CellMapper 1.4.0
Brad Nelms
| Snapshot Date: 2018-04-11 16:45:18 -0400 (Wed, 11 Apr 2018) |
| URL: https://git.bioconductor.org/packages/CellMapper |
| Branch: RELEASE_3_6 |
| Last Commit: 19d7d16 |
| Last Changed Date: 2017-10-30 12:41:21 -0400 (Mon, 30 Oct 2017) |
| malbec1 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | OK | OK | WARNINGS | |  |
| tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | WARNINGS | OK | |
| veracruz1 | 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 CellMapper
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* checking for file ‘CellMapper/DESCRIPTION’ ... OK
* preparing ‘CellMapper’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
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, cbind, colMeans, colSums, 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, rowMeans, rowSums, rownames, sapply,
setdiff, sort, table, tapply, union, unique, unsplit, which,
which.max, which.min
Loading required package: AnnotationHub
snapshotDate(): 2017-10-30
Warning: replacing previous import ‘stats::sd’ by ‘S4Vectors::sd’ when loading ‘CellMapper’
Warning: replacing previous import ‘stats::var’ by ‘S4Vectors::var’ when loading ‘CellMapper’
see ?CellMapperData and browseVignettes('CellMapperData') for documentation
loading from cache ‘/Users/biocbuild//.ExperimentHub/170’
snapshotDate(): 2017-10-30
see ?CellMapperData and browseVignettes('CellMapperData') for documentation
loading from cache ‘/Users/biocbuild//.ExperimentHub/170’
* Running CellMapper with query gene(s) '2571'...
see ?CellMapperData and browseVignettes('CellMapperData') for documentation
loading from cache ‘/Users/biocbuild//.ExperimentHub/171’
see ?CellMapperData and browseVignettes('CellMapperData') for documentation
loading from cache ‘/Users/biocbuild//.ExperimentHub/172’
see ?CellMapperData and browseVignettes('CellMapperData') for documentation
loading from cache ‘/Users/biocbuild//.ExperimentHub/173’
* Running CellMapper on 'Dataset 1' with query gene(s) '3856'...
* Running CellMapper on 'Dataset 2' with query gene(s) '3856'...
* Running CellMapper on 'Dataset 3' with query gene(s) '3856'...
* Pooling results...
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:ExperimentHub’:
cache
The following object is masked from ‘package:AnnotationHub’:
cache
* Scaling the data matrix...
* Computing the singular-value decomposition of the data matrix...
* Preparing data for CellMapper...
* Running CellMapper with query gene(s) '1000_at'...
see ?HumanAffyData and browseVignettes('HumanAffyData') for documentation
loading from cache ‘/Users/biocbuild//.ExperimentHub/177’
* Scaling the data matrix...
* Computing the singular-value decomposition of the data matrix...
* Preparing data for CellMapper...
see ?HumanAffyData and browseVignettes('HumanAffyData') for documentation
loading from cache ‘/Users/biocbuild//.ExperimentHub/176’
Warning in load(cache(getHub(x))) : lzma decoder corrupt data
Error: processing vignette 'CellMapper.Rnw' failed with diagnostics:
chunk 26
Error : failed to load resource
name: EH176
title: GEO accession data GSE64985 as an ExpressionSet
reason: error reading from connection
Execution halted