Laurent Gatto
| Snapshot Date: 2017-10-17 17:00:52 -0400 (Tue, 17 Oct 2017) |
| URL: https://git.bioconductor.org/packages/MSnbase |
| Branch: RELEASE_3_5 |
| Last Commit: d6e8fb7 |
| Last Changed Date: 2017-04-24 15:45:44 -0400 (Mon, 24 Apr 2017) |
| Back to the "Multiple platform build/check report" | A B C D E F G H I J K L [M] N O P Q R S T U V W X Y Z |
This page was generated on 2017-10-18 14:14:01 -0400 (Wed, 18 Oct 2017).
| Package 861/1381 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| MSnbase 2.2.0 Laurent Gatto
| malbec2 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | OK | OK | [ ERROR ] | |||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | | ||||||
| veracruz2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | |
| Package: MSnbase |
| Version: 2.2.0 |
| Command: /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD check --no-vignettes --timings MSnbase_2.2.0.tar.gz |
| StartedAt: 2017-10-18 01:01:57 -0400 (Wed, 18 Oct 2017) |
| EndedAt: 2017-10-18 01:16:14 -0400 (Wed, 18 Oct 2017) |
| EllapsedTime: 857.6 seconds |
| RetCode: 1 |
| Status: ERROR |
| CheckDir: MSnbase.Rcheck |
| Warnings: NA |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD check --no-vignettes --timings MSnbase_2.2.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.5-bioc/meat/MSnbase.Rcheck’
* using R version 3.4.2 (2017-09-28)
* 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 ‘2.2.0’
* 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 ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘MSnbase’ can be installed ... OK
* checking installed package size ... NOTE
installed size is 9.0Mb
sub-directories of 1Mb or more:
data 1.9Mb
doc 4.3Mb
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Authors@R field gives more than one person with maintainer role:
Laurent Gatto <lg390@cam.ac.uk> [aut, cre]
Johannes Rainer <Johannes.Rainer@eurac.edu> [aut, cre]
Sebastian Gibb <mail@sebastiangibb.de> [aut, cre]
* 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’
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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
OnDiskMSnExp-class 12.012 0.120 12.803
MSnSet-class 6.496 0.028 6.548
averageMSnSet 6.464 0.040 6.768
MzTab-class 2.244 0.088 6.198
quantify-methods 2.036 0.248 5.303
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’
ERROR
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
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
testthat results ================================================================
OK: 1326 SKIPPED: 0 FAILED: 2
1. Failure: Combine MSnSet features (L) (@test_MSnSet.R#128)
2. Failure: Compare OnDiskMSnExp and MSnExp extractPrecSpectra (@test_OnDiskMSnExp_other_methods.R#120)
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, 3 NOTEs
See
‘/home/biocbuild/bbs-3.5-bioc/meat/MSnbase.Rcheck/00check.log’
for details.
testthat.Rout.fail:
R version 3.4.2 (2017-09-28) -- "Short Summer"
Copyright (C) 2017 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, 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 2.2.0
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
> setMSnbaseVerbose(FALSE)
> register(SerialParam()) ## see issue 205
>
> test_check("MSnbase")
Experiment data
Experimenter name: Laurent Gatto
Laboratory: Cambridge Centre for Proteomics (CCP)
Contact information: Laurent Gatto
Contact email: lg390@cam.ac.uk
Title: Example 'MSnExp' data set
URL:
PMIDs:
No abstract available.
Instrument :
Model: test (1)
Manufacturer:
Customisations:
Use 'msInfo(object)' for more MIAPE-MS information.
Experiment data
Experimenter name: Laurent Gatto
Laboratory: Cambridge Centre for Proteomics (CCP)
Contact information: Laurent Gatto
Contact email: lg390@cam.ac.uk
Title: Example 'MSnExp' data set
URL:
PMIDs:
No abstract available.
notes:
Note1:
First note
MIAPE-MS information:
1. General features:
Date stamp:
Contact: Laurent Gatto
Name: Laurent Gatto
Laboratory: Cambridge Centre for Proteomics (CCP)
Instument model: test
Manufacturer:
Customisations:
Software:
Version:
Switching:
Param file:
2. Ion source
Source:
Source details:
3. Post-source componentry
Analyzer:
Analyzer details:
Collision gas:
Pressure: bars
Energy:
Detector type:
Sensitivity:
Attaching package: 'AnnotationHub'
The following object is masked from 'package:Biobase':
cache
snapshotDate(): 2017-04-25
loading from cache '/home/biocbuild//.AnnotationHub/55314'
1
Object of class "MSmap"
Map [75, 401]
[1] Retention time: 30:1 - 34:58
[2] M/Z: 521 - 523 (res 0.005)
Object of class "MSmap"
Map [401, 75]
[1] M/Z: 521 - 523 (res 0.005)
[2] Retention time: 30:1 - 34:58
1
1
1. Failure: Combine MSnSet features (L) (@test_MSnSet.R#128) -------------------
combineFeatures(ee, L, redundancy.handler = "unique", cv = FALSE) showed 0 warnings
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.
MSn experiment data ("OnDiskMSnExp")
Object size in memory: 0.13 Mb
- - - Spectra data - - -
MS level(s): 1 2
Number of spectra: 509
MSn retention times: 18:28 - 22:3 minutes
- - - Processing information - - -
Data loaded [Wed Oct 18 01:12:06 2017]
MSnbase version: 2.2.0
- - - Meta data - - -
phenoData
rowNames:
TMT_Erwinia_1uLSike_Top10HCD_isol2_45stepped_60min_01.mzML.gz
varLabels: sampleNames
varMetadata: labelDescription
Loaded from:
TMT_Erwinia_1uLSike_Top10HCD_isol2_45stepped_60min_01.mzML.gz
protocolData: none
featureData
featureNames: X001.1 X002.1 ... X509.1 (509 total)
fvarLabels: fileIdx spIdx ... spectrum (27 total)
fvarMetadata: labelDescription
experimentData: use 'experimentData(object)'
2. Failure: Compare OnDiskMSnExp and MSnExp extractPrecSpectra (@test_OnDiskMSnExp_other_methods.R#120)
unname(precMzs[sort(exP)]) not identical to unname(precursorMz(extsp2)).
Lengths differ: 20 vs 21
Object of class "ReporterIons"
TMT10HCD: '10-plex TMT HCD' with 10 reporter ions
- 126.1277 +/- 0.002 (#8DD3C7)
- 127.1248 +/- 0.002 (#FFFFB3)
- 127.1311 +/- 0.002 (#BEBADA)
- 128.1281 +/- 0.002 (#FB8072)
- 128.1344 +/- 0.002 (#80B1D3)
- 129.1315 +/- 0.002 (#FDB462)
- 129.1378 +/- 0.002 (#B3DE69)
- 130.1348 +/- 0.002 (#FCCDE5)
- 130.1411 +/- 0.002 (#D9D9D9)
- 131.1382 +/- 0.002 (#BC80BD)
Object of class "Spectrum1"
Retention time: 0:0
MSn level: 1
Total ion count: 684
Polarity: 1
This is pRolocdata version 1.14.0.
Use 'pRolocdata()' to list available data sets.
MSn experiment data ("MSnExp")
Object size in memory: 0.18 Mb
- - - Spectra data - - -
MS level(s): 2
Number of spectra: 5
MSn retention times: 25:1 - 25:2 minutes
- - - Processing information - - -
Data loaded: Wed Oct 18 01:14:11 2017
MSnbase version: 2.2.0
- - - Meta data - - -
phenoData
rowNames: dummyiTRAQ.mzXML
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)'
MSn experiment data ("MSnExp")
Object size in memory: 0.2 Mb
- - - Spectra data - - -
MS level(s): 2
Number of spectra: 5
MSn retention times: 25:1 - 25:2 minutes
- - - Processing information - - -
Data loaded: Wed Oct 18 01:14:11 2017
MSnbase version: 2.2.0
- - - Meta data - - -
phenoData
rowNames: dummyiTRAQ.mzXML
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)'
1
Object of class "FeaturesOfInterest"
Created on Wed Oct 18 01:14:55 2017
Description:
small foi
3 features of interest:
P20353, P53501, Q7KU78
Traceable object of class "FeaturesOfInterest"
Created on Wed Oct 18 01:14:55 2017
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
testthat results ================================================================
OK: 1326 SKIPPED: 0 FAILED: 2
1. Failure: Combine MSnSet features (L) (@test_MSnSet.R#128)
2. Failure: Compare OnDiskMSnExp and MSnExp extractPrecSpectra (@test_OnDiskMSnExp_other_methods.R#120)
Error: testthat unit tests failed
Execution halted
MSnbase.Rcheck/00install.out:
* installing *source* package ‘MSnbase’ ...
** libs
g++ -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG -I"/home/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I/usr/local/include -fpic -g -O2 -Wall -c RcppExports.cpp -o RcppExports.o
gcc -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG -I"/home/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I/usr/local/include -fpic -g -O2 -Wall -c Spectrum1_class.c -o Spectrum1_class.o
Spectrum1_class.c:8:13: warning: ‘_new_Spectrum1’ defined but not used [-Wunused-function]
static SEXP _new_Spectrum1(SEXP msLevel, SEXP peaksCount, SEXP rt,
^
gcc -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG -I"/home/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I/usr/local/include -fpic -g -O2 -Wall -c Spectrum2_class.c -o Spectrum2_class.o
Spectrum2_class.c:9:13: warning: ‘_new_Spectrum2’ defined but not used [-Wunused-function]
static SEXP _new_Spectrum2(SEXP msLevel, SEXP peaksCount, SEXP rt,
^
g++ -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG -I"/home/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I/usr/local/include -fpic -g -O2 -Wall -c imp_neighbour_avg.cpp -o imp_neighbour_avg.o
gcc -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG -I"/home/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I/usr/local/include -fpic -g -O2 -Wall -c utils.c -o utils.o
utils.c: In function ‘compar_double_dd_for_stable_asc_order’:
utils.c:92:15: warning: unused variable ‘ret’ [-Wunused-variable]
int i1, i2, ret;
^
utils.c: In function ‘compar_double_dd_for_stable_desc_order’:
utils.c:107:15: warning: unused variable ‘ret’ [-Wunused-variable]
int i1, i2, ret;
^
utils.c: In function ‘compar_double_asc_order’:
utils.c:123:18: warning: unused variable ‘ret’ [-Wunused-variable]
double d1, d2, ret;
^
utils.c: In function ‘compar_double_desc_order’:
utils.c:133:18: warning: unused variable ‘ret’ [-Wunused-variable]
double d1, d2, ret;
^
utils.c: At top level:
utils.c:121:12: warning: ‘compar_double_asc_order’ defined but not used [-Wunused-function]
static int compar_double_asc_order(const void *p1, const void *p2)
^
utils.c:131:12: warning: ‘compar_double_desc_order’ defined but not used [-Wunused-function]
static int compar_double_desc_order(const void *p1, const void *p2)
^
g++ -shared -L/home/biocbuild/bbs-3.5-bioc/R/lib -L/usr/local/lib -o MSnbase.so RcppExports.o Spectrum1_class.o Spectrum2_class.o imp_neighbour_avg.o utils.o -L/home/biocbuild/bbs-3.5-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.5-bioc/meat/MSnbase.Rcheck/MSnbase/libs
** R
** data
*** moving datasets to lazyload DB
Creating a new generic function for ‘smooth’ in package ‘MSnbase’
Creating a new generic function for ‘trimws’ in package ‘MSnbase’
in method for ‘coerce’ with signature ‘"IBSpectra","MSnSet"’: no definition for class “IBSpectra”
** inst
** preparing package for lazy loading
Creating a new generic function for ‘smooth’ in package ‘MSnbase’
Creating a new generic function for ‘trimws’ in package ‘MSnbase’
in method for ‘coerce’ with signature ‘"IBSpectra","MSnSet"’: no definition for class “IBSpectra”
** 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 | 0.296 | 0.008 | 0.340 | |
| FeaturesOfInterest-class | 0.080 | 0.000 | 0.077 | |
| MSmap-class | 0.004 | 0.000 | 0.001 | |
| MSnExp-class | 0.448 | 0.000 | 0.447 | |
| MSnProcess-class | 0.000 | 0.000 | 0.002 | |
| MSnSet-class | 6.496 | 0.028 | 6.548 | |
| MSnSetList-class | 2.844 | 0.000 | 2.845 | |
| MzTab-class | 2.244 | 0.088 | 6.198 | |
| NAnnotatedDataFrame-class | 0.040 | 0.000 | 0.038 | |
| OnDiskMSnExp-class | 12.012 | 0.120 | 12.803 | |
| ProcessingStep-class | 0.004 | 0.000 | 0.005 | |
| ReporterIons-class | 0.020 | 0.000 | 0.019 | |
| TMT6 | 0.012 | 0.000 | 0.014 | |
| addIdentificationData-methods | 0.728 | 0.000 | 0.727 | |
| aggvar | 4.244 | 0.008 | 4.270 | |
| averageMSnSet | 6.464 | 0.040 | 6.768 | |
| bin-methods | 0.972 | 0.000 | 0.973 | |
| calculateFragments-methods | 0.856 | 0.004 | 0.859 | |
| chromatogram-methods | 0.092 | 0.108 | 0.263 | |
| clean-methods | 0.844 | 0.072 | 0.916 | |
| combineFeatures | 0.824 | 0.004 | 0.828 | |
| commonFeatureNames | 0.412 | 0.000 | 0.412 | |
| compareSpectra-methods | 0.248 | 0.004 | 0.255 | |
| estimateNoise-method | 0.012 | 0.000 | 0.013 | |
| exprsToRatios-methods | 0.080 | 0.000 | 0.078 | |
| extractPrecSpectra-methods | 0.576 | 0.000 | 0.576 | |
| featureCV | 0.024 | 0.004 | 0.029 | |
| fillUp | 0.012 | 0.000 | 0.013 | |
| formatRt | 0.000 | 0.000 | 0.001 | |
| get.amino.acids | 0.000 | 0.000 | 0.003 | |
| get.atomic.mass | 0.000 | 0.000 | 0.001 | |
| getVariableName | 0.004 | 0.000 | 0.004 | |
| iPQF | 0.472 | 0.004 | 0.475 | |
| iTRAQ4 | 0.008 | 0.000 | 0.010 | |
| imageNA2 | 3.280 | 0.004 | 3.285 | |
| impute-methods | 0.848 | 0.000 | 0.989 | |
| itraqdata | 0.104 | 0.000 | 0.104 | |
| listOf | 0.004 | 0.000 | 0.003 | |
| makeNaData | 0.820 | 0.004 | 0.824 | |
| missing-data | 3.440 | 0.008 | 3.448 | |
| nFeatures | 0.532 | 0.024 | 0.559 | |
| nQuants | 0.120 | 0.000 | 0.122 | |
| naplot | 0.068 | 0.000 | 0.067 | |
| navMS | 3.484 | 0.040 | 4.109 | |
| normalise-methods | 0.016 | 0.000 | 0.016 | |
| npcv | 0.004 | 0.000 | 0.004 | |
| pSet-class | 0.004 | 0.000 | 0.002 | |
| pickPeaks-method | 0.408 | 0.000 | 0.410 | |
| plot-methods | 1.644 | 0.004 | 1.651 | |
| plot2d-methods | 0.676 | 0.004 | 0.680 | |
| plotDensity-methods | 0.928 | 0.000 | 0.926 | |
| plotMzDelta-methods | 1.616 | 0.004 | 1.621 | |
| plotNA-methods | 0.436 | 0.004 | 0.439 | |
| plotSpectrumSpectrum-methods | 0.840 | 0.004 | 0.842 | |
| precSelection | 0.016 | 0.000 | 0.017 | |
| purityCorrect-methods | 0.084 | 0.000 | 0.084 | |
| quantify-methods | 2.036 | 0.248 | 5.303 | |
| readMSData | 1.032 | 0.000 | 1.034 | |
| readMSnSet | 0.456 | 0.004 | 0.479 | |
| readMgfData | 2.576 | 0.004 | 2.583 | |
| readMzTabData | 1.952 | 0.028 | 2.802 | |
| readMzTabData_v0.9 | 0.496 | 0.004 | 0.925 | |
| removeNoId-methods | 1.308 | 0.004 | 1.314 | |
| removePeaks-methods | 0.724 | 0.000 | 0.723 | |
| removeReporters-methods | 0.640 | 0.000 | 0.639 | |
| selectFeatureData | 0.112 | 0.008 | 0.132 | |
| smooth-methods | 0.224 | 0.000 | 0.225 | |
| trimMz-methods | 0.176 | 0.000 | 0.173 | |
| writeMgfData-methods | 0.000 | 0.000 | 0.001 | |
| xic-methods | 0.000 | 0.000 | 0.001 | |