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This page was generated on 2015-10-27 12:12:48 -0400 (Tue, 27 Oct 2015).
| Package 416/1104 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | |||||
| genomation 1.3.1 Altuna Akalin
| linux2.bioconductor.org | Linux (Ubuntu 14.04.2 LTS) / x86_64 | OK | OK | [ ERROR ] | ||||||
| windows2.bioconductor.org | Windows Server 2012 R2 Enterprise SP1 (64-bit) / x64 | OK | OK | ERROR | OK |
| Package: genomation |
| Version: 1.3.1 |
| Command: /home/biocbuild/bbs-3.3-bioc/R/bin/R CMD check --no-vignettes --timings genomation_1.3.1.tar.gz |
| StartedAt: 2015-10-27 04:10:54 -0400 (Tue, 27 Oct 2015) |
| EndedAt: 2015-10-27 04:14:11 -0400 (Tue, 27 Oct 2015) |
| EllapsedTime: 196.4 seconds |
| RetCode: 1 |
| Status: ERROR |
| CheckDir: genomation.Rcheck |
| Warnings: NA |
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### Running command:
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### /home/biocbuild/bbs-3.3-bioc/R/bin/R CMD check --no-vignettes --timings genomation_1.3.1.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.3-bioc/meat/genomation.Rcheck’
* using R Under development (unstable) (2015-09-09 r69333)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘genomation/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘genomation’ version ‘1.3.1’
* package encoding: latin1
* 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 ‘genomation’ can be installed ... [16s/16s] 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:
‘BiocGenerics:::testPackage’ ‘GenomicAlignments:::invertRleStrand’
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 ... NOTE
heatMeta: no visible binding for global variable ‘a’
ScoreMatrixBin,GRanges-GRanges: no visible global function definition
for ‘runValue’
plotGeneAnnotation,list: no visible binding for global variable
‘SampleName’
plotGeneAnnotation,list: no visible binding for global variable ‘value’
randomizeFeature,GRanges : <anonymous>: no visible global function
definition for ‘Rle’
randomizeFeature,GRanges: no visible global function definition for
‘runValue’
Undefined global functions or variables:
Rle SampleName a runValue value
* 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 Makefiles ... OK
* checking for GNU extensions in Makefiles ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... NOTE
The following directory looks like a leftover from 'knitr':
‘cache’
Please remove from your package.
* checking examples ... [26s/26s] OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘genomation_unit_tests.R’ [24s/24s]
ERROR
Running the tests in ‘tests/genomation_unit_tests.R’ failed.
Last 13 lines of output:
Test files with failing tests
test_ScoreMatrix.R
test_ScoreMatrix_character_GRanges
test_ScoreMatrixBin.R
test_ScoreMatrixBin_character_GRanges
Error in BiocGenerics:::testPackage("genomation") :
unit tests failed for package genomation
Calls: <Anonymous> -> <Anonymous>
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-3.3-bioc/meat/genomation.Rcheck/00check.log’
for details.
genomation.Rcheck/tests/genomation_unit_tests.Rout.fail:
R Under development (unstable) (2015-09-09 r69333) -- "Unsuffered Consequences"
Copyright (C) 2015 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.
> (require("genomation") & require("GenomicRanges") & require("GenomicAlignments") & require("rtracklayer") & require("readr") & require("Biostrings")) || stop("unable to load genomation package")
Loading required package: genomation
Loading required package: grid
Loading required package: GenomicRanges
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: S4Vectors
Loading required package: stats4
Attaching package: 'S4Vectors'
The following object is masked from 'package:base':
expand.grid
Loading required package: IRanges
Loading required package: GenomeInfoDb
Loading required package: GenomicAlignments
Loading required package: SummarizedExperiment
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: Biostrings
Loading required package: XVector
Loading required package: Rsamtools
Loading required package: rtracklayer
Loading required package: readr
[1] TRUE
> genomation:::.test()
Normalizing to rpm ...
Timing stopped at: 0.981 0 0.983
Error : The strand setter for GAlignmentPairs objects is defunct. You can use
strandMode() to control the behavior of the strand() getter in
accordance with the stranded protocol that was used to generate the
paired-end data (see '?strandMode').
testing:min
testing:max
testing:median
Normalizing to rpm ...
Timing stopped at: 1.465 0 1.465
Error : The strand setter for GAlignmentPairs objects is defunct. You can use
strandMode() to control the behavior of the strand() getter in
accordance with the stranded protocol that was used to generate the
paired-end data (see '?strandMode').
working on
working on
working on
working on
working on tar1
working on tar2
working on
Normalizing to rpm ...
working on
Normalizing to rpm ...
working on
working on
working on tar1
working on tar2
working on tar1
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working on tar1
working on tar2
working on tar1
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working on tar2
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RUNIT TEST PROTOCOL -- Tue Oct 27 04:14:08 2015
***********************************************
Number of test functions: 20
Number of errors: 2
Number of failures: 0
1 Test Suite :
genomation RUnit Tests - 20 test functions, 2 errors, 0 failures
ERROR in test_ScoreMatrix_character_GRanges: Error : The strand setter for GAlignmentPairs objects is defunct. You can use
strandMode() to control the behavior of the strand() getter in
accordance with the stranded protocol that was used to generate the
paired-end data (see '?strandMode').
ERROR in test_ScoreMatrixBin_character_GRanges: Error : The strand setter for GAlignmentPairs objects is defunct. You can use
strandMode() to control the behavior of the strand() getter in
accordance with the stranded protocol that was used to generate the
paired-end data (see '?strandMode').
Test files with failing tests
test_ScoreMatrix.R
test_ScoreMatrix_character_GRanges
test_ScoreMatrixBin.R
test_ScoreMatrixBin_character_GRanges
Error in BiocGenerics:::testPackage("genomation") :
unit tests failed for package genomation
Calls: <Anonymous> -> <Anonymous>
Execution halted
genomation.Rcheck/00install.out:
* installing *source* package ‘genomation’ ... ** R ** data ** inst ** preparing package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded * DONE (genomation)
genomation.Rcheck/genomation-Ex.timings:
| name | user | system | elapsed | |
| AnnotationByGeneParts-methods | 0.777 | 0.008 | 0.824 | |
| ScoreMatrix-methods | 3.877 | 0.048 | 3.934 | |
| ScoreMatrixBin-methods | 0.561 | 0.000 | 0.562 | |
| ScoreMatrixList-methods | 0.687 | 0.000 | 0.687 | |
| annotateWithFeature-methods | 0.028 | 0.000 | 0.028 | |
| annotateWithFeatureFlank-methods | 0.163 | 0.000 | 0.163 | |
| annotateWithGeneParts-methods | 0.364 | 0.004 | 0.368 | |
| binMatrix-methods | 0.140 | 0.000 | 0.141 | |
| convertBed2Exons-methods | 0.06 | 0.00 | 0.06 | |
| convertBed2Introns-methods | 0.072 | 0.000 | 0.072 | |
| findFeatureComb-methods | 0.257 | 0.000 | 0.257 | |
| getFeatsWithTargetsStats-methods | 0.358 | 0.000 | 0.358 | |
| getFlanks-methods | 0.1 | 0.0 | 0.1 | |
| getRandomEnrichment-methods | 0.002 | 0.000 | 0.002 | |
| getTargetAnnotationStats-methods | 0.350 | 0.004 | 0.354 | |
| gffToGRanges | 0.065 | 0.000 | 0.064 | |
| heatMatrix | 1.059 | 0.017 | 1.078 | |
| heatMeta | 1.093 | 0.008 | 1.101 | |
| intersectScoreMatrixList-methods | 0.222 | 0.000 | 0.223 | |
| multiHeatMatrix | 1.539 | 0.000 | 1.546 | |
| orderBy-methods | 1.197 | 0.008 | 1.217 | |
| patternMatrix-methods | 0.148 | 0.000 | 0.148 | |
| plotGeneAnnotation-methods | 1.117 | 0.011 | 1.129 | |
| plotMeta | 0.890 | 0.004 | 0.894 | |
| plotTargetAnnotation-methods | 0.94 | 0.00 | 0.94 | |
| readBed | 0.087 | 0.004 | 0.092 | |
| readBroadPeak | 0.056 | 0.004 | 0.060 | |
| readFeatureFlank-methods | 0.151 | 0.004 | 0.156 | |
| readGeneric | 0.052 | 0.008 | 0.061 | |
| readNarrowPeak | 0.053 | 0.008 | 0.062 | |
| readTranscriptFeatures-methods | 0.300 | 0.008 | 0.308 | |
| scaleScoreMatrix-methods | 0.247 | 0.000 | 0.246 | |
| scaleScoreMatrixList | 1.207 | 0.004 | 1.211 | |