BioC 2.13: CHECK report for clonotypeR on moscato1

Package: clonotypeR

Version: 1.0.0

Command: rm -rf clonotypeR.buildbin-libdir && mkdir clonotypeR.buildbin-libdir && D:\biocbld\bbs-2.13-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=clonotypeR.buildbin-libdir clonotypeR_1.0.0.tar.gz >clonotypeR-install.out 2>&1 && D:\biocbld\bbs-2.13-bioc\R\bin\R.exe CMD check --library=clonotypeR.buildbin-libdir --install="check:clonotypeR-install.out" --force-multiarch --no-vignettes --timings clonotypeR_1.0.0.tar.gz && mv clonotypeR.buildbin-libdir/* clonotypeR.Rcheck/ && rmdir clonotypeR.buildbin-libdir

StartedAt: 2014-04-05 03:06:26 -0700 (Sat, 05 Apr 2014)

EndedAt: 2014-04-05 03:07:01 -0700 (Sat, 05 Apr 2014)

EllapsedTime: 35.2 seconds

RetCode: 0

Status:  OK

CheckDir: clonotypeR.Rcheck

Warnings: 0

* using log directory 'D:/biocbld/bbs-2.13-bioc/meat/clonotypeR.Rcheck'
* using R version 3.0.3 (2014-03-06)
* using platform: i386-w64-mingw32 (32-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'clonotypeR/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'clonotypeR' version '1.0.0'
* 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 'clonotypeR' 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
* 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 dependencies in R code ... NOTE
Package in Depends field not imported from: 'methods'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
See the information on DESCRIPTION files in the chapter 'Creating R
packages' of the 'Writing R Extensions' manual.
* 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' ... [1s] OK
** running examples for arch 'x64' ... [1s] OK
* checking for unstated dependencies in tests ... OK
* checking tests ...
** running tests for arch 'i386'
  Running 'runTests.R' [1s]
 [1s] OK
** running tests for arch 'x64'
  Running 'runTests.R' [1s]
 [1s] 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

NOTE: There was 1 note.
See
  'D:/biocbld/bbs-2.13-bioc/meat/clonotypeR.Rcheck/00check.log'
for details.

install for i386

* installing *source* package 'clonotypeR' ...
** 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 'clonotypeR' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'clonotypeR' as clonotypeR_1.0.0.zip
* DONE (clonotypeR)

name	user	system	elapsed
clonotype_table	0.03	0.01	0.04
clonotyper_extdata	0.02	0.00	0.02
common_clonotypes	0.03	0.00	0.03
is_unproductive	0.00	0.02	0.01
read_clonotypes	0.02	0.00	0.02
unique_clonotypes	0.03	0.00	0.03
yassai_identifier	0.11	0.00	0.11

name	user	system	elapsed
clonotype_table	0.06	0.00	0.06
clonotyper_extdata	0.03	0.00	0.03
common_clonotypes	0.04	0.00	0.05
is_unproductive	0.05	0.00	0.04
read_clonotypes	0.02	0.00	0.02
unique_clonotypes	0.03	0.00	0.03
yassai_identifier	0.12	0.00	0.12