BioC experimental data: CHECK report for ceuhm3 on malbec1

Package: ceuhm3

Version: 0.12.0

Command: /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings ceuhm3_0.12.0.tar.gz

StartedAt: 2017-04-15 10:44:23 -0400 (Sat, 15 Apr 2017)

EndedAt: 2017-04-15 10:46:32 -0400 (Sat, 15 Apr 2017)

EllapsedTime: 128.7 seconds

RetCode: 0

Status:  OK

CheckDir: ceuhm3.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings ceuhm3_0.12.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.4-data-experiment/meat/ceuhm3.Rcheck’
* using R version 3.3.3 (2017-03-06)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘ceuhm3/DESCRIPTION’ ... OK
* this is package ‘ceuhm3’ version ‘0.12.0’
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘ceuhm3’ can be installed ... OK
* checking installed package size ... NOTE
  installed size is 45.2Mb
  sub-directories of 1Mb or more:
    data   25.9Mb
    parts  19.1Mb
* checking package directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Description field: should contain one or more complete sentences.
* 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 ... NOTE
Namespace in Imports field not imported from: ‘GGtools’
  All declared Imports should be used.
Package in Depends field not imported from: ‘GGBase’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
File ‘ceuhm3/R/zzz.R’:
  .onLoad calls:
    packageStartupMessage(paste("To get a tailored smlSet, use getSS(\"",     pkgname, "\", [chrvec])", sep = ""))
    packageStartupMessage("available chromosomes are named ", selectSome(cn))

See section ‘Good practice’ in '?.onAttach'.
* 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 ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                user system elapsed
ceuhm3-package 9.672  0.456   11.52
* checking PDF version of manual ... OK
* DONE

Status: 4 NOTEs
See
  ‘/home/biocbuild/bbs-3.4-data-experiment/meat/ceuhm3.Rcheck/00check.log’
for details.

* installing *source* package ‘ceuhm3’ ...
** R
** data
** inst
** preparing package for lazy loading
Warning: replacing previous import ‘IRanges::which’ by ‘Matrix::which’ when loading ‘GGBase’
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
Warning: replacing previous import ‘IRanges::which’ by ‘Matrix::which’ when loading ‘GGBase’
* DONE (ceuhm3)

name	user	system	elapsed
ceuhm3-package	9.672	0.456	11.520