RefNet 1.19.0
Paul Shannon
| Snapshot Date: 2019-04-08 17:01:18 -0400 (Mon, 08 Apr 2019) |
| URL: https://git.bioconductor.org/packages/RefNet |
| Branch: master |
| Last Commit: f384aed |
| Last Changed Date: 2018-10-30 11:54:32 -0400 (Tue, 30 Oct 2018) |
| 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 | OK | OK | OK |  |
| merida2 | 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 RefNet
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* checking for file ‘RefNet/DESCRIPTION’ ... OK
* preparing ‘RefNet’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
Loading required package: IRanges
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
Loading required package: stats4
Attaching package: ‘S4Vectors’
The following object is masked from ‘package:base’:
expand.grid
Loading required package: PSICQUIC
Loading required package: biomaRt
Loading required package: httr
Loading required package: plyr
Attaching package: ‘plyr’
The following object is masked from ‘package:IRanges’:
desc
The following object is masked from ‘package:S4Vectors’:
rename
Warning: replacing previous import ‘IRanges::desc’ by ‘plyr::desc’ when loading ‘PSICQUIC’
Loading required package: AnnotationHub
Loading required package: BiocFileCache
Loading required package: dbplyr
Loading required package: RCurl
Loading required package: bitops
Loading required package: shiny
Using temporary cache /tmp/RtmpyB5Bq8/BiocFileCache
snapshotDate(): 2019-04-03
Using temporary cache /tmp/RtmpyB5Bq8/BiocFileCache
Using temporary cache /tmp/RtmpyB5Bq8/BiocFileCache
Using temporary cache /tmp/RtmpyB5Bq8/BiocFileCache
downloading 1 resources
retrieving 1 resource
Using temporary cache /tmp/RtmpyB5Bq8/BiocFileCache
loading from cache
‘AH10364 : 10364’
Using temporary cache /tmp/RtmpyB5Bq8/BiocFileCache
Using temporary cache /tmp/RtmpyB5Bq8/BiocFileCache
Using temporary cache /tmp/RtmpyB5Bq8/BiocFileCache
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Using temporary cache /tmp/RtmpyB5Bq8/BiocFileCache
downloading 1 resources
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Using temporary cache /tmp/RtmpyB5Bq8/BiocFileCache
loading from cache
‘AH10365 : 10365’
Using temporary cache /tmp/RtmpyB5Bq8/BiocFileCache
Using temporary cache /tmp/RtmpyB5Bq8/BiocFileCache
Using temporary cache /tmp/RtmpyB5Bq8/BiocFileCache
Using temporary cache /tmp/RtmpyB5Bq8/BiocFileCache
Using temporary cache /tmp/RtmpyB5Bq8/BiocFileCache
downloading 1 resources
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Using temporary cache /tmp/RtmpyB5Bq8/BiocFileCache
loading from cache
‘AH12810 : 12810’
Using temporary cache /tmp/RtmpyB5Bq8/BiocFileCache
Using temporary cache /tmp/RtmpyB5Bq8/BiocFileCache
Using temporary cache /tmp/RtmpyB5Bq8/BiocFileCache
Using temporary cache /tmp/RtmpyB5Bq8/BiocFileCache
Using temporary cache /tmp/RtmpyB5Bq8/BiocFileCache
downloading 1 resources
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Using temporary cache /tmp/RtmpyB5Bq8/BiocFileCache
loading from cache
‘AH12814 : 12814’
Using temporary cache /tmp/RtmpyB5Bq8/BiocFileCache
Using temporary cache /tmp/RtmpyB5Bq8/BiocFileCache
Using temporary cache /tmp/RtmpyB5Bq8/BiocFileCache
Using temporary cache /tmp/RtmpyB5Bq8/BiocFileCache
Using temporary cache /tmp/RtmpyB5Bq8/BiocFileCache
downloading 1 resources
retrieving 1 resource
Using temporary cache /tmp/RtmpyB5Bq8/BiocFileCache
loading from cache
‘AH22338 : 27766’
Using temporary cache /tmp/RtmpyB5Bq8/BiocFileCache
Using temporary cache /tmp/RtmpyB5Bq8/BiocFileCache
Using temporary cache /tmp/RtmpyB5Bq8/BiocFileCache
Using temporary cache /tmp/RtmpyB5Bq8/BiocFileCache
Using temporary cache /tmp/RtmpyB5Bq8/BiocFileCache
downloading 1 resources
retrieving 1 resource
Using temporary cache /tmp/RtmpyB5Bq8/BiocFileCache
loading from cache
‘AH22339 : 27767’
Using temporary cache /tmp/RtmpyB5Bq8/BiocFileCache
Using temporary cache /tmp/RtmpyB5Bq8/BiocFileCache
Using temporary cache /tmp/RtmpyB5Bq8/BiocFileCache
Using temporary cache /tmp/RtmpyB5Bq8/BiocFileCache
Using temporary cache /tmp/RtmpyB5Bq8/BiocFileCache
downloading 1 resources
retrieving 1 resource
Using temporary cache /tmp/RtmpyB5Bq8/BiocFileCache
loading from cache
‘AH22340 : 27768’
Using temporary cache /tmp/RtmpyB5Bq8/BiocFileCache
Using temporary cache /tmp/RtmpyB5Bq8/BiocFileCache
Using temporary cache /tmp/RtmpyB5Bq8/BiocFileCache
Using temporary cache /tmp/RtmpyB5Bq8/BiocFileCache
Using temporary cache /tmp/RtmpyB5Bq8/BiocFileCache
downloading 1 resources
retrieving 1 resource
Using temporary cache /tmp/RtmpyB5Bq8/BiocFileCache
loading from cache
‘AH22341 : 27769’
Using temporary cache /tmp/RtmpyB5Bq8/BiocFileCache
Using temporary cache /tmp/RtmpyB5Bq8/BiocFileCache
Using temporary cache /tmp/RtmpyB5Bq8/BiocFileCache
checking for biomart access...
does 'http://www.ensembl.org' respond?
creating ensembl mart
hsapiens_gene_ensembl dataset provided?
connecting to biomart...
Loading required package: AnnotationDbi
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")'.
Attaching package: ‘Biobase’
The following object is masked from ‘package:AnnotationHub’:
cache
The following object is masked from ‘package:httr’:
content
Error: processing vignette 'RefNet.Rnw' failed with diagnostics:
chunk 12 (label = eliminateDups)
Error in getBM(filters = biomart.filter, values = uniprots, attributes = columns, :
The query to the BioMart webservice returned an invalid result: biomaRt expected a character string of length 1.
Please report this on the support site at http://support.bioconductor.org
Execution halted