plot	1.67	0.00	1.67
SRV_lod.plot	0.08	0.00	0.08
Top_SRV.plot	1.52	0.03	1.55
alignSp	0.70	0.02	0.72
align_mQTL	39.04	0.12	39.16
attachSegments	0.65	0.00	0.65
circle_mQTL	0.16	0.00	0.16
configureRSPA	0	0	0
format_mGWA	0.82	0.02	0.84
format_mQTL	0.93	0.00	0.94
load_datafiles	0.02	0.00	0.01
load_demo_data	0	0	0
mQTL.NMR-package	41.59	0.12	41.78
matchSegments	0.64	0.00	0.65
normalise	0.19	0.00	0.19
normalise_mQTL	2.58	0.05	2.62
peakPeaks	0.39	0.00	0.39
post_mQTL	0.09	0.12	0.22
ppersp	0.05	0.03	0.08
pplot	0.00	0.03	0.03
pre_mQTL	40.84	0.07	40.92
process_mGWA	5.09	0.01	5.12
process_mQTL	0.69	0.00	0.69
segmentateSp	0.67	0.02	0.69
selectRefSp	1.28	0.00	1.28
setupRSPA	0	0	0
sgolay	0	0	0
sgolayDeriv	0.18	0.00	0.19
simple.plot	1.49	0.02	1.50
summary_mQTL	0.01	0.00	0.01