FELLA 1.4.1
Sergio Picart-Armada
| Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019) |
| URL: https://git.bioconductor.org/packages/FELLA |
| Branch: RELEASE_3_9 |
| Last Commit: 36e66c6 |
| Last Changed Date: 2019-07-14 04:16:52 -0400 (Sun, 14 Jul 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 | |
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### Running command:
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### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data FELLA
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* checking for file ‘FELLA/DESCRIPTION’ ... OK
* preparing ‘FELLA’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘musmusculus.Rmd’ using rmarkdown
Loading required package: AnnotationDbi
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, 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,
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: IRanges
Loading required package: S4Vectors
Attaching package: 'S4Vectors'
The following object is masked from 'package:base':
expand.grid
Attaching package: 'igraph'
The following object is masked from 'package:IRanges':
union
The following object is masked from 'package:S4Vectors':
union
The following objects are masked from 'package:BiocGenerics':
normalize, path, union
The following objects are masked from 'package:stats':
decompose, spectrum
The following object is masked from 'package:base':
union
Building through KEGGREST...
Quitting from lines 42-67 (musmusculus.Rmd)
Error: processing vignette 'musmusculus.Rmd' failed with diagnostics:
Not Found (HTTP 404).
--- failed re-building ‘musmusculus.Rmd’
--- re-building ‘quickstart.Rmd’ using rmarkdown
No background compounds specified. Default background will be used.
Warning in defineCompounds(compounds = input.fail, data = FELLA.sample) :
Some compounds were introduced as affected but they do not belong to the background. These compounds will be excluded from the analysis. Use 'getExcluded' to see them.
No background compounds specified. Default background will be used.
Warning in defineCompounds(compounds = compounds, compoundsBackground = compoundsBackground, :
Some compounds were introduced as affected but they do not belong to the background. These compounds will be excluded from the analysis. Use 'getExcluded' to see them.
Running hypergeom...
Starting hypergeometric p-values calculation...
Done.
Running diffusion...
Computing p-scores through the specified distribution.
Done.
Running PageRank...
Computing p-scores through the specified distribution.
Using provided damping factor...
Done.
Warning in has_utility("convert", "ImageMagick") :
ImageMagick not installed or not in PATH
--- finished re-building ‘quickstart.Rmd’
--- re-building ‘zebrafish.Rmd’ using rmarkdown
Building through KEGGREST...
Quitting from lines 51-74 (zebrafish.Rmd)
Error: processing vignette 'zebrafish.Rmd' failed with diagnostics:
Not Found (HTTP 404).
--- failed re-building ‘zebrafish.Rmd’
--- re-building ‘FELLA.Rnw’ using Sweave
Building through KEGGREST...
Error: processing vignette 'FELLA.Rnw' failed with diagnostics:
chunk 2 (label = 01_graph)
Error in .getUrl(url, .listParser, nameColumn = 1, valueColumn = 2) :
Not Found (HTTP 404).
--- failed re-building ‘FELLA.Rnw’
SUMMARY: processing the following files failed:
‘musmusculus.Rmd’ ‘zebrafish.Rmd’ ‘FELLA.Rnw’
Error: Vignette re-building failed.
Execution halted