BioC 3.0: CHECK report for MinimumDistance on moscato1

Package: MinimumDistance

Version: 1.10.2

Command: rm -rf MinimumDistance.buildbin-libdir MinimumDistance.Rcheck && mkdir MinimumDistance.buildbin-libdir MinimumDistance.Rcheck && D:\biocbld\bbs-3.0-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=MinimumDistance.buildbin-libdir MinimumDistance_1.10.2.tar.gz >MinimumDistance.Rcheck\00install.out 2>&1 && cp MinimumDistance.Rcheck\00install.out MinimumDistance-install.out && D:\biocbld\bbs-3.0-bioc\R\bin\R.exe CMD check --library=MinimumDistance.buildbin-libdir --install="check:MinimumDistance-install.out" --force-multiarch --no-vignettes --timings MinimumDistance_1.10.2.tar.gz

StartedAt: 2015-04-10 03:08:29 -0700 (Fri, 10 Apr 2015)

EndedAt: 2015-04-10 03:20:47 -0700 (Fri, 10 Apr 2015)

EllapsedTime: 738.2 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 MinimumDistance.Rcheck && mkdir MinimumDistance.buildbin-libdir MinimumDistance.Rcheck && D:\biocbld\bbs-3.0-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=MinimumDistance.buildbin-libdir MinimumDistance_1.10.2.tar.gz >MinimumDistance.Rcheck\00install.out 2>&1 && cp MinimumDistance.Rcheck\00install.out MinimumDistance-install.out  && D:\biocbld\bbs-3.0-bioc\R\bin\R.exe CMD check --library=MinimumDistance.buildbin-libdir --install="check:MinimumDistance-install.out" --force-multiarch --no-vignettes --timings MinimumDistance_1.10.2.tar.gz
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* using log directory 'D:/biocbld/bbs-3.0-bioc/meat/MinimumDistance.Rcheck'
* using R version 3.1.3 (2015-03-09)
* 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 '1.10.2'
* 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 ... NOTE
Found the following hidden files and directories:
  .gigignore
These were most likely included in error. See section 'Package
structure' in the 'Writing R Extensions' manual.
* 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 ... NOTE
package 'methods' is used but not declared
* 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 line endings in Makefiles ... OK
* checking for GNU extensions in Makefiles ... OK
* checking installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... [61s] OK
Examples with CPU or elapsed time > 5s
               user system elapsed
FilterParamMD 28.61   0.29   28.90
pedigreeGrid  11.50   0.09   12.73
TrioSet        1.59   0.00    6.52
** running examples for arch 'x64' ... [64s] OK
Examples with CPU or elapsed time > 5s
               user system elapsed
FilterParamMD 33.46   0.28   33.74
pedigreeGrid  12.14   0.04   12.17
* checking for unstated dependencies in tests ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'doRUnit.R' [98s]
 [98s] OK
** running tests for arch 'x64' ...
  Running 'doRUnit.R' [107s]
 [107s] OK
* checking for unstated dependencies in vignettes ... NOTE
'library' or 'require' call not declared from: 'BSgenome.Hsapiens.UCSC.hg18'
* 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

NOTE: There were 3 notes.
See
  'D:/biocbld/bbs-3.0-bioc/meat/MinimumDistance.Rcheck/00check.log'
for details.

install for i386

* installing *source* package 'MinimumDistance' ...
** R
** data
** inst
** preparing package for lazy loading
Creating a generic function for 'colMads' from package 'matrixStats' 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_1.10.2.zip
* DONE (MinimumDistance)

name	user	system	elapsed
DNAcopyParam	0.03	0.00	0.03
FilterParamMD	28.61	0.29	28.90
MAP2	0.36	0.03	0.39
MDRanges-class	0.03	0.00	0.03
MinDistGRanges-class	0.07	0.00	0.08
MinDistGRanges	0.05	0.00	0.05
ParentOffspring-class	0	0	0
ParentOffspringList-class	0	0	0
Pedigree	0	0	0
TrioSet	1.59	0.00	6.52
acf2	0	0	0
md_exp	0.01	0.00	0.02
pedigreeGrid	11.50	0.09	12.73
pedigreeViewports	0.02	0.00	0.02

name	user	system	elapsed
DNAcopyParam	0.01	0.00	0.02
FilterParamMD	33.46	0.28	33.74
MAP2	0.34	0.04	0.39
MDRanges-class	0.03	0.00	0.03
MinDistGRanges-class	0.09	0.00	0.10
MinDistGRanges	0.05	0.00	0.04
ParentOffspring-class	0.01	0.00	0.02
ParentOffspringList-class	0	0	0
Pedigree	0	0	0
TrioSet	1.7	0.0	1.7
acf2	0	0	0
md_exp	0	0	0
pedigreeGrid	12.14	0.04	12.17
pedigreeViewports	0	0	0