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This page was generated on 2021-10-15 15:06:35 -0400 (Fri, 15 Oct 2021).

CHECK results for flowMap on machv2

To the developers/maintainers of the flowMap package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/flowMap.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 653/2041HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
flowMap 1.30.0  (landing page)
Chiaowen Joyce Hsiao
Snapshot Date: 2021-10-14 04:50:12 -0400 (Thu, 14 Oct 2021)
git_url: https://git.bioconductor.org/packages/flowMap
git_branch: RELEASE_3_13
git_last_commit: 040845e
git_last_commit_date: 2021-05-19 12:01:13 -0400 (Wed, 19 May 2021)
nebbiolo1Linux (Ubuntu 20.04.2 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published

Summary

Package: flowMap
Version: 1.30.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:flowMap.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings flowMap_1.30.0.tar.gz
StartedAt: 2021-10-14 19:07:38 -0400 (Thu, 14 Oct 2021)
EndedAt: 2021-10-14 19:08:38 -0400 (Thu, 14 Oct 2021)
EllapsedTime: 60.4 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: flowMap.Rcheck
Warnings: 2

Command output

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### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:flowMap.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings flowMap_1.30.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.13-bioc/meat/flowMap.Rcheck’
* using R version 4.1.1 (2021-08-10)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘flowMap/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘flowMap’ version ‘1.30.0’
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Depends: includes the non-default packages:
  'ade4', 'doParallel', 'abind', 'reshape2', 'scales', 'Matrix'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
* 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:
  .git_fetch_output.txt
  .git_merge_output.txt
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 ‘flowMap’ can be installed ... OK
* 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 ... WARNING
'library' or 'require' call not declared from: ‘igraph’
'library' or 'require' call to ‘Matrix’ which was already attached by Depends.
  Please remove these calls from your code.
'library' or 'require' call to ‘igraph’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Packages in Depends field not imported from:
  ‘Matrix’ ‘abind’ ‘ade4’ ‘doParallel’ ‘methods’ ‘reshape2’ ‘scales’
  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
getFR: no visible global function definition for ‘dist’
getFR: no visible global function definition for ‘pnorm’
getFRest: no visible global function definition for ‘detectCores’
getFRest: no visible global function definition for
  ‘registerDoParallel’
getFRest: no visible global function definition for ‘%dopar%’
getFRest: no visible global function definition for ‘foreach’
getFRest: no visible binding for global variable ‘i’
getFRest: no visible global function definition for ‘new’
makeDistmat: no visible global function definition for ‘forceSymmetric’
makeFRMST: no visible global function definition for ‘dist’
makeFRMST: no visible global function definition for ‘as.dist’
makeFRMST: no visible global function definition for ‘graph.adjacency’
makeFRMST: no visible global function definition for
  ‘set.edge.attribute’
makeFRMST: no visible global function definition for ‘E’
makeFRMST: no visible global function definition for ‘E<-’
makeFRMST: no visible global function definition for ‘V’
makeFRMST: no visible global function definition for ‘V<-’
makeFRMST: no visible global function definition for ‘pnorm’
statCrossLists: no visible global function definition for ‘abind’
Undefined global functions or variables:
  %dopar% E E<- V V<- abind as.dist detectCores dist forceSymmetric
  foreach graph.adjacency i new pnorm registerDoParallel
  set.edge.attribute
Consider adding
  importFrom("methods", "new")
  importFrom("stats", "as.dist", "dist", "pnorm")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* 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 ... WARNING
Undocumented arguments in documentation object 'getFRest'
  ‘ncores’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
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 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: 2 WARNINGs, 3 NOTEs
See
  ‘/Users/biocbuild/bbs-3.13-bioc/meat/flowMap.Rcheck/00check.log’
for details.



Installation output

flowMap.Rcheck/00install.out

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL flowMap
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.1/Resources/library’
* installing *source* package ‘flowMap’ ...
** using staged installation
** R
** inst
** 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 (flowMap)

Tests output


Example timings

flowMap.Rcheck/flowMap-Ex.timings

nameusersystemelapsed
frstats-class0.0000.0000.001
getFR0.0000.0010.000
getFRest0.0000.0010.000