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BioC 3.5: CHECK report for flowTrans on toluca2

This page was generated on 2017-04-23 14:35:15 -0400 (Sun, 23 Apr 2017).

Package 470/1377HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
flowTrans 1.27.1
Greg Finak
Snapshot Date: 2017-04-22 17:18:01 -0400 (Sat, 22 Apr 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/flowTrans
Last Changed Rev: 122770 / Revision: 129046
Last Changed Date: 2016-10-18 14:44:37 -0400 (Tue, 18 Oct 2016)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  NotNeeded  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository
toluca2 Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK [ OK ] OK 
veracruz2 OS X 10.11.6 El Capitan / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: flowTrans
Version: 1.27.1
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings flowTrans_1.27.1.tar.gz
StartedAt: 2017-04-23 03:56:29 -0400 (Sun, 23 Apr 2017)
EndedAt: 2017-04-23 03:58:25 -0400 (Sun, 23 Apr 2017)
EllapsedTime: 116.7 seconds
RetCode: 0
Status:  OK 
CheckDir: flowTrans.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings flowTrans_1.27.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/flowTrans.Rcheck’
* using R Under development (unstable) (2017-02-15 r72187)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘flowTrans/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘flowTrans’ version ‘1.27.1’
* 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 ‘flowTrans’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Packages listed in more than one of Depends, Imports, Suggests, Enhances:
  ‘flowCore’ ‘flowViz’ ‘flowClust’
A package should be listed in only one of these fields.
* 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
Unexported object imported by a ':::' call: ‘flowCore:::biexponential_transform’
  See the note in ?`:::` about the use of this operator.
There are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
  ‘linlog’
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... NOTE
Foreign function call to a different package:
  .Call("flowCore_biexponential_transform", ..., PACKAGE = "flowCore")
See chapter ‘System and foreign language interfaces’ in the ‘Writing R
Extensions’ manual.
* 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 ... NOTE
S3 methods shown with full name in documentation object 'summary.flowTransResult':
  ‘summary.flowTransResult’

The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... 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
flowTrans-package 5.412   0.17   5.631
* 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: 4 NOTEs
See
  ‘/Users/biocbuild/bbs-3.5-bioc/meat/flowTrans.Rcheck/00check.log’
for details.


flowTrans.Rcheck/00install.out:

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

flowTrans.Rcheck/flowTrans-Ex.timings:

nameusersystemelapsed
extractParams0.4510.0170.469
flowTrans-package5.4120.1705.631
flowTrans1.4300.1031.544
flowTransResult-class0.3300.0050.337
summary.flowTransResult0.3180.0020.321