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CHECK report for flowTrans on malbec2

This page was generated on 2019-04-09 11:28:57 -0400 (Tue, 09 Apr 2019).

Package 572/1703HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
flowTrans 1.35.1
Greg Finak
Snapshot Date: 2019-04-08 17:01:18 -0400 (Mon, 08 Apr 2019)
URL: https://git.bioconductor.org/packages/flowTrans
Branch: master
Last Commit: e598539
Last Changed Date: 2019-01-04 13:32:59 -0400 (Fri, 04 Jan 2019)
malbec2 Linux (Ubuntu 18.04.2 LTS) / x86_64  OK  OK [ OK ]UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
celaya2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
merida2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK 

Summary

Package: flowTrans
Version: 1.35.1
Command: /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:flowTrans.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings flowTrans_1.35.1.tar.gz
StartedAt: 2019-04-09 00:33:34 -0400 (Tue, 09 Apr 2019)
EndedAt: 2019-04-09 00:34:36 -0400 (Tue, 09 Apr 2019)
EllapsedTime: 62.3 seconds
RetCode: 0
Status:  OK 
CheckDir: flowTrans.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:flowTrans.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings flowTrans_1.35.1.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.9-bioc/meat/flowTrans.Rcheck’
* using R Under development (unstable) (2019-03-18 r76245)
* using platform: x86_64-pc-linux-gnu (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 ‘1.35.1’
* 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 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 ... NOTE
Found the following apparent S3 methods exported but not registered:
  summary.flowTransResult
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
* 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 files in ‘vignettes’ ... OK
* checking examples ... 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: 5 NOTEs
See
  ‘/home/biocbuild/bbs-3.9-bioc/meat/flowTrans.Rcheck/00check.log’
for details.



Installation output

flowTrans.Rcheck/00install.out

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### Running command:
###
###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD INSTALL flowTrans
###
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* installing to library ‘/home/biocbuild/bbs-3.9-bioc/R/library’
* installing *source* package ‘flowTrans’ ...
** using staged installation
** R
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (flowTrans)

Tests output


Example timings

flowTrans.Rcheck/flowTrans-Ex.timings

nameusersystemelapsed
extractParams0.3820.0000.381
flowTrans-package3.7090.0483.764
flowTrans1.0840.0241.108
flowTransResult-class0.3310.0000.331
summary.flowTransResult0.3410.0000.341