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This page was generated on 2016-04-23 10:11:40 -0700 (Sat, 23 Apr 2016).
| Package 680/1103 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | |||||
| MSnbase 1.18.1 Laurent Gatto
| zin1 | Linux (Ubuntu 14.04.2 LTS) / x86_64 | OK | OK | [ ERROR ] | ||||||
| moscato1 | Windows Server 2008 R2 Standard (64-bit) / x64 | OK | OK | OK | OK |  | |||||
| oaxaca | Mac OS X Mavericks (10.9.5) / x86_64 | OK | OK | OK | OK | |
| Package: MSnbase |
| Version: 1.18.1 |
| Command: /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings MSnbase_1.18.1.tar.gz |
| StartedAt: 2016-04-23 03:14:50 -0700 (Sat, 23 Apr 2016) |
| EndedAt: 2016-04-23 03:19:12 -0700 (Sat, 23 Apr 2016) |
| EllapsedTime: 261.6 seconds |
| RetCode: 1 |
| Status: ERROR |
| CheckDir: MSnbase.Rcheck |
| Warnings: NA |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings MSnbase_1.18.1.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.2-bioc/meat/MSnbase.Rcheck’
* using R version 3.2.4 Revised (2016-03-16 r70336)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘MSnbase/DESCRIPTION’ ... OK
* this is package ‘MSnbase’ version ‘1.18.1’
* 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 ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘MSnbase’ can be installed ... [18s/18s] 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 dependencies in R code ... NOTE
Unexported objects imported by ':::' calls:
‘Biobase:::.showAnnotatedDataFrame’ ‘MALDIquant:::.estimateNoise’
‘MALDIquant:::.localMaxima’ ‘MALDIquant:::.movingAverage’
‘MALDIquant:::.savitzkyGolay’ ‘MALDIquant:::.which.closest’
See the note in ?`:::` about the use of this operator.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* 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 line endings in C/C++/Fortran sources/headers ... OK
* checking compiled code ... OK
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [56s/91s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
quantify-methods 7.283 1.186 3.967
averageMSnSet 5.945 0.154 6.752
MSnSet-class 5.312 0.028 5.352
writeMzTabData 2.645 0.016 37.587
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’ [52s/46s]
ERROR
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
30: match(name, names(x))
31: (function (x)
x$.self$finalize())(<environment>)
Error in signalCondition(e) :
no function to return from, jumping to top level
Calls: <Anonymous> -> .handleSimpleError -> h -> signalCondition
testthat results ================================================================
OK: 496 SKIPPED: 0 FAILED: 1
1. Error: topN for MSnSet (@test_topN.R#54)
Error: testthat unit tests failed
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, 1 NOTE
See
‘/home/biocbuild/bbs-3.2-bioc/meat/MSnbase.Rcheck/00check.log’
for details.
testthat.Rout.fail:
R version 3.2.4 Revised (2016-03-16 r70336) -- "Very Secure Dishes"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> # setting R_TESTS to empty string because of
> # https://github.com/hadley/testthat/issues/144
> # revert this when that issue in R is fixed.
> Sys.setenv("R_TESTS" = "")
> library(testthat)
> 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, xtabs
The following objects are masked from 'package:base':
Filter, Find, Map, Position, Reduce, anyDuplicated, append,
as.data.frame, as.vector, 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, unlist, unsplit
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 1.18.1
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
>
> test_check("MSnbase")
Object of class "MzTab".
Description: mzTab example file for reporting a summary report of
quantification data quantified on the protein level
Mode: Complete
Type: Quantification
Available data: Proteins PSMs
Instance of class 'MSnSetList' containig 3 objects.
Object of class "MSnExp"
Object size in memory: 0.2 Mb
- - - Spectra data - - -
MS level(s): 2
Number of MS1 acquisitions: 1
Number of MSn scans: 5
Number of precursor ions: 5
4 unique MZs
Precursor MZ's: 437.8 - 716.34
MSn M/Z range: 100 2016.66
MSn retention times: 25:1 - 25:2 minutes
- - - Processing information - - -
Data loaded: Sat Apr 23 03:18:37 2016
MSnbase version: 1.18.1
- - - Meta data - - -
phenoData
rowNames: 1
varLabels: sampleNames
varMetadata: labelDescription
Loaded from:
dummyiTRAQ.mzXML
protocolData: none
featureData
featureNames: X1.1 X2.1 ... X5.1 (5 total)
fvarLabels: spectrum
fvarMetadata: labelDescription
experimentData: use 'experimentData(object)'
Object of class "MSnExp"
Object size in memory: 0.2 Mb
- - - Spectra data - - -
MS level(s): 2
Number of MS1 acquisitions: 1
Number of MSn scans: 5
Number of precursor ions: 5
4 unique MZs
Precursor MZ's: 437.8 - 716.34
MSn M/Z range: 100 2016.66
MSn retention times: 25:1 - 25:2 minutes
- - - Processing information - - -
Data loaded: Sat Apr 23 03:18:37 2016
MSnbase version: 1.18.1
- - - Meta data - - -
phenoData
rowNames: 1
varLabels: sampleNames
varMetadata: labelDescription
Loaded from:
dummyiTRAQ.mzXML
protocolData: none
featureData
featureNames: X1.1 X2.1 ... X5.1 (5 total)
fvarLabels: spectrum
fvarMetadata: labelDescription
experimentData: use 'experimentData(object)'
common unique1 unique2
all 2 2 2
common unique1 unique2
all 0 4 4
A 0 1 0
B 0 1 0
C 0 1 0
D 0 1 0
F 0 0 2
G 0 0 2
common unique1 unique2
all 2 2 2
C 0 1 0
D 0 1 0
E 0 1 0
F 0 1 2
G 0 0 2
Object of class "FeaturesOfInterest"
Created on Sat Apr 23 03:18:39 2016
Description:
small foi
3 features of interest:
P20353, P53501, Q7KU78
Traceable object of class "FeaturesOfInterest"
Created on Sat Apr 23 03:18:39 2016
Description:
my description
10 features of interest:
P20353, P53501 ... Q9VCK0, Q9VIU7
A collection of 1 features of interest.
A collection of 10 features of interest.
Iterations of EM:
1...2...3...4...5...6...7...8...9...10...11...
[1] 0.07947339
Reading 5 MS2 spectra from file dummyiTRAQ.mzXML
|
| | 0%
|
|============== | 20%
|
|============================ | 40%
|
|========================================== | 60%
|
|======================================================== | 80%
|
|======================================================================| 100%
Reading 5 MS2 spectra from file dummyiTRAQ2.mzXML
|
| | 0%
|
|============== | 20%
|
|============================ | 40%
|
|========================================== | 60%
|
|======================================================== | 80%
|
|======================================================================| 100%
Creating 'MSnExp' object
|
| | 0%
|
|======================= | 33%
|
|=============================================== | 67%
|
|======================================================================| 100%
1. Error: topN for MSnSet (@test_topN.R#54) ------------------------------------
attempt to apply non-function
1: quantify(itraqdata, reporters = iTRAQ4, method = "max", verbose = FALSE, BPPARAM = SerialParam()) at testthat/test_topN.R:54
2: quantify(itraqdata, reporters = iTRAQ4, method = "max", verbose = FALSE, BPPARAM = SerialParam())
3: .local(object, ...)
4: quantify_MSnExp(object, method, reporters, strict, BPPARAM, qual, verbose)
5: bplapply(spectraList, quantify, method, reporters, strict, BPPARAM = BPPARAM)
6: bplapply(spectraList, quantify, method, reporters, strict, BPPARAM = BPPARAM)
7: lapply(X, FUN, ...)
8: FUN(X[[i]], ...)
9: FUN(X[[i]], ...)
10: .local(object, ...)
11: quantify_Spectrum(object, match.arg(method), reporters, strict)
12: curveData(spectrum, reporters[i])
13: reporters[i]
14: reporters[i]
15: .local(x, i, j, ..., drop)
16: `[.ReporterIons`(x, i)
17: new("ReporterIons", name = paste(x@name, "[", paste(i, collapse = ":"), "]", sep = ""),
description = paste("subset of", x@description, sep = " "), reporterNames = x@reporterNames[i],
mz = x@mz[i], col = x@col[i], width = x@width)
18: initialize(value, ...)
19: initialize(value, ...)
20: callNextMethod()
21: .nextMethod(.Object = .Object, ... = ...)
22: .local(.Object, ...)
23: callNextMethod(.Object, ...)
24: addNextMethod(method, f, envir = methodEnv)
25: addNextMethod(method, f, envir = methodEnv)
26: .findNextFromTable(method, f, optional, envir)
27: .findInheritedMethods(defined, fdef, mtable = NULL, excluded = excluded)
28: (function (cl, name, valueClass)
{
ClassDef <- getClass(cl)
slotClass <- elNamed(ClassDef@slots, name)
if (is.null(slotClass))
stop(gettextf("%s is not a slot in class %s", sQuote(name), dQuote(cl)),
domain = NA)
if (.identC(slotClass, valueClass))
return(TRUE)
ok <- possibleExtends(valueClass, slotClass, ClassDef2 = getClassDef(slotClass,
where = .classEnv(ClassDef)))
if (identical(ok, FALSE))
stop(gettextf("assignment of an object of class %s is not valid for @%s in an object of class %s; is(value, \"%s\") is not TRUE",
dQuote(valueClass), sQuote(name), dQuote(cl), slotClass), domain = NA)
TRUE
})(structure("derivedDefaultMethod", package = "methods"), "target", structure("signature", package = "methods"))
29: elNamed(ClassDef@slots, name)
30: match(name, names(x))
31: (function (x)
x$.self$finalize())(<environment>)
Error in signalCondition(e) :
no function to return from, jumping to top level
Calls: <Anonymous> -> .handleSimpleError -> h -> signalCondition
testthat results ================================================================
OK: 496 SKIPPED: 0 FAILED: 1
1. Error: topN for MSnSet (@test_topN.R#54)
Error: testthat unit tests failed
Execution halted
MSnbase.Rcheck/00install.out:
* installing *source* package ‘MSnbase’ ... ** libs g++ -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-3.2-bioc/R/library/Rcpp/include" -fpic -g -O2 -Wall -c RcppExports.cpp -o RcppExports.o g++ -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-3.2-bioc/R/library/Rcpp/include" -fpic -g -O2 -Wall -c imp_neighbour_avg.cpp -o imp_neighbour_avg.o g++ -shared -L/home/biocbuild/bbs-3.2-bioc/R/lib -L/usr/local/lib -o MSnbase.so RcppExports.o imp_neighbour_avg.o -L/home/biocbuild/bbs-3.2-bioc/R/lib -lR installing to /home/biocbuild/bbs-3.2-bioc/meat/MSnbase.Rcheck/MSnbase/libs ** R ** data *** moving datasets to lazyload DB ** inst ** preparing package for lazy loading Creating a new generic function for ‘smooth’ in package ‘MSnbase’ Creating a generic function for ‘t’ from package ‘base’ in package ‘MSnbase’ Creating a generic function for ‘scale’ from package ‘base’ in package ‘MSnbase’ in method for ‘coerce’ with signature ‘"IBSpectra","MSnSet"’: no definition for class “IBSpectra” Creating a generic function for ‘split’ from package ‘base’ in package ‘MSnbase’ ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded * DONE (MSnbase)
MSnbase.Rcheck/MSnbase-Ex.timings:
| name | user | system | elapsed | |
| FeatComp-class | 0.198 | 0.004 | 0.239 | |
| FeaturesOfInterest-class | 0.083 | 0.000 | 0.082 | |
| MSmap-class | 0.001 | 0.000 | 0.001 | |
| MSnExp-class | 0.325 | 0.000 | 0.342 | |
| MSnProcess-class | 0.001 | 0.000 | 0.002 | |
| MSnSet-class | 5.312 | 0.028 | 5.352 | |
| MSnSetList-class | 3.520 | 0.012 | 3.530 | |
| MzTab-class | 1.165 | 0.024 | 4.072 | |
| NAnnotatedDataFrame-class | 0.015 | 0.000 | 0.016 | |
| ReporterIons-class | 0.013 | 0.000 | 0.013 | |
| TMT6 | 0.010 | 0.000 | 0.009 | |
| addIdentificationData-methods | 0.504 | 0.000 | 0.504 | |
| averageMSnSet | 5.945 | 0.154 | 6.752 | |
| bin-methods | 0.281 | 0.004 | 0.285 | |
| calculateFragments-methods | 0.515 | 0.004 | 0.519 | |
| chromatogram-methods | 0.039 | 0.008 | 0.097 | |
| clean-methods | 0.821 | 0.032 | 0.851 | |
| combineFeatures | 0.753 | 0.000 | 0.756 | |
| commonFeatureNames | 0.553 | 0.004 | 0.558 | |
| compareSpectra-methods | 0.145 | 0.000 | 0.146 | |
| exprsToRatios-methods | 0.071 | 0.000 | 0.071 | |
| extractPrecSpectra-methods | 0.474 | 0.000 | 0.477 | |
| featureCV | 0.037 | 0.004 | 0.041 | |
| fillUp | 0.006 | 0.000 | 0.006 | |
| formatRt | 0.000 | 0.000 | 0.001 | |
| get.amino.acids | 0.004 | 0.000 | 0.004 | |
| get.atomic.mass | 0.001 | 0.000 | 0.001 | |
| getVariableName | 0.001 | 0.000 | 0.002 | |
| iPQF | 0.304 | 0.004 | 0.311 | |
| iTRAQ4 | 0.018 | 0.000 | 0.017 | |
| imageNA2 | 2.224 | 0.044 | 2.283 | |
| impute-methods | 0.744 | 0.008 | 0.780 | |
| itraqdata | 0.036 | 0.000 | 0.036 | |
| listOf | 0.003 | 0.000 | 0.003 | |
| missing-data | 1.956 | 0.004 | 1.958 | |
| nQuants | 0.193 | 0.000 | 0.193 | |
| normalise-methods | 0.018 | 0.000 | 0.019 | |
| npcv | 0.003 | 0.000 | 0.002 | |
| pSet-class | 0.002 | 0.000 | 0.002 | |
| pickPeaks-method | 0.189 | 0.000 | 0.189 | |
| plot-methods | 1.107 | 0.000 | 1.107 | |
| plot2d-methods | 0.604 | 0.000 | 0.603 | |
| plotDensity-methods | 0.646 | 0.004 | 0.649 | |
| plotMzDelta-methods | 1.451 | 0.012 | 1.462 | |
| plotNA-methods | 0.438 | 0.000 | 0.438 | |
| plotSpectrumSpectrum-methods | 0.695 | 0.004 | 0.699 | |
| precSelection | 0.008 | 0.004 | 0.013 | |
| purityCorrect-methods | 0.026 | 0.000 | 0.025 | |
| quantify-methods | 7.283 | 1.186 | 3.967 | |
| readIspyData | 0 | 0 | 0 | |
| readMSData | 0.461 | 0.000 | 0.461 | |
| readMSnSet | 0.001 | 0.000 | 0.000 | |
| readMgfData | 2.326 | 0.036 | 2.360 | |
| readMzTabData | 2.298 | 0.024 | 2.646 | |
| readMzTabData_v0.9 | 0.182 | 0.004 | 0.748 | |
| removeNoId-methods | 1.024 | 0.000 | 1.030 | |
| removePeaks-methods | 1.023 | 0.004 | 1.027 | |
| removeReporters-methods | 0.568 | 0.000 | 0.569 | |
| smooth-methods | 0.157 | 0.000 | 0.157 | |
| trimMz-methods | 0.101 | 0.000 | 0.102 | |
| writeMgfData-methods | 0.001 | 0.000 | 0.001 | |
| writeMzTabData | 2.645 | 0.016 | 37.587 | |
| xic-methods | 0.001 | 0.000 | 0.000 | |