PCAtools 0.99.13
Kevin Blighe , Myles Lewis
| Snapshot Date: 2019-04-08 17:01:18 -0400 (Mon, 08 Apr 2019) |
| URL: https://git.bioconductor.org/packages/PCAtools |
| Branch: master |
| Last Commit: d0c6fad |
| Last Changed Date: 2019-01-26 07:59:42 -0400 (Sat, 26 Jan 2019) |
| malbec2 | Linux (Ubuntu 18.04.2 LTS) / x86_64 | OK | OK | OK | |  |
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | |
| 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 PCAtools
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* checking for file ‘PCAtools/DESCRIPTION’ ... OK
* preparing ‘PCAtools’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
Loading required package: ggplot2
Registered S3 methods overwritten by 'ggplot2':
method from
[.quosures rlang
c.quosures rlang
print.quosures rlang
Loading required package: ggrepel
Loading required package: reshape2
Loading required package: lattice
Loading required package: cowplot
Attaching package: 'cowplot'
The following object is masked from 'package:ggplot2':
ggsave
Attaching package: 'PCAtools'
The following objects are masked from 'package:stats':
biplot, screeplot
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
Welcome to Bioconductor
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
Setting options('download.file.method.GEOquery'='auto')
Setting options('GEOquery.inmemory.gpl'=FALSE)
Found 1 file(s)
GSE2990_series_matrix.txt.gz
trying URL 'https://ftp.ncbi.nlm.nih.gov/geo/series/GSE2nnn/GSE2990/matrix/GSE2990_series_matrix.txt.gz'
Content type 'application/x-gzip' length 16680570 bytes (15.9 MB)
==================================================
downloaded 15.9 MB
Parsed with column specification:
cols(
.default = col_double(),
ID_REF = col_character()
)
See spec(...) for full column specifications.
-- removing the lower 10% of variables based on variance
-- variables retained:
215281_x_at, 214464_at, 204533_at, 210163_at, 211122_s_at, 205225_at, 202037_s_at, 205044_at, 209351_at, 204540_at, 212671_s_at, 214768_x_at, 215176_x_at, 219415_at, 208650_s_at, 37892_at, 205358_at, 205380_at, 205825_at, 206754_s_at
Warning in eigencorplot(p, metavars = c("Age", "Distant.RFS", "ER", "GGI", :
Distant.RFS is not numeric - please check the source data as everything will be converted to a matrix
Warning in eigencorplot(p, metavars = c("Age", "Distant.RFS", "ER", "GGI", :
ER is not numeric - please check the source data as everything will be converted to a matrix
Warning in eigencorplot(p, metavars = c("Age", "Distant.RFS", "ER", "GGI", :
Grade is not numeric - please check the source data as everything will be converted to a matrix
Scale for 'colour' is already present. Adding another scale for
'colour', which will replace the existing scale.
Scale for 'colour' is already present. Adding another scale for
'colour', which will replace the existing scale.
-- variables retained:
215281_x_at, 214464_at, 211122_s_at, 205225_at, 202037_s_at, 204540_at, 215176_x_at, 205044_at, 208650_s_at, 205380_at
Quitting from lines 363-378 (PCAtools.Rmd)
Error: processing vignette 'PCAtools.Rmd' failed with diagnostics:
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