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This page was generated on 2022-07-07 11:11:06 -0400 (Thu, 07 Jul 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.2.0 Patched (2022-06-02 r82447) -- "Vigorous Calisthenics" 4343
palomino4Windows Server 2022 Datacenterx644.2.0 Patched (2022-06-02 r82447 ucrt) -- "Vigorous Calisthenics" 4148
lconwaymacOS 12.2.1 Montereyx86_644.2.0 Patched (2022-05-29 r82424) -- "Vigorous Calisthenics" 4160
kjohnsonmacOS 12.4 Montereyarm644.2.0 Patched (2022-06-09 r82473) -- "Vigorous Calisthenics" 3115
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

BUILD results for fcoex on kjohnson


To the developers/maintainers of the fcoex package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/fcoex.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? 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 648/2124HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
fcoex 1.11.0  (landing page)
Tiago Lubiana
Snapshot Date: 2022-07-06 14:00:06 -0400 (Wed, 06 Jul 2022)
git_url: https://git.bioconductor.org/packages/fcoex
git_branch: master
git_last_commit: 03f66a9
git_last_commit_date: 2022-04-26 12:01:03 -0400 (Tue, 26 Apr 2022)
nebbiolo2Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
palomino4Windows Server 2022 Datacenter / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
lconwaymacOS 12.2.1 Monterey / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
kjohnsonmacOS 12.4 Monterey / arm64  OK    ERROR  skippedskipped

Summary

Package: fcoex
Version: 1.11.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data fcoex
StartedAt: 2022-07-06 20:49:33 -0400 (Wed, 06 Jul 2022)
EndedAt: 2022-07-06 20:51:43 -0400 (Wed, 06 Jul 2022)
EllapsedTime: 129.8 seconds
RetCode: 1
Status:   ERROR  
PackageFile: None
PackageFileSize: NA

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data fcoex
###
##############################################################################
##############################################################################


* checking for file ‘fcoex/DESCRIPTION’ ... OK
* preparing ‘fcoex’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘fcoex.Rmd’ using rmarkdown


Attaching package: 'MatrixGenerics'

The following objects are masked from 'package:matrixStats':

    colAlls, colAnyNAs, colAnys, colAvgsPerRowSet, colCollapse,
    colCounts, colCummaxs, colCummins, colCumprods, colCumsums,
    colDiffs, colIQRDiffs, colIQRs, colLogSumExps, colMadDiffs,
    colMads, colMaxs, colMeans2, colMedians, colMins, colOrderStats,
    colProds, colQuantiles, colRanges, colRanks, colSdDiffs, colSds,
    colSums2, colTabulates, colVarDiffs, colVars, colWeightedMads,
    colWeightedMeans, colWeightedMedians, colWeightedSds,
    colWeightedVars, rowAlls, rowAnyNAs, rowAnys, rowAvgsPerColSet,
    rowCollapse, rowCounts, rowCummaxs, rowCummins, rowCumprods,
    rowCumsums, rowDiffs, rowIQRDiffs, rowIQRs, rowLogSumExps,
    rowMadDiffs, rowMads, rowMaxs, rowMeans2, rowMedians, rowMins,
    rowOrderStats, rowProds, rowQuantiles, rowRanges, rowRanks,
    rowSdDiffs, rowSds, rowSums2, rowTabulates, rowVarDiffs, rowVars,
    rowWeightedMads, rowWeightedMeans, rowWeightedMedians,
    rowWeightedSds, rowWeightedVars


Attaching package: 'BiocGenerics'

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, basename, cbind, colnames, dirname, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
    pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
    tapply, union, unique, unsplit, which.max, which.min


Attaching package: 'S4Vectors'

The following objects are masked from 'package:base':

    I, expand.grid, unname

Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.


Attaching package: 'Biobase'

The following object is masked from 'package:MatrixGenerics':

    rowMedians

The following objects are masked from 'package:matrixStats':

    anyMissing, rowMedians

Created new fcoex object.
Getting SU scores for each gene
Running FCBF to find module headers
Calculating adjacency matrix
Trimming and getting modules from adjacency matrix
12 modules were found.
Quitting from lines 130-143 (fcoex.Rmd) 
Error: processing vignette 'fcoex.Rmd' failed with diagnostics:
object 'gmt_in' not found
--- failed re-building ‘fcoex.Rmd’

--- re-building ‘fcoex_and_seurat.Rmd’ using rmarkdown
Warning in xtfrm.data.frame(x) : cannot xtfrm data frames
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Quitting from lines 67-75 (fcoex_and_seurat.Rmd) 
Error: processing vignette 'fcoex_and_seurat.Rmd' failed with diagnostics:
invalid 'nchars' argument
--- failed re-building ‘fcoex_and_seurat.Rmd’

SUMMARY: processing the following files failed:
  ‘fcoex.Rmd’ ‘fcoex_and_seurat.Rmd’

Error: Vignette re-building failed.
Execution halted