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This page was generated on 2022-10-19 13:20:21 -0400 (Wed, 19 Oct 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 20.04.5 LTS)x86_644.2.1 (2022-06-23) -- "Funny-Looking Kid" 4386
palomino3Windows Server 2022 Datacenterx644.2.1 (2022-06-23 ucrt) -- "Funny-Looking Kid" 4138
merida1macOS 10.14.6 Mojavex86_644.2.1 (2022-06-23) -- "Funny-Looking Kid" 4205
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 GRaNIE on nebbiolo1


To the developers/maintainers of the GRaNIE package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/GRaNIE.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 839/2140HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
GRaNIE 1.0.7  (landing page)
Christian Arnold
Snapshot Date: 2022-10-18 13:55:19 -0400 (Tue, 18 Oct 2022)
git_url: https://git.bioconductor.org/packages/GRaNIE
git_branch: RELEASE_3_15
git_last_commit: 2ff0659
git_last_commit_date: 2022-09-27 06:50:11 -0400 (Tue, 27 Sep 2022)
nebbiolo1Linux (Ubuntu 20.04.5 LTS) / x86_64  OK    ERROR  skipped
palomino3Windows Server 2022 Datacenter / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published

Summary

Package: GRaNIE
Version: 1.0.7
Command: /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data GRaNIE
StartedAt: 2022-10-18 16:48:21 -0400 (Tue, 18 Oct 2022)
EndedAt: 2022-10-18 16:52:09 -0400 (Tue, 18 Oct 2022)
EllapsedTime: 228.3 seconds
RetCode: 1
Status:   ERROR  
PackageFile: None
PackageFileSize: NA

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data GRaNIE
###
##############################################################################
##############################################################################


* checking for file ‘GRaNIE/DESCRIPTION’ ... OK
* preparing ‘GRaNIE’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘GRaNIE_workflow.Rmd’ using rmarkdown
── Attaching packages ─────────────────────────────────────── tidyverse 1.3.2 ──
✔ ggplot2 3.3.6      ✔ purrr   0.3.5 
✔ tibble  3.1.8      ✔ dplyr   1.0.10
✔ tidyr   1.2.1      ✔ stringr 1.4.1 
✔ readr   2.1.3      ✔ forcats 0.5.2 
── Conflicts ────────────────────────────────────────── tidyverse_conflicts() ──
✖ dplyr::filter() masks stats::filter()
✖ dplyr::lag()    masks stats::lag()
Loading required package: topGO
Loading required package: BiocGenerics

Attaching package: 'BiocGenerics'

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

    combine, intersect, setdiff, union

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

Loading required package: graph

Attaching package: 'graph'

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

    boundary

Loading required package: Biobase
Welcome to Bioconductor

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

Loading required package: GO.db
Loading required package: AnnotationDbi
Loading required package: stats4
Loading required package: IRanges
Loading required package: S4Vectors

Attaching package: 'S4Vectors'

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

    first, rename

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

    expand

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

    I, expand.grid, unname


Attaching package: 'IRanges'

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

    collapse, desc, slice

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

    reduce


Attaching package: 'AnnotationDbi'

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

    select


Loading required package: SparseM

Attaching package: 'SparseM'

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

    backsolve


groupGOTerms: 	GOBPTerm, GOMFTerm, GOCCTerm environments built.

Attaching package: 'topGO'

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

    members


Welcome to the GRaNIE package and thank you for using our software. This is GRaNIE version 1.0.7.
All project-related information, guidance, help, documentation and ways to contact us can be found in the R help or here:
https://grp-zaugg.embl-community.io/GRaNIE

Loading required package: Matrix

Attaching package: 'Matrix'

The following object is masked from 'package:S4Vectors':

    expand

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

    expand, pack, unpack

Ensembl site unresponsive, trying asia mirror
Quitting from lines 356-359 (GRaNIE_workflow.Rmd) 
Error: processing vignette 'GRaNIE_workflow.Rmd' failed with diagnostics:
Gateway Timeout (HTTP 504).
--- failed re-building ‘GRaNIE_workflow.Rmd’

SUMMARY: processing the following file failed:
  ‘GRaNIE_workflow.Rmd’

Error: Vignette re-building failed.
Execution halted