BioC 3.2: CHECK report for systemPipeRdata on perceval

Package: systemPipeRdata

Version: 0.99.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings systemPipeRdata_0.99.0.tar.gz

StartedAt: 2015-09-15 10:32:27 -0400 (Tue, 15 Sep 2015)

EndedAt: 2015-09-15 10:33:21 -0400 (Tue, 15 Sep 2015)

EllapsedTime: 54.8 seconds

RetCode: 0

Status:  OK

CheckDir: systemPipeRdata.Rcheck

Warnings: 0

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings systemPipeRdata_0.99.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.2-bioc/meat/systemPipeRdata.Rcheck’
* using R version 3.2.2 Patched (2015-08-14 r69078)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘systemPipeRdata/DESCRIPTION’ ... OK
* this is package ‘systemPipeRdata’ version ‘0.99.0’
* 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 ... NOTE
Found the following hidden files and directories:
  inst/extdata/param/.BatchJobs.R
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* checking for portable file names ... NOTE
Found the following non-portable file paths:
  systemPipeRdata/vignettes/systemPipeRdata_cache/html/documentation_systemPipeR_c79d7d0bccd16d6a1a8601f6dcaaa9b4.RData
  systemPipeRdata/vignettes/systemPipeRdata_cache/html/documentation_systemPipeR_c79d7d0bccd16d6a1a8601f6dcaaa9b4.rdb
  systemPipeRdata/vignettes/systemPipeRdata_cache/html/documentation_systemPipeR_c79d7d0bccd16d6a1a8601f6dcaaa9b4.rdx
  systemPipeRdata/vignettes/systemPipeRdata_cache/html/documentation_systemPipeRdata_bbf89884b369a56c0e25a0eee2d5c67b.RData
  systemPipeRdata/vignettes/systemPipeRdata_cache/html/documentation_systemPipeRdata_bbf89884b369a56c0e25a0eee2d5c67b.rdb
  systemPipeRdata/vignettes/systemPipeRdata_cache/html/documentation_systemPipeRdata_bbf89884b369a56c0e25a0eee2d5c67b.rdx
  systemPipeRdata/vignettes/systemPipeRdata_cache/html/generate_workenvir_0c6d4c51337d681e880eae4946c2f74f.RData
  systemPipeRdata/vignettes/systemPipeRdata_cache/html/generate_workenvir_0c6d4c51337d681e880eae4946c2f74f.rdb
  systemPipeRdata/vignettes/systemPipeRdata_cache/html/generate_workenvir_0c6d4c51337d681e880eae4946c2f74f.rdx
  systemPipeRdata/vignettes/systemPipeRdata_cache/html/generate_workenvir_from_shell_e6af8809e77cb0c390cb6f3f16deb9ec.RData
  systemPipeRdata/vignettes/systemPipeRdata_cache/html/generate_workenvir_from_shell_e6af8809e77cb0c390cb6f3f16deb9ec.rdb
  systemPipeRdata/vignettes/systemPipeRdata_cache/html/generate_workenvir_from_shell_e6af8809e77cb0c390cb6f3f16deb9ec.rdx
  systemPipeRdata/vignettes/systemPipeRdata_cache/html/load_systemPipeR_e12409b4ef174e7562368018651bd280.RData
  systemPipeRdata/vignettes/systemPipeRdata_cache/html/load_systemPipeR_e12409b4ef174e7562368018651bd280.rdb
  systemPipeRdata/vignettes/systemPipeRdata_cache/html/load_systemPipeR_e12409b4ef174e7562368018651bd280.rdx
  systemPipeRdata/vignettes/systemPipeRdata_cache/html/load_systemPipeRdata_94c2325c16bfad2a6fc456bd6bcab330.RData
  systemPipeRdata/vignettes/systemPipeRdata_cache/html/load_systemPipeRdata_94c2325c16bfad2a6fc456bd6bcab330.rdb
  systemPipeRdata/vignettes/systemPipeRdata_cache/html/load_systemPipeRdata_94c2325c16bfad2a6fc456bd6bcab330.rdx
  systemPipeRdata/vignettes/systemPipeRdata_cache/html/return_samplepaths_ccb111a1e3b525d7cd78bc7152dd7503.RData
  systemPipeRdata/vignettes/systemPipeRdata_cache/html/return_samplepaths_ccb111a1e3b525d7cd78bc7152dd7503.rdb
  systemPipeRdata/vignettes/systemPipeRdata_cache/html/return_samplepaths_ccb111a1e3b525d7cd78bc7152dd7503.rdx
  systemPipeRdata/vignettes/systemPipeRdata_cache/html/sessionInfo_b3166f2822b5a4f7707049554463255b.RData
  systemPipeRdata/vignettes/systemPipeRdata_cache/html/sessionInfo_b3166f2822b5a4f7707049554463255b.rdb
  systemPipeRdata/vignettes/systemPipeRdata_cache/html/sessionInfo_b3166f2822b5a4f7707049554463255b.rdx

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 for sufficient/correct file permissions ... OK
* checking whether package ‘systemPipeRdata’ can be installed ... [3s/7s] OK
* checking installed package size ... NOTE
  installed size is 235.6Mb
  sub-directories of 1Mb or more:
    extdata  235.4Mb
* 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
* 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 ... OK
* 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 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 ... [1s/1s] OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.R’ [1s/1s]
 [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
* DONE

Status: 3 NOTEs
See
  ‘/Users/biocbuild/bbs-3.2-bioc/meat/systemPipeRdata.Rcheck/00check.log’
for details.

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

name	user	system	elapsed
genWorkenvir	0.005	0.001	0.005
pathList	0.005	0.001	0.005