Back to Multiple platform build/check report for BioC 3.13
[A]BCDEFGHIJKLMNOPQRSTUVWXYZ

This page was generated on 2021-10-15 15:06:28 -0400 (Fri, 15 Oct 2021).

BUILD results for AffyExpress on machv2

To the developers/maintainers of the AffyExpress package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/AffyExpress.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 28/2041HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
AffyExpress 1.58.0  (landing page)
Xuejun Arthur Li
Snapshot Date: 2021-10-14 04:50:12 -0400 (Thu, 14 Oct 2021)
git_url: https://git.bioconductor.org/packages/AffyExpress
git_branch: RELEASE_3_13
git_last_commit: 3b0f72d
git_last_commit_date: 2021-05-19 11:39:35 -0400 (Wed, 19 May 2021)
nebbiolo1Linux (Ubuntu 20.04.2 LTS) / x86_64  OK    ERROR  skipped
tokay2Windows Server 2012 R2 Standard / x64  OK    ERROR  skippedskipped
machv2macOS 10.14.6 Mojave / x86_64  OK    ERROR  skippedskipped

Summary

Package: AffyExpress
Version: 1.58.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data AffyExpress
StartedAt: 2021-10-14 10:31:58 -0400 (Thu, 14 Oct 2021)
EndedAt: 2021-10-14 10:32:16 -0400 (Thu, 14 Oct 2021)
EllapsedTime: 18.0 seconds
RetCode: 1
Status:   ERROR  
PackageFile: None
PackageFileSize: NA

Command output

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


* checking for file ‘AffyExpress/DESCRIPTION’ ... OK
* preparing ‘AffyExpress’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘AffyExpress.Rnw’ using Sweave
Loading required package: affy
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: ‘BiocGenerics’

The following objects are masked from ‘package:parallel’:

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

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: 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: limma

Attaching package: ‘limma’

The following object is masked from ‘package:BiocGenerics’:

    plotMA

Warning: Package 'AffyExpress' is deprecated and will be removed from
  Bioconductor version 3.14

Attaching package: ‘AffyExpress’

The following object is masked from ‘package:BiocGenerics’:

    Filter

The following object is masked from ‘package:base’:

    Filter

Loading required package: R2HTML
Loading required package: affyPLM
Loading required package: gcrma
Loading required package: preprocessCore
Loading required package: simpleaffy
Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called ‘simpleaffy’

Error: processing vignette 'AffyExpress.Rnw' failed with diagnostics:
 chunk 2 
Error in setQCEnvironment(genome) : 
  could not find function "setQCEnvironment"

--- failed re-building ‘AffyExpress.Rnw’

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

Error: Vignette re-building failed.
Execution halted