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BUILD report for MOFA on merida2

This page was generated on 2019-04-09 13:39:39 -0400 (Tue, 09 Apr 2019).

Package 1015/1703HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
MOFA 0.99.14
Britta Velten
Snapshot Date: 2019-04-08 17:01:18 -0400 (Mon, 08 Apr 2019)
URL: https://git.bioconductor.org/packages/MOFA
Branch: master
Last Commit: f81da40
Last Changed Date: 2019-03-27 07:58:34 -0400 (Wed, 27 Mar 2019)
malbec2 Linux (Ubuntu 18.04.2 LTS) / x86_64  OK  ERROR  skipped 
tokay2 Windows Server 2012 R2 Standard / x64  OK  ERROR  skipped  skipped 
celaya2 OS X 10.11.6 El Capitan / x86_64  OK  ERROR  skipped  skipped 
merida2 OS X 10.11.6 El Capitan / x86_64  OK [ ERROR ] skipped  skipped 

Summary

Package: MOFA
Version: 0.99.14
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data MOFA
StartedAt: 2019-04-08 22:53:52 -0400 (Mon, 08 Apr 2019)
EndedAt: 2019-04-08 22:56:12 -0400 (Mon, 08 Apr 2019)
EllapsedTime: 139.7 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 MOFA
###
##############################################################################
##############################################################################


* checking for file ‘MOFA/DESCRIPTION’ ... OK
* preparing ‘MOFA’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
Loading required package: SummarizedExperiment
Loading required package: GenomicRanges
Loading required package: stats4
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, colMeans, colSums, 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, rowMeans,
    rowSums, rownames, sapply, setdiff, sort, table, tapply, union,
    unique, unsplit, which, which.max, which.min

Loading required package: S4Vectors

Attaching package: 'S4Vectors'

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

    expand.grid

Loading required package: IRanges
Loading required package: GenomeInfoDb
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: DelayedArray
Loading required package: matrixStats

Attaching package: 'matrixStats'

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

    anyMissing, rowMedians

Loading required package: BiocParallel

Attaching package: 'DelayedArray'

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

    colMaxs, colMins, colRanges, rowMaxs, rowMins, rowRanges

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

    aperm, apply, rowsum

Registered S3 methods overwritten by 'ggplot2':
  method         from 
  [.quosures     rlang
  c.quosures     rlang
  print.quosures rlang

Attaching package: 'MOFA'

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

    featureNames, featureNames<-, sampleNames, sampleNames<-

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

    predict

Creating MOFA object from a MultiAssayExperiment object...
sh: line 1: 20636 Abort trap: 6           'convert' 'MOFA_example_CLL_files/figure-html/unnamed-chunk-4-1.png' -trim 'MOFA_example_CLL_files/figure-html/unnamed-chunk-4-1.png' > /dev/null
sh: line 1: 20782 Abort trap: 6           'convert' 'MOFA_example_CLL_files/figure-html/unnamed-chunk-12-1.png' -trim 'MOFA_example_CLL_files/figure-html/unnamed-chunk-12-1.png' > /dev/null
sh: line 1: 20790 Abort trap: 6           'convert' 'MOFA_example_CLL_files/figure-html/unnamed-chunk-13-1.png' -trim 'MOFA_example_CLL_files/figure-html/unnamed-chunk-13-1.png' > /dev/null
sh: line 1: 20803 Abort trap: 6           'convert' 'MOFA_example_CLL_files/figure-html/unnamed-chunk-14-1.png' -trim 'MOFA_example_CLL_files/figure-html/unnamed-chunk-14-1.png' > /dev/null
sh: line 1: 20805 Abort trap: 6           'convert' 'MOFA_example_CLL_files/figure-html/unnamed-chunk-14-2.png' -trim 'MOFA_example_CLL_files/figure-html/unnamed-chunk-14-2.png' > /dev/null
sh: line 1: 20819 Abort trap: 6           'convert' 'MOFA_example_CLL_files/figure-html/unnamed-chunk-15-1.png' -trim 'MOFA_example_CLL_files/figure-html/unnamed-chunk-15-1.png' > /dev/null
sh: line 1: 20870 Abort trap: 6           'convert' 'MOFA_example_CLL_files/figure-html/unnamed-chunk-16-1.png' -trim 'MOFA_example_CLL_files/figure-html/unnamed-chunk-16-1.png' > /dev/null
sh: line 1: 20876 Abort trap: 6           'convert' 'MOFA_example_CLL_files/figure-html/unnamed-chunk-17-1.png' -trim 'MOFA_example_CLL_files/figure-html/unnamed-chunk-17-1.png' > /dev/null
sh: line 1: 20975 Abort trap: 6           'convert' 'MOFA_example_CLL_files/figure-html/unnamed-chunk-19-1.png' -trim 'MOFA_example_CLL_files/figure-html/unnamed-chunk-19-1.png' > /dev/null
sh: line 1: 20985 Abort trap: 6           'convert' 'MOFA_example_CLL_files/figure-html/unnamed-chunk-20-1.png' -trim 'MOFA_example_CLL_files/figure-html/unnamed-chunk-20-1.png' > /dev/null
sh: line 1: 20990 Abort trap: 6           'convert' 'MOFA_example_CLL_files/figure-html/unnamed-chunk-21-1.png' -trim 'MOFA_example_CLL_files/figure-html/unnamed-chunk-21-1.png' > /dev/null
sh: line 1: 21010 Abort trap: 6           'convert' 'MOFA_example_CLL_files/figure-html/unnamed-chunk-22-1.png' -trim 'MOFA_example_CLL_files/figure-html/unnamed-chunk-22-1.png' > /dev/null
sh: line 1: 21015 Abort trap: 6           'convert' 'MOFA_example_CLL_files/figure-html/unnamed-chunk-23-1.png' -trim 'MOFA_example_CLL_files/figure-html/unnamed-chunk-23-1.png' > /dev/null
sh: line 1: 21025 Abort trap: 6           'convert' 'MOFA_example_CLL_files/figure-html/unnamed-chunk-27-1.png' -trim 'MOFA_example_CLL_files/figure-html/unnamed-chunk-27-1.png' > /dev/null
sh: line 1: 21027 Abort trap: 6           'convert' 'MOFA_example_CLL_files/figure-html/unnamed-chunk-27-2.png' -trim 'MOFA_example_CLL_files/figure-html/unnamed-chunk-27-2.png' > /dev/null
sh: line 1: 21032 Abort trap: 6           'convert' 'MOFA_example_CLL_files/figure-html/unnamed-chunk-28-1.png' -trim 'MOFA_example_CLL_files/figure-html/unnamed-chunk-28-1.png' > /dev/null
sh: line 1: 21034 Abort trap: 6           'convert' 'MOFA_example_CLL_files/figure-html/unnamed-chunk-28-2.png' -trim 'MOFA_example_CLL_files/figure-html/unnamed-chunk-28-2.png' > /dev/null
sh: line 1: 21040 Abort trap: 6           'convert' 'MOFA_example_CLL_files/figure-html/unnamed-chunk-29-1.png' -trim 'MOFA_example_CLL_files/figure-html/unnamed-chunk-29-1.png' > /dev/null
sh: line 1: 21098 Abort trap: 6           'convert' 'MOFA_example_scMT_files/figure-html/unnamed-chunk-4-1.png' -trim 'MOFA_example_scMT_files/figure-html/unnamed-chunk-4-1.png' > /dev/null
sh: line 1: 21443 Abort trap: 6           'convert' 'MOFA_example_scMT_files/figure-html/unnamed-chunk-11-1.png' -trim 'MOFA_example_scMT_files/figure-html/unnamed-chunk-11-1.png' > /dev/null
sh: line 1: 21568 Abort trap: 6           'convert' 'MOFA_example_scMT_files/figure-html/unnamed-chunk-12-1.png' -trim 'MOFA_example_scMT_files/figure-html/unnamed-chunk-12-1.png' > /dev/null
sh: line 1: 21570 Abort trap: 6           'convert' 'MOFA_example_scMT_files/figure-html/unnamed-chunk-12-2.png' -trim 'MOFA_example_scMT_files/figure-html/unnamed-chunk-12-2.png' > /dev/null
sh: line 1: 21572 Abort trap: 6           'convert' 'MOFA_example_scMT_files/figure-html/unnamed-chunk-13-1.png' -trim 'MOFA_example_scMT_files/figure-html/unnamed-chunk-13-1.png' > /dev/null
sh: line 1: 21576 Abort trap: 6           'convert' 'MOFA_example_scMT_files/figure-html/unnamed-chunk-14-1.png' -trim 'MOFA_example_scMT_files/figure-html/unnamed-chunk-14-1.png' > /dev/null
sh: line 1: 21622 Abort trap: 6           'convert' 'MOFA_example_scMT_files/figure-html/unnamed-chunk-15-1.png' -trim 'MOFA_example_scMT_files/figure-html/unnamed-chunk-15-1.png' > /dev/null
sh: line 1: 21664 Abort trap: 6           'convert' 'MOFA_example_scMT_files/figure-html/unnamed-chunk-16-1.png' -trim 'MOFA_example_scMT_files/figure-html/unnamed-chunk-16-1.png' > /dev/null
sh: line 1: 21668 Abort trap: 6           'convert' 'MOFA_example_scMT_files/figure-html/unnamed-chunk-16-2.png' -trim 'MOFA_example_scMT_files/figure-html/unnamed-chunk-16-2.png' > /dev/null
sh: line 1: 21676 Abort trap: 6           'convert' 'MOFA_example_scMT_files/figure-html/unnamed-chunk-17-1.png' -trim 'MOFA_example_scMT_files/figure-html/unnamed-chunk-17-1.png' > /dev/null
sh: line 1: 21689 Abort trap: 6           'convert' 'MOFA_example_scMT_files/figure-html/unnamed-chunk-18-1.png' -trim 'MOFA_example_scMT_files/figure-html/unnamed-chunk-18-1.png' > /dev/null
sh: line 1: 21697 Abort trap: 6           'convert' 'MOFA_example_scMT_files/figure-html/unnamed-chunk-19-1.png' -trim 'MOFA_example_scMT_files/figure-html/unnamed-chunk-19-1.png' > /dev/null
sh: line 1: 21706 Abort trap: 6           'convert' 'MOFA_example_scMT_files/figure-html/unnamed-chunk-20-1.png' -trim 'MOFA_example_scMT_files/figure-html/unnamed-chunk-20-1.png' > /dev/null
sh: line 1: 21738 Abort trap: 6           'convert' 'MOFA_example_scMT_files/figure-html/unnamed-chunk-21-1.png' -trim 'MOFA_example_scMT_files/figure-html/unnamed-chunk-21-1.png' > /dev/null
sh: line 1: 21748 Abort trap: 6           'convert' 'MOFA_example_scMT_files/figure-html/unnamed-chunk-23-1.png' -trim 'MOFA_example_scMT_files/figure-html/unnamed-chunk-23-1.png' > /dev/null
sh: line 1: 21752 Abort trap: 6           'convert' 'MOFA_example_scMT_files/figure-html/unnamed-chunk-23-2.png' -trim 'MOFA_example_scMT_files/figure-html/unnamed-chunk-23-2.png' > /dev/null
sh: line 1: 21759 Abort trap: 6           'convert' 'MOFA_example_scMT_files/figure-html/unnamed-chunk-24-1.png' -trim 'MOFA_example_scMT_files/figure-html/unnamed-chunk-24-1.png' > /dev/null
Quitting from lines 42-56 (MOFA_example_simulated.Rmd) 
Error: processing vignette 'MOFA_example_simulated.Rmd' failed with diagnostics:
mofapy package not found. Make sure that Reticulate is pointing to the right Python binary.
         Please read the instructions here: https://github.com/bioFAM/MOFA#installation
Execution halted