BioC 3.5: CHECK report for CellMapper on veracruz2

Package: CellMapper

Version: 1.2.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings CellMapper_1.2.0.tar.gz

StartedAt: 2017-08-16 00:41:37 -0400 (Wed, 16 Aug 2017)

EndedAt: 2017-08-16 00:45:05 -0400 (Wed, 16 Aug 2017)

EllapsedTime: 207.8 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: CellMapper.Rcheck

Warnings: 1

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings CellMapper_1.2.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/CellMapper.Rcheck’
* using R version 3.4.1 (2017-06-30)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘CellMapper/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘CellMapper’ version ‘1.2.0’
* 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:
  .BBSoptions
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘CellMapper’ can be installed ... WARNING
Found the following significant warnings:
  Warning: replacing previous import ‘stats::sd’ by ‘S4Vectors::sd’ when loading ‘CellMapper’
  Warning: replacing previous import ‘stats::var’ by ‘S4Vectors::var’ when loading ‘CellMapper’
See ‘/Users/biocbuild/bbs-3.5-bioc/meat/CellMapper.Rcheck/00install.out’ for details.
* checking installed package size ... OK
* 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 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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                       user system elapsed
ReplicateManuscript 137.719 25.311 167.681
* 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: 1 WARNING, 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.5-bioc/meat/CellMapper.Rcheck/00check.log’
for details.

* installing *source* package ‘CellMapper’ ...
** R
** data
** inst
** preparing package for lazy loading
Warning: replacing previous import ‘stats::sd’ by ‘S4Vectors::sd’ when loading ‘CellMapper’
Warning: replacing previous import ‘stats::var’ by ‘S4Vectors::var’ when loading ‘CellMapper’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Warning: replacing previous import ‘stats::sd’ by ‘S4Vectors::sd’ when loading ‘CellMapper’
Warning: replacing previous import ‘stats::var’ by ‘S4Vectors::var’ when loading ‘CellMapper’
* DONE (CellMapper)

name	user	system	elapsed
CMprep	0.202	0.010	0.224
CMsearch	0.225	0.005	0.232
CellMapperList-class	0.098	0.003	0.101
ExampleGeneLists	0.011	0.002	0.013
ReplicateManuscript	137.719	25.311	167.681