CluMSID 1.3.0
Tobias Depke
| Snapshot Date: 2020-01-15 16:46:30 -0500 (Wed, 15 Jan 2020) |
| URL: https://git.bioconductor.org/packages/CluMSID |
| Branch: master |
| Last Commit: aec22b6 |
| Last Changed Date: 2019-10-29 13:43:25 -0500 (Tue, 29 Oct 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 CluMSID
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* checking for file ‘CluMSID/DESCRIPTION’ ... OK
* preparing ‘CluMSID’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘CluMSID_DI-MSMS.Rmd’ using rmarkdown
Registered S3 method overwritten by 'GGally':
method from
+.gg ggplot2
--- finished re-building ‘CluMSID_DI-MSMS.Rmd’
--- re-building ‘CluMSID_GC-EI-MS.Rmd’ using rmarkdown
Loading required package: CAMERA
Loading required package: Biobase
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, 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
Welcome to Bioconductor
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
Loading required package: xcms
Loading required package: BiocParallel
Loading required package: MSnbase
Loading required package: mzR
Loading required package: Rcpp
Loading required package: S4Vectors
Loading required package: stats4
Attaching package: 'S4Vectors'
The following object is masked from 'package:base':
expand.grid
Loading required package: ProtGenerics
Attaching package: 'ProtGenerics'
The following object is masked from 'package:stats':
smooth
This is MSnbase version 2.13.2
Visit https://lgatto.github.io/MSnbase/ to get started.
Attaching package: 'MSnbase'
The following object is masked from 'package:base':
trimws
This is xcms version 3.9.2
Attaching package: 'xcms'
The following object is masked from 'package:stats':
sigma
Warning: replacing previous import 'xcms::plot' by 'graphics::plot' when loading 'CAMERA'
--- finished re-building ‘CluMSID_GC-EI-MS.Rmd’
--- re-building ‘CluMSID_MTBLS.Rmd’ using rmarkdown
Loading required package: magrittr
Parsed with column specification:
cols(
.default = col_double(),
database_identifier = col_character(),
chemical_formula = col_character(),
smiles = col_character(),
inchi = col_character(),
metabolite_identification = col_character(),
fragmentation = col_logical(),
modifications = col_logical(),
charge = col_logical(),
taxid = col_character(),
species = col_character(),
database = col_logical(),
database_version = col_logical(),
reliability = col_logical(),
uri = col_logical(),
search_engine = col_logical(),
search_engine_score = col_logical(),
smallmolecule_abundance_sub = col_logical(),
smallmolecule_abundance_stdev_sub = col_logical(),
smallmolecule_abundance_std_error_sub = col_logical()
)
See spec(...) for full column specifications.
--- finished re-building ‘CluMSID_MTBLS.Rmd’
--- re-building ‘CluMSID_lowres-LC-MSMS.Rmd’ using rmarkdown
--- finished re-building ‘CluMSID_lowres-LC-MSMS.Rmd’
--- re-building ‘CluMSID_tutorial.Rmd’ using rmarkdown
Warning: Missing column names filled in: 'X1' [1]
Parsed with column specification:
cols(
.default = col_double(),
name = col_character(),
CV = col_logical(),
isotopes = col_character(),
adduct = col_character()
)
See spec(...) for full column specifications.
Quitting from lines 504-505 (CluMSID_tutorial.Rmd)
Error: processing vignette 'CluMSID_tutorial.Rmd' failed with diagnostics:
Unknown colour name: 2
--- failed re-building ‘CluMSID_tutorial.Rmd’
SUMMARY: processing the following file failed:
‘CluMSID_tutorial.Rmd’
Error: Vignette re-building failed.
Execution halted