InterMineR 1.9.2
InterMine Team
| Snapshot Date: 2020-01-15 16:46:30 -0500 (Wed, 15 Jan 2020) |
| URL: https://git.bioconductor.org/packages/InterMineR |
| Branch: master |
| Last Commit: e05e70a |
| Last Changed Date: 2019-11-18 12:00:04 -0500 (Mon, 18 Nov 2019) |
| malbec2 | Linux (Ubuntu 18.04.3 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 InterMineR
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* checking for file ‘InterMineR/DESCRIPTION’ ... OK
* preparing ‘InterMineR’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘Enrichment_Analysis_and_Visualization.Rmd’ using rmarkdown
Loading required package: igraph
Attaching package: 'igraph'
The following objects are masked from 'package:stats':
decompose, spectrum
The following object is masked from 'package:base':
union
Loading required package: RCurl
Loading required package: bitops
Loading required package: annotate
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:igraph':
normalize, path, union
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
Loading required package: XML
Loading required package: RSQLite
Loading required package: MASS
Attaching package: 'MASS'
The following object is masked from 'package:AnnotationDbi':
select
Loading required package: Heatplus
Loading required package: RColorBrewer
Warning: replacing previous import 'stats::decompose' by 'igraph::decompose' when loading 'GeneAnswers'
Warning: replacing previous import 'stats::spectrum' by 'igraph::spectrum' when loading 'GeneAnswers'
Loading required package: GO.db
Loading required package: org.Hs.eg.db
Warning in has_utility("convert", "ImageMagick") :
ImageMagick not installed or not in PATH
--- finished re-building ‘Enrichment_Analysis_and_Visualization.Rmd’
--- re-building ‘FlyMine_Genomic_Visualizations.Rmd’ using rmarkdown
Loading required package: GenomicRanges
Loading required package: GenomeInfoDb
Loading required package: grid
--- finished re-building ‘FlyMine_Genomic_Visualizations.Rmd’
--- re-building ‘InterMineR.Rmd’ using rmarkdown
Quitting from lines 173-177 (InterMineR.Rmd)
Error: processing vignette 'InterMineR.Rmd' failed with diagnostics:
Bad Request (HTTP 400). Failed to query <query name="Gene_Orth" model="genomic" view="Gene.primaryIdentifier Gene.symbol Gene.homologues.homologue.primaryIdentifier Gene.homologues.homologue.symbol Gene.homologues.homologue.organism.shortName" longDescription="For a given Gene (or List of Genes) in named organism (default: Human) returns the orthologues in a different organisms. [keywords: homologue, homolog, paralogue, paralogue, ortholog]" sortOrder="Gene.symbol ASC">
<constraint path="Gene" value="PPARG" code="A" op="LOOKUP" extraValue="H. sapiens"/>
</query> .
--- failed re-building ‘InterMineR.Rmd’
SUMMARY: processing the following file failed:
‘InterMineR.Rmd’
Error: Vignette re-building failed.
Execution halted