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This page was generated on 2024-03-27 11:35:51 -0400 (Wed, 27 Mar 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 22.04.3 LTS)x86_644.3.3 (2024-02-29) -- "Angel Food Cake" 4667
palomino4Windows Server 2022 Datacenterx644.3.3 (2024-02-29 ucrt) -- "Angel Food Cake" 4403
merida1macOS 12.7.1 Montereyx86_644.3.3 (2024-02-29) -- "Angel Food Cake" 4426
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

Package 731/2266HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
flowMap 1.40.0  (landing page)
Chiaowen Joyce Hsiao
Snapshot Date: 2024-03-25 14:05:07 -0400 (Mon, 25 Mar 2024)
git_url: https://git.bioconductor.org/packages/flowMap
git_branch: RELEASE_3_18
git_last_commit: a8a8982
git_last_commit_date: 2023-10-24 09:56:15 -0400 (Tue, 24 Oct 2023)
nebbiolo2Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    ERROR  
palomino4Windows Server 2022 Datacenter / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
merida1macOS 12.7.1 Monterey / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.1 Ventura / arm64see weekly results here

CHECK results for flowMap on nebbiolo2


To the developers/maintainers of the flowMap package:
- 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 Troubleshooting Build Report for more information.
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results


Summary

Package: flowMap
Version: 1.40.0
Command: /home/biocbuild/bbs-3.18-bioc/R/bin/R CMD check --install=check:flowMap.install-out.txt --library=/home/biocbuild/bbs-3.18-bioc/R/site-library --timings flowMap_1.40.0.tar.gz
StartedAt: 2024-03-25 22:21:46 -0400 (Mon, 25 Mar 2024)
EndedAt: 2024-03-25 22:22:26 -0400 (Mon, 25 Mar 2024)
EllapsedTime: 39.9 seconds
RetCode: 1
Status:   ERROR  
CheckDir: flowMap.Rcheck
Warnings: NA

Command output

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###
### Running command:
###
###   /home/biocbuild/bbs-3.18-bioc/R/bin/R CMD check --install=check:flowMap.install-out.txt --library=/home/biocbuild/bbs-3.18-bioc/R/site-library --timings flowMap_1.40.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.18-bioc/meat/flowMap.Rcheck’
* using R version 4.3.3 (2024-02-29)
* using platform: x86_64-pc-linux-gnu (64-bit)
* R was compiled by
    gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
    GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
* running under: Ubuntu 22.04.4 LTS
* using session charset: UTF-8
* checking for file ‘flowMap/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘flowMap’ version ‘1.40.0’
* 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 ... OK
* 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 loading without being on the library search path ... 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 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 ...
  ‘flowMap.Rnw’... OK
 NONE
* checking re-building of vignette outputs ... ERROR
Error(s) in re-building vignettes:
  ...
--- re-building ‘flowMap.Rnw’ using knitr

Quitting from lines 97-120 [makeplotSelfruns1] (flowMap.Rnw)
Error: processing vignette 'flowMap.Rnw' failed with diagnostics:
there is no package called 'igraph'
--- failed re-building ‘flowMap.Rnw’

SUMMARY: processing the following file failed:
  ‘flowMap.Rnw’

Error: Vignette re-building failed.
Execution halted

* checking PDF version of manual ... OK
* DONE

Status: 1 ERROR, 2 WARNINGs, 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.18-bioc/meat/flowMap.Rcheck/00check.log’
for details.


Installation output

flowMap.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.18-bioc/R/bin/R CMD INSTALL flowMap
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.18-bioc/R/site-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-class0.0010.0000.000
getFR000
getFRest000