BioC experimental data: CHECK report for MafDb.ESP6500SI.V2.SSA137.dbSNP138 on moscato2

Package: MafDb.ESP6500SI.V2.SSA137.dbSNP138

Version: 1.0.0

Command: rm -rf MafDb.ESP6500SI.V2.SSA137.dbSNP138.buildbin-libdir && mkdir MafDb.ESP6500SI.V2.SSA137.dbSNP138.buildbin-libdir && E:\biocbld\bbs-2.14-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=MafDb.ESP6500SI.V2.SSA137.dbSNP138.buildbin-libdir MafDb.ESP6500SI.V2.SSA137.dbSNP138_1.0.0.tar.gz >MafDb.ESP6500SI.V2.SSA137.dbSNP138-install.out 2>&1 && E:\biocbld\bbs-2.14-bioc\R\bin\R.exe CMD check --library=MafDb.ESP6500SI.V2.SSA137.dbSNP138.buildbin-libdir --install="check:MafDb.ESP6500SI.V2.SSA137.dbSNP138-install.out" --force-multiarch --no-vignettes --timings MafDb.ESP6500SI.V2.SSA137.dbSNP138_1.0.0.tar.gz && mv MafDb.ESP6500SI.V2.SSA137.dbSNP138.buildbin-libdir/* MafDb.ESP6500SI.V2.SSA137.dbSNP138.Rcheck/ && rmdir MafDb.ESP6500SI.V2.SSA137.dbSNP138.buildbin-libdir

StartedAt: 2014-04-15 14:06:02 -0700 (Tue, 15 Apr 2014)

EndedAt: 2014-04-15 14:15:28 -0700 (Tue, 15 Apr 2014)

EllapsedTime: 565.7 seconds

RetCode: 0

Status: OK

CheckDir: MafDb.ESP6500SI.V2.SSA137.dbSNP138.Rcheck

Warnings: 0

Command output

* using log directory 'E:/biocbld/bbs-2.14-data-experiment/meat/MafDb.ESP6500SI.V2.SSA137.dbSNP138.Rcheck'
* using R version 3.1.0 RC (2014-04-02 r65358)
* using platform: i386-w64-mingw32 (32-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'MafDb.ESP6500SI.V2.SSA137.dbSNP138/DESCRIPTION' ... OK
* this is package 'MafDb.ESP6500SI.V2.SSA137.dbSNP138' 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 ... NOTE
Found the following non-portable file path:
  MafDb.ESP6500SI.V2.SSA137.dbSNP138/inst/MafDbPkgTemplate/man/MafDb.ESP6500SI.V2.SSA137.dbSNP138-package.Rd

Tarballs are only required to store paths of up to 100 bytes and cannot
store those of more than 256 bytes, with restrictions including to 100
bytes for the final component.
See section 'Package structure' in the 'Writing R Extensions' manual.
* checking whether package 'MafDb.ESP6500SI.V2.SSA137.dbSNP138' can be installed ... OK
* checking installed package size ... NOTE
  installed size is 76.9Mb
  sub-directories of 1Mb or more:
    extdata  76.8Mb
* checking package 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
Missing object imported by a ':::' call: 'VariantFiltering:::dbEasyQuery'
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 examples ...
** running examples for arch 'i386' ... [10s] OK
** running examples for arch 'x64' ... [13s] OK
* checking PDF version of manual ... OK

NOTE: There were 3 notes.
See
  'E:/biocbld/bbs-2.14-data-experiment/meat/MafDb.ESP6500SI.V2.SSA137.dbSNP138.Rcheck/00check.log'
for details.


install for i386

* installing *source* package 'MafDb.ESP6500SI.V2.SSA137.dbSNP138' ...
** R
** inst
** preparing package for lazy loading
Note: the specification for S3 class "AsIs" in package 'RJSONIO' seems equivalent to one from package 'BiocGenerics': not turning on duplicate class definitions for this class.
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
Note: the specification for S3 class "AsIs" in package 'RJSONIO' seems equivalent to one from package 'BiocGenerics': not turning on duplicate class definitions for this class.

install for x64

* installing *source* package 'MafDb.ESP6500SI.V2.SSA137.dbSNP138' ...
** testing if installed package can be loaded
Note: the specification for S3 class "AsIs" in package 'RJSONIO' seems equivalent to one from package 'BiocGenerics': not turning on duplicate class definitions for this class.
* MD5 sums
packaged installation of 'MafDb.ESP6500SI.V2.SSA137.dbSNP138' as MafDb.ESP6500SI.V2.SSA137.dbSNP138_1.0.0.zip
* DONE (MafDb.ESP6500SI.V2.SSA137.dbSNP138)

MafDb.ESP6500SI.V2.SSA137.dbSNP138.Rcheck/examples_i386/MafDb.ESP6500SI.V2.SSA137.dbSNP138-Ex.timings:

name	user	system	elapsed
MafDb.ESP6500SI.V2.SSA137.dbSNP138-package	0	0	0
makeMafDbPackage	0	0	0

MafDb.ESP6500SI.V2.SSA137.dbSNP138.Rcheck/examples_x64/MafDb.ESP6500SI.V2.SSA137.dbSNP138-Ex.timings:

BioC experimental data: CHECK report for MafDb.ESP6500SI.V2.SSA137.dbSNP138 on moscato2

Summary

Command output