BioC 2.13: CHECK report for RMAPPER on moscato1

Package: RMAPPER

Version: 1.12.0

Command: rm -rf RMAPPER.buildbin-libdir && mkdir RMAPPER.buildbin-libdir && D:\biocbld\bbs-2.13-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=RMAPPER.buildbin-libdir RMAPPER_1.12.0.tar.gz >RMAPPER-install.out 2>&1 && D:\biocbld\bbs-2.13-bioc\R\bin\R.exe CMD check --library=RMAPPER.buildbin-libdir --install="check:RMAPPER-install.out" --force-multiarch --no-vignettes --timings RMAPPER_1.12.0.tar.gz && mv RMAPPER.buildbin-libdir/* RMAPPER.Rcheck/ && rmdir RMAPPER.buildbin-libdir

StartedAt: 2014-04-05 06:22:45 -0700 (Sat, 05 Apr 2014)

EndedAt: 2014-04-05 06:25:09 -0700 (Sat, 05 Apr 2014)

EllapsedTime: 143.8 seconds

RetCode: 1

Status:  ERROR

CheckDir: RMAPPER.Rcheck

Warnings: NA

* using log directory 'D:/biocbld/bbs-2.13-bioc/meat/RMAPPER.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 'RMAPPER/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'RMAPPER' version '1.12.0'
* 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 'RMAPPER' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Non-standard license specification:
  Artistic 2.0
Standardizable: TRUE
Standardized license specification:
  Artistic-2.0
* 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 ... NOTE
readMAPPER: warning in read.delim(tc, sep = "\t", skip = 1, h = TRUE):
  partial argument match of 'h' to 'header'
* 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 for old-style vignette sources ... NOTE
Vignette sources only in 'inst/doc':
  'readMAPPER.Rnw'
A 'vignettes' directory will be required as from R 3.1.0
* checking examples ...
** running examples for arch 'i386' ... ERROR
Running examples in 'RMAPPER-Ex.R' failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: readMAPPER
> ### Title: Retrieve a set of predicted transcription factor binding sites
> ###   from the MAPPER database
> ### Aliases: readMAPPER
> ### Keywords: models
> 
> ### ** Examples
> 
>  # Run an example retrieving data from the MAPPER RPC interface for gene ID = NM_009696
>  mh = readMAPPER(gene="NM_009696", perc="95", models="M00027")
Warning in file(con, "r") : cannot open: HTTP status was '0 (nil)'
Error in file(con, "r") : cannot open the connection
Calls: readMAPPER -> readLines -> file
Execution halted
** running examples for arch 'x64' ... ERROR
Running examples in 'RMAPPER-Ex.R' failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: readMAPPER
> ### Title: Retrieve a set of predicted transcription factor binding sites
> ###   from the MAPPER database
> ### Aliases: readMAPPER
> ### Keywords: models
> 
> ### ** Examples
> 
>  # Run an example retrieving data from the MAPPER RPC interface for gene ID = NM_009696
>  mh = readMAPPER(gene="NM_009696", perc="95", models="M00027")
Warning in file(con, "r") : cannot open: HTTP status was '0 (nil)'
Error in file(con, "r") : cannot open the connection
Calls: readMAPPER -> readLines -> file
Execution halted

install for i386

* installing *source* package 'RMAPPER' ...
** 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 'RMAPPER' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'RMAPPER' as RMAPPER_1.12.0.zip
* DONE (RMAPPER)

name	user	system	elapsed
hits	0	0	0
mapperHits-class	0	0	0
query	0	0	0

name	user	system	elapsed
hits	0	0	0
mapperHits-class	0	0	0
query	0.03	0.00	0.03