BgeeDB 2.0.0
Andrea Komljenovic , Frederic Bastian
| Snapshot Date: 2017-04-14 17:17:13 -0400 (Fri, 14 Apr 2017) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_4/madman/Rpacks/BgeeDB | | Last Changed Rev: 122710 / Revision: 128728 | | Last Changed Date: 2016-10-17 14:45:06 -0400 (Mon, 17 Oct 2016) |
| malbec1 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | OK | [ ERROR ] | skipped | | |
| tokay1 | Windows Server 2012 R2 Standard / x64 | OK | ERROR | skipped | skipped | |
| morelia | Mac OS X Mavericks (10.9.5) / x86_64 | OK | ERROR | skipped | skipped | |
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### Running command:
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### /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data BgeeDB
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* checking for file ‘BgeeDB/DESCRIPTION’ ... OK
* preparing ‘BgeeDB’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
Loading required package: topGO
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, xtabs
The following objects are masked from 'package:base':
Filter, Find, Map, Position, Reduce, anyDuplicated, append,
as.data.frame, cbind, 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, rownames, sapply, setdiff, sort,
table, tapply, union, unique, unsplit, which, which.max,
which.min
Loading required package: graph
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: GO.db
Loading required package: AnnotationDbi
Loading required package: stats4
Loading required package: IRanges
Loading required package: S4Vectors
Attaching package: 'S4Vectors'
The following objects are masked from 'package:base':
colMeans, colSums, expand.grid, rowMeans, rowSums
Loading required package: SparseM
Attaching package: 'SparseM'
The following object is masked from 'package:base':
backsolve
groupGOTerms: GOBPTerm, GOMFTerm, GOCCTerm environments built.
Attaching package: 'topGO'
The following object is masked from 'package:IRanges':
members
Loading required package: tidyr
Attaching package: 'tidyr'
The following object is masked from 'package:S4Vectors':
expand
trying URL 'http://r13_2.bgee.org/?page=species&display_type=tsv'
Content type 'text/tab-separated-values;charset=UTF-8' length unknown
downloaded 707 bytes
trying URL 'http://r13_2.bgee.org/?page=species&display_type=tsv'
Content type 'text/tab-separated-values;charset=UTF-8' length unknown
downloaded 707 bytes
trying URL 'http://r13_2.bgee.org/?page=species&display_type=tsv'
Content type 'text/tab-separated-values;charset=UTF-8' length unknown
downloaded 707 bytes
trying URL 'ftp://ftp.bgee.org/bgee_v13_2/download/processed_expr_values/rna_seq/Mus_musculus/Mus_musculus_RNA-Seq_experiments_libraries.zip'
ftp data connection made, file length 9292 bytes
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downloaded 9292 bytes
trying URL 'ftp://ftp.bgee.org/bgee_v13_2/download/processed_expr_values/rna_seq/Mus_musculus/Mus_musculus_RNA-Seq_read_counts_RPKM.zip'
ftp data connection made, file length 32872528 bytes
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downloaded 31.3 MB
trying URL 'ftp://ftp.bgee.org/bgee_v13_2/download/processed_expr_values/rna_seq/Mus_musculus/Mus_musculus_RNA-Seq_read_counts_RPKM_GSE30617.tsv.zip'
ftp data connection made, file length 10651169 bytes
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downloaded 10.2 MB
trying URL 'http://r13_2.bgee.org/?page=dao&action=org.bgee.model.dao.api.ontologycommon.RelationDAO.getAnatEntityRelations&display_type=tsv&species_list=7955&attr_list=SOURCE_ID&attr_list=TARGET_ID&api_key=a7967ba6caa351588255fad2669329f74721bcff82e5a82df4890a4c0401d40e3dc43f790e07a8ffbb7574bc4e0dff41397ec02b2be4a358ca9595c517575cc5&source=BgeeDB_R_package&source_version=2.0.0'
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downloaded 638 KB
trying URL 'http://r13_2.bgee.org/?page=dao&action=org.bgee.model.dao.api.anatdev.AnatEntityDAO.getAnatEntities&display_type=tsv&species_list=7955&attr_list=ID&attr_list=NAME&api_key=a7967ba6caa351588255fad2669329f74721bcff82e5a82df4890a4c0401d40e3dc43f790e07a8ffbb7574bc4e0dff41397ec02b2be4a358ca9595c517575cc5&source=BgeeDB_R_package&source_version=2.0.0'
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downloaded 475 KB
trying URL 'http://r13_2.bgee.org/?page=dao&action=org.bgee.model.dao.api.expressiondata.ExpressionCallDAO.getExpressionCalls&display_type=tsv&species_list=7955&attr_list=GENE_ID&attr_list=ANAT_ENTITY_ID&api_key=a7967ba6caa351588255fad2669329f74721bcff82e5a82df4890a4c0401d40e3dc43f790e07a8ffbb7574bc4e0dff41397ec02b2be4a358ca9595c517575cc5&source=BgeeDB_R_package&source_version=2.0.0'
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downloaded 7.0 MB
Quitting from lines 157-177 (BgeeDB_Manual.Rmd)
Error: processing vignette 'BgeeDB_Manual.Rmd' failed with diagnostics:
Invalid filters(s): go_id
Please use the function 'listFilters' to get valid filter names
Execution halted