BioC 2.14: CHECK report for MinimumDistance on moscato2

Package: MinimumDistance

Version: 1.8.1

Command: rm -rf MinimumDistance.buildbin-libdir && mkdir MinimumDistance.buildbin-libdir && E:\biocbld\bbs-2.14-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=MinimumDistance.buildbin-libdir MinimumDistance_1.8.1.tar.gz >MinimumDistance-install.out 2>&1 && E:\biocbld\bbs-2.14-bioc\R\bin\R.exe CMD check --library=MinimumDistance.buildbin-libdir --install="check:MinimumDistance-install.out" --force-multiarch --no-vignettes --timings MinimumDistance_1.8.1.tar.gz

StartedAt: 2014-10-08 02:56:20 -0700 (Wed, 08 Oct 2014)

EndedAt: 2014-10-08 03:08:57 -0700 (Wed, 08 Oct 2014)

EllapsedTime: 756.8 seconds

RetCode: 0

Status:  OK

CheckDir: MinimumDistance.Rcheck

Warnings: 0

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### Running command:
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###   rm -rf MinimumDistance.buildbin-libdir && mkdir MinimumDistance.buildbin-libdir && E:\biocbld\bbs-2.14-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=MinimumDistance.buildbin-libdir MinimumDistance_1.8.1.tar.gz >MinimumDistance-install.out 2>&1 && E:\biocbld\bbs-2.14-bioc\R\bin\R.exe CMD check --library=MinimumDistance.buildbin-libdir --install="check:MinimumDistance-install.out" --force-multiarch --no-vignettes --timings MinimumDistance_1.8.1.tar.gz
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* using log directory 'E:/biocbld/bbs-2.14-bioc/meat/MinimumDistance.Rcheck'
* using R version 3.1.1 (2014-07-10)
* using platform: i386-w64-mingw32 (32-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'MinimumDistance/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'MinimumDistance' version '1.8.1'
* 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 'MinimumDistance' 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 ... OK
* 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 contents of 'data' directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... [69s] OK
Examples with CPU or elapsed time > 5s
                    user system elapsed
computeBayesFactor 28.15   0.41   28.57
callDenovoSegments 14.03   0.04   14.11
** running examples for arch 'x64' ... [85s] OK
Examples with CPU or elapsed time > 5s
                    user system elapsed
computeBayesFactor 33.57   0.84   34.41
callDenovoSegments 18.72   0.14   18.86
narrow              5.08   0.05    5.13
* checking for unstated dependencies in tests ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'doRUnit.R' [170s]
 [170s] OK
** running tests for arch 'x64' ...
  Running 'doRUnit.R' [159s]
 [159s] OK
* 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

install for i386

* installing *source* package 'MinimumDistance' ...
** R
** data
** inst
** preparing package for lazy loading
Creating a generic function for 'xyplot' from package 'lattice' in package 'MinimumDistance'
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded

install for x64

* installing *source* package 'MinimumDistance' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'MinimumDistance' as MinimumDistance_1.8.1.zip
* DONE (MinimumDistance)

name	user	system	elapsed
Pedigree-class	0.02	0.00	0.02
Pedigree	0.00	0.02	0.01
TrioSet-class	1.76	0.04	1.81
TrioSet	2.81	0.02	3.31
TrioSetList-class	0.36	0.03	0.39
TrioSetListLD	2.71	0.05	2.76
calculateMindist	0.38	0.03	0.41
callDenovoSegments	14.03	0.04	14.11
computeBayesFactor	28.15	0.41	28.57
isDenovo	0.07	0.02	0.08
lrr.segs	0	0	0
mad2	0.42	0.00	0.42
narrow	4.25	0.03	4.27
phenoData	0.33	0.00	0.33
segment2	0	0	0
stackRangedDataList	0.19	0.00	0.18
trioSetList	2.49	0.04	2.55
trioSetListExample	0.52	0.00	0.51
xyplotTrio	1.39	0.02	1.40

name	user	system	elapsed
Pedigree-class	0.02	0.00	0.02
Pedigree	0.01	0.01	0.03
TrioSet-class	2.45	0.03	2.48
TrioSet	2.83	0.02	2.84
TrioSetList-class	0.36	0.01	0.37
TrioSetListLD	4.07	0.04	4.10
calculateMindist	0.39	0.00	0.39
callDenovoSegments	18.72	0.14	18.86
computeBayesFactor	33.57	0.84	34.41
isDenovo	0.11	0.00	0.45
lrr.segs	0	0	0
mad2	0.53	0.00	0.53
narrow	5.08	0.05	5.13
phenoData	0.26	0.00	0.26
segment2	0	0	0
stackRangedDataList	0.21	0.00	0.20
trioSetList	2.47	0.09	2.56
trioSetListExample	0.47	0.00	0.47
xyplotTrio	1.56	0.00	1.56