BioC experimental data: CHECK report for faahKO on zin2

Package: faahKO

Version: 1.4.4

Command: /home/biocbuild/bbs-2.14-bioc/R/bin/R CMD check --no-vignettes --timings faahKO_1.4.4.tar.gz

StartedAt: 2014-10-04 09:10:19 -0700 (Sat, 04 Oct 2014)

EndedAt: 2014-10-04 09:11:13 -0700 (Sat, 04 Oct 2014)

EllapsedTime: 53.3 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: faahKO.Rcheck

Warnings: 4

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### Running command:
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###   /home/biocbuild/bbs-2.14-bioc/R/bin/R CMD check --no-vignettes --timings faahKO_1.4.4.tar.gz
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* using log directory ‘/home/biocbuild/bbs-2.14-data-experiment/meat/faahKO.Rcheck’
* using R version 3.1.1 (2014-07-10)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘faahKO/DESCRIPTION’ ... OK
* this is package ‘faahKO’ version ‘1.4.4’
* 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 ... WARNING
Found the following file with a non-portable file name:
  inst/s_Proteomic profiling of yeast TFs.txt
These are not fully portable file names.
See section ‘Package structure’ in the ‘Writing R Extensions’ manual.
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘faahKO’ can be installed ... [5s/5s] OK
* checking installed package size ... NOTE
  installed size is 42.8Mb
  sub-directories of 1Mb or more:
    cdf  42.4Mb
* 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
* 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 ... WARNING
Error: .onLoad failed in loadNamespace() for 'faahKO', details:
  call: filepaths(faahko) <- nms
  error: could not find function "filepaths<-"
In addition: Warning message:
class "C++Object" is defined (with package slot ‘Rcpp’) but no metadata object found to revise subclass information---not exported?  Making a copy in package ‘.GlobalEnv’ 
Execution halted

A namespace must be able to be loaded with just the base namespace
loaded: otherwise if the namespace gets loaded by a saved object, the
session will be unable to start.

Probably some imports need to be declared in the NAMESPACE file.
* checking whether the namespace can be unloaded cleanly ... WARNING
Error: .onLoad failed in loadNamespace() for 'faahKO', details:
  call: filepaths(faahko) <- nms
  error: could not find function "filepaths<-"
In addition: Warning message:
class "C++Object" is defined (with package slot ‘Rcpp’) but no metadata object found to revise subclass information---not exported?  Making a copy in package ‘.GlobalEnv’ 
Execution halted
* checking dependencies in R code ... NOTE
Package in Depends field not imported from: ‘xcms’
  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
.onLoad: warning in assign("faahko", faahko, env =
  getNamespace("faahKO")): partial argument match of 'env' to 'envir'
* 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 ... WARNING
  Warning message:
  class "C++Object" is defined (with package slot ‘Rcpp’) but no metadata object found to revise subclass information---not exported?  Making a copy in package ‘.GlobalEnv’ 
* checking examples ... [2s/3s] OK
* checking PDF version of manual ... OK

WARNING: There were 4 warnings.
NOTE: There were 3 notes.
See
  ‘/home/biocbuild/bbs-2.14-data-experiment/meat/faahKO.Rcheck/00check.log’
for details.

* installing *source* package ‘faahKO’ ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
* DONE (faahKO)

name	user	system	elapsed
faahko	0.212	0.016	0.332