MSstats 3.9.0
Meena Choi
| Snapshot Date: 2017-08-15 17:18:21 -0400 (Tue, 15 Aug 2017) | | URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/MSstats | | Last Changed Rev: 129129 / Revision: 131943 | | Last Changed Date: 2017-04-24 15:50:57 -0400 (Mon, 24 Apr 2017) |
| malbec1 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | NotNeeded | OK | ERROR | | |
| tokay1 | Windows Server 2012 R2 Standard / x64 | ...NOT SUPPORTED...NOT SUPPORTED...NOT SUPPORTED... |
| veracruz1 | OS X 10.11.6 El Capitan / x86_64 | NotNeeded | OK | [ ERROR ] | OK | |
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### Running command:
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### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings MSstats_3.9.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.6-bioc/meat/MSstats.Rcheck’
* using R version 3.4.1 (2017-06-30)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘MSstats/DESCRIPTION’ ... OK
* this is package ‘MSstats’ version ‘3.9.0’
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... NOTE
Found the following hidden files and directories:
.BBSoptions
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘MSstats’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking dependencies in R code ... NOTE
Namespaces in Imports field not imported from:
‘MSnbase’ ‘Rcpp’ ‘data.table’ ‘limma’ ‘minpack.lm’ ‘preprocessCore’
‘reshape’
All declared Imports should be used.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
.iter.wls.fit.model: no visible binding for global variable ‘weight’
.multiplot: no visible global function definition for ‘grid.newpage’
.multiplot: no visible global function definition for ‘pushViewport’
.multiplot: no visible global function definition for ‘grid.layout’
.runQuantification: no visible binding for global variable
‘datafeature’
dataProcess: no visible global function definition for
‘normalize.quantiles’
dataProcess: no visible binding for global variable ‘RUN’
dataProcess: no visible binding for global variable ‘LABEL’
dataProcessPlots: no visible binding for global variable ‘RUN’
dataProcessPlots: no visible binding for global variable ‘ABUNDANCE’
dataProcessPlots: no visible binding for global variable ‘Name’
dataProcessPlots: no visible binding for global variable ‘analysis’
dataProcessPlots: no visible binding for global variable ‘Mean’
dataProcessPlots: no visible binding for global variable ‘ciw’
groupComparisonPlots: no visible binding for global variable ‘Protein’
groupComparisonPlots: no visible binding for global variable ‘logFC’
groupComparisonPlots: no visible binding for global variable ‘ciw’
linear_quantlim: no visible binding for global variable ‘label’
linear_quantlim: no visible global function definition for ‘nlsLM’
linear_quantlim: no visible global function definition for
‘nls.lm.control’
modelBasedQCPlots: no visible binding for global variable ‘residual’
nonlinear_quantlim: no visible binding for global variable ‘label’
nonlinear_quantlim: no visible global function definition for ‘nlsLM’
nonlinear_quantlim: no visible global function definition for
‘nls.lm.control’
plot_quantlim: no visible binding for global variable ‘x’
plot_quantlim: no visible binding for global variable ‘y’
plot_quantlim: no visible binding for global variable ‘ymin’
plot_quantlim: no visible binding for global variable ‘ymax’
plot_quantlim: no visible binding for global variable ‘shape’
transformMSnSetToMSstats: no visible global function definition for
‘pData’
transformMSnSetToMSstats: no visible global function definition for
‘fData’
transformMSnSetToMSstats: no visible global function definition for
‘exprs’
transformMSstatsToMSnSet: no visible global function definition for
‘MSnSet’
transformMSstatsToMSnSet: no visible global function definition for
‘sampleNames<-’
transformMSstatsToMSnSet: no visible global function definition for
‘featureNames<-’
transformMSstatsToMSnSet: no visible global function definition for
‘fData’
Undefined global functions or variables:
ABUNDANCE LABEL MSnSet Mean Name Protein RUN analysis ciw datafeature
exprs fData featureNames<- grid.layout grid.newpage label logFC
nls.lm.control nlsLM normalize.quantiles pData pushViewport residual
sampleNames<- shape weight x y ymax ymin
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... ERROR
Running examples in ‘MSstats-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: transformMSnSetToMSstats
> ### Title: Transforms a MSnSet class dataset into a required input for
> ### MSstats
> ### Aliases: transformMSnSetToMSstats
>
> ### ** Examples
>
>
> library("MSnbase")
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: 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: mzR
Loading required package: Rcpp
Loading required package: BiocParallel
Loading required package: ProtGenerics
This is MSnbase version 2.3.9
Read '?MSnbase' and references therein for information
about the package and how to get started.
Attaching package: ‘MSnbase’
The following object is masked from ‘package:stats’:
smooth
The following object is masked from ‘package:base’:
trimws
> data(itraqdata)
> class(itraqdata)
[1] "MSnExp"
attr(,"package")
[1] "MSnbase"
>
> msnset <- quantify(itraqdata[10:15], method = "trap", reporters = iTRAQ4, verbose = FALSE)
> msnset
MSnSet (storageMode: lockedEnvironment)
assayData: 6 features, 4 samples
element names: exprs
protocolData: none
phenoData
sampleNames: iTRAQ4.114 iTRAQ4.115 iTRAQ4.116 iTRAQ4.117
varLabels: mz reporters
varMetadata: labelDescription
featureData
featureNames: X18 X19 ... X22 (6 total)
fvarLabels: spectrum ProteinAccession ... collision.energy (15 total)
fvarMetadata: labelDescription
experimentData: use 'experimentData(object)'
Annotation: No annotation
- - - Processing information - - -
Data loaded: Wed May 11 18:54:39 2011
Updated from version 0.3.0 to 0.3.1 [Fri Jul 8 20:23:25 2016]
Data [numerically] subsetted 6 spectra: Wed Aug 16 06:02:27 2017
iTRAQ4 quantification by trapezoidation: Wed Aug 16 06:02:27 2017
MSnbase version: 1.1.22
>
> pData(msnset)$group<-c("control","disease","control","disease")
>
> transformMSnSetToMSstats(data=msnset,Condition="group")
Error in transformMSnSetToMSstats(data = msnset, Condition = "group") :
Please check the variable name. The provided variable name file is not present in the data set.
Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: 1 ERROR, 3 NOTEs
See
‘/Users/biocbuild/bbs-3.6-bioc/meat/MSstats.Rcheck/00check.log’
for details.