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BioC 3.6: BUILD report for MAIT on malbec1

This page was generated on 2017-08-16 13:22:32 -0400 (Wed, 16 Aug 2017).

Package 754/1410HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
MAIT 1.11.1
Francesc Fernandez-Albert
Snapshot Date: 2017-08-15 17:18:21 -0400 (Tue, 15 Aug 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/MAIT
Last Changed Rev: 131484 / Revision: 131943
Last Changed Date: 2017-07-21 11:56:42 -0400 (Fri, 21 Jul 2017)
malbec1 Linux (Ubuntu 16.04.1 LTS) / x86_64  NotNeeded [ ERROR ] skipped 
tokay1 Windows Server 2012 R2 Standard / x64  NotNeeded  ERROR  skipped  skipped 
veracruz1 OS X 10.11.6 El Capitan / x86_64  NotNeeded  ERROR  skipped  skipped 

Summary

Package: MAIT
Version: 1.11.1
Command: /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data MAIT
StartedAt: 2017-08-15 19:47:19 -0400 (Tue, 15 Aug 2017)
EndedAt: 2017-08-15 19:48:41 -0400 (Tue, 15 Aug 2017)
EllapsedTime: 81.2 seconds
RetCode: 1
Status:  ERROR 
PackageFile: None
PackageFileSize: NA

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data MAIT
###
##############################################################################
##############################################################################


* checking for file ‘MAIT/DESCRIPTION’ ... OK
* preparing ‘MAIT’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
Loading required package: CAMERA
Loading required package: Biobase
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, cbind, colMeans, colSums, colnames, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, lengths, mapply, match, mget, order, paste, pmax, pmax.int,
    pmin, pmin.int, rank, rbind, rowMeans, rowSums, rownames, sapply,
    setdiff, sort, table, tapply, union, unique, unsplit, which,
    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")'.

Loading required package: xcms
Loading required package: BiocParallel
Loading required package: MSnbase
Loading required package: mzR
Loading required package: Rcpp
Loading required package: ProtGenerics

This is MSnbase version 2.3.9 
  Read '?MSnbase' and references therein for information
  about the package and how to get started.


Attaching package: ‘MSnbase’

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

    smooth

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

    trimws


This is xcms version 2.99.6 


Attaching package: ‘xcms’

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

    sigma

Loading required package: pls

Attaching package: ‘pls’

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

    loadings


Attaching package: ‘MAIT’

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

    loadings, scores

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

    model

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

    plotPCA

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

    loadings

Processing 3201 mz slices ... OK
Performing retention time correction using 1 peak groups.
Warning in do_adjustRtime_peakGroups(peaks = peakmat, peakIndex = object@groupidx,  :
  Too few peak groups for 'loess', reverting to linear method

Error: processing vignette 'MAIT_Vignette.Rnw' failed with diagnostics:
 chunk 2 (label = sampleProcessing) 
Error in do_adjustRtime_peakGroups(peaks = peakmat, peakIndex = object@groupidx,  : 
  Not enough peak groups even for linear smoothing available!
Execution halted