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This page was generated on 2022-10-19 13:21:34 -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 GEOmetadb on palomino3


To the developers/maintainers of the GEOmetadb package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/GEOmetadb.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 789/2140HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
GEOmetadb 1.58.1  (landing page)
Jack Zhu
Snapshot Date: 2022-10-18 13:55:19 -0400 (Tue, 18 Oct 2022)
git_url: https://git.bioconductor.org/packages/GEOmetadb
git_branch: RELEASE_3_15
git_last_commit: b6816ff
git_last_commit_date: 2022-08-29 16:18:33 -0400 (Mon, 29 Aug 2022)
nebbiolo1Linux (Ubuntu 20.04.5 LTS) / x86_64  OK    ERROR  skipped
palomino3Windows Server 2022 Datacenter / x64  OK    ERROR  skippedskipped
merida1macOS 10.14.6 Mojave / x86_64  OK    ERROR  skippedskipped

Summary

Package: GEOmetadb
Version: 1.58.1
Command: chmod a+r GEOmetadb -R && F:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD build --keep-empty-dirs --no-resave-data GEOmetadb
StartedAt: 2022-10-18 18:48:25 -0400 (Tue, 18 Oct 2022)
EndedAt: 2022-10-18 18:49:00 -0400 (Tue, 18 Oct 2022)
EllapsedTime: 34.8 seconds
RetCode: 1
Status:   ERROR  
PackageFile: None
PackageFileSize: NA

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   chmod a+r GEOmetadb -R && F:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD build --keep-empty-dirs --no-resave-data GEOmetadb
###
##############################################################################
##############################################################################


* checking for file 'GEOmetadb/DESCRIPTION' ... OK
* preparing 'GEOmetadb':
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building 'GEOmetadb.Rmd' using rmarkdown
Loading required package: GEOquery
Loading required package: Biobase
Loading required package: BiocGenerics

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

Welcome to Bioconductor

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

Setting options('download.file.method.GEOquery'='auto')
Setting options('GEOquery.inmemory.gpl'=FALSE)
Loading required package: RSQLite
trying URL 'https://gbnci.cancer.gov/geo/GEOmetadb_demo.sqlite.gz'
Warning in download.file(url_geo, destfile = localfile, mode = "wb") :
  URL 'https://gbnci.cancer.gov/geo/GEOmetadb_demo.sqlite.gz': Timeout of 300 seconds was reached
Quitting from lines 88-97 (GEOmetadb.Rmd) 
Error: processing vignette 'GEOmetadb.Rmd' failed with diagnostics:
cannot open URL 'https://gbnci.cancer.gov/geo/GEOmetadb_demo.sqlite.gz'
--- failed re-building 'GEOmetadb.Rmd'

SUMMARY: processing the following file failed:
  'GEOmetadb.Rmd'

Error: Vignette re-building failed.
Execution halted