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CHECK report for AllelicImbalance on merida2

This page was generated on 2019-04-09 13:28:43 -0400 (Tue, 09 Apr 2019).

Package 42/1703HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
AllelicImbalance 1.21.2
Jesper R Gadin
Snapshot Date: 2019-04-08 17:01:18 -0400 (Mon, 08 Apr 2019)
URL: https://git.bioconductor.org/packages/AllelicImbalance
Branch: master
Last Commit: 16a3ffe
Last Changed Date: 2019-04-02 07:25:49 -0400 (Tue, 02 Apr 2019)
malbec2 Linux (Ubuntu 18.04.2 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  ERROR  skipped  skipped 
celaya2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
merida2 OS X 10.11.6 El Capitan / x86_64  OK  OK [ ERROR ] OK 

Summary

Package: AllelicImbalance
Version: 1.21.2
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:AllelicImbalance.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings AllelicImbalance_1.21.2.tar.gz
StartedAt: 2019-04-08 23:11:15 -0400 (Mon, 08 Apr 2019)
EndedAt: 2019-04-08 23:19:00 -0400 (Mon, 08 Apr 2019)
EllapsedTime: 464.8 seconds
RetCode: 1
Status:  ERROR 
CheckDir: AllelicImbalance.Rcheck
Warnings: NA

Command output

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:AllelicImbalance.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings AllelicImbalance_1.21.2.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/AllelicImbalance.Rcheck’
* using R Under development (unstable) (2018-11-27 r75683)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘AllelicImbalance/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘AllelicImbalance’ version ‘1.21.2’
* package encoding: UTF-8
* 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 ‘AllelicImbalance’ 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 dependencies in R code ... OK
* 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                       user system elapsed
getSnpIdFromLocation 21.861  1.516  23.467
import-bam           18.981  0.384  19.502
lva                   9.783  0.020   9.862
annotation-wrappers   6.326  0.571   7.719
ASEset-glocationplot  5.505  0.185   5.738
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘test-all.R’
 ERROR
Running the tests in ‘tests/test-all.R’ failed.
Last 13 lines of output:
  ── 4. Failure: test store and access of phase (@test_phase.R#37)  ──────────────
  `x` not equal to `expected`.
  2/4 mismatches (average diff: 1)
  [1] 1 - 0 ==  1
  [2] 0 - 1 == -1
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 92 SKIPPED: 1 FAILED: 4
  1. Failure: test store and access of phase (@test_phase.R#31) 
  2. Failure: test store and access of phase (@test_phase.R#32) 
  3. Failure: test store and access of phase (@test_phase.R#36) 
  4. Failure: test store and access of phase (@test_phase.R#37) 
  
  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
See
  ‘/Users/biocbuild/bbs-3.9-bioc/meat/AllelicImbalance.Rcheck/00check.log’
for details.


Installation output

AllelicImbalance.Rcheck/00install.out

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL AllelicImbalance
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library’
* installing *source* package ‘AllelicImbalance’ ...
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
Creating a generic function for 'chisq.test' from package 'stats' in package 'AllelicImbalance'
Creating a generic function for 'binom.test' from package 'stats' in package 'AllelicImbalance'
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (AllelicImbalance)

Tests output

AllelicImbalance.Rcheck/tests/test-all.Rout.fail


R Under development (unstable) (2018-11-27 r75683) -- "Unsuffered Consequences"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin15.6.0 (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.

> library(testthat)
> test_check("AllelicImbalance")
Loading required package: AllelicImbalance
Loading required package: grid
Loading required package: GenomicRanges
Loading required package: stats4
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, colMeans, colSums, 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, rowMeans, rowSums,
    rownames, sapply, setdiff, sort, table, tapply, union, unique,
    unsplit, which, which.max, which.min

Loading required package: S4Vectors

Attaching package: 'S4Vectors'

The following object is masked from 'package:base':

    expand.grid

Loading required package: IRanges
Loading required package: GenomeInfoDb
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: DelayedArray
Loading required package: matrixStats

Attaching package: 'matrixStats'

The following objects are masked from 'package:Biobase':

    anyMissing, rowMedians

Loading required package: BiocParallel

Attaching package: 'DelayedArray'

The following objects are masked from 'package:matrixStats':

    colMaxs, colMins, colRanges, rowMaxs, rowMins, rowRanges

The following objects are masked from 'package:base':

    aperm, apply, rowsum

Loading required package: GenomicAlignments
Loading required package: Biostrings
Loading required package: XVector

Attaching package: 'Biostrings'

The following object is masked from 'package:DelayedArray':

    type

The following object is masked from 'package:base':

    strsplit

Loading required package: Rsamtools
── 1. Failure: test store and access of phase (@test_phase.R#31)  ──────────────
`x` not equal to `expected`.
4/4 mismatches
x[1]: "1/0"
y[1]: "1|1"

x[2]: "1|1"
y[2]: "0/0"

x[3]: "0|1"
y[3]: "1/0"

x[4]: "0|1"
y[4]: "1/0"

── 2. Failure: test store and access of phase (@test_phase.R#32)  ──────────────
`x` not equal to `expected`.
3/4 mismatches
x[1]: "1|0"
y[1]: "0/0"

x[2]: "0/1"
y[2]: "0|1"

x[3]: "0|1"
y[3]: "0|0"

── 3. Failure: test store and access of phase (@test_phase.R#36)  ──────────────
`x` not equal to `expected`.
3/4 mismatches (average diff: 1)
[2] 1 - 0 ==  1
[3] 0 - 1 == -1
[4] 0 - 1 == -1

── 4. Failure: test store and access of phase (@test_phase.R#37)  ──────────────
`x` not equal to `expected`.
2/4 mismatches (average diff: 1)
[1] 1 - 0 ==  1
[2] 0 - 1 == -1

══ testthat results  ═══════════════════════════════════════════════════════════
OK: 92 SKIPPED: 1 FAILED: 4
1. Failure: test store and access of phase (@test_phase.R#31) 
2. Failure: test store and access of phase (@test_phase.R#32) 
3. Failure: test store and access of phase (@test_phase.R#36) 
4. Failure: test store and access of phase (@test_phase.R#37) 

Error: testthat unit tests failed
Execution halted

Example timings

AllelicImbalance.Rcheck/AllelicImbalance-Ex.timings

nameusersystemelapsed
ASEset-barplot0.3690.0100.383
ASEset-class0.5840.0360.631
ASEset-filters0.0890.0030.091
ASEset-gbarplot0.0800.0020.082
ASEset-glocationplot5.5050.1855.738
ASEset-gviztrack0.7140.0730.796
ASEset-scanForHeterozygotes1.9080.0171.939
ASEset.old0.0000.0010.001
ASEset.sim000
ASEsetFromBam0.0030.0030.005
DetectedAI-class0.2160.0020.223
DetectedAI-plot2.0860.0132.128
DetectedAI-summary0.1920.0060.200
GRvariants0.0020.0020.005
GlobalAnalysis-class0.0020.0020.003
LinkVariantAlmlof-class000
LinkVariantAlmlof-plot2.4570.0082.488
RegionSummary-class0.0010.0000.001
RiskVariant-class000
annotation-wrappers6.3260.5717.719
annotationBarplot000
barplot-lattice-support0.2320.0010.237
binom.test0.1020.0020.104
chisq.test0.2290.0040.233
cigar-utilities0.010.000.01
countAllelesFromBam0.0020.0010.003
coverageMatrixListFromGAL0.8560.0440.906
decorateWithExons0.0020.0020.004
decorateWithGenes0.0020.0020.004
defaultMapBias0.0390.0030.042
defaultPhase0.0010.0000.002
detectAI0.1890.0020.192
fractionPlotDf0.0400.0010.041
gba0.0000.0000.001
genomatrix000
genotype2phase0.0360.0040.041
getAlleleCounts3.9780.0294.041
getAlleleQuality3.3590.0493.435
getAreaFromGeneNames0.2880.0060.296
getDefaultMapBiasExpMean0.0400.0020.041
getSnpIdFromLocation21.861 1.51623.467
histplot0.0000.0010.000
implodeList-old0.0070.0000.006
import-bam-20.0080.0000.008
import-bam18.981 0.38419.502
import-bcf0.8960.0230.923
inferAlleles0.0390.0020.041
inferAltAllele0.0350.0020.038
inferGenotypes0.0680.0010.069
initialize-ASEset0.0640.0000.064
initialize-DetectedAI0.1370.0020.139
initialize-GlobalAnalysis0.0060.0030.007
initialize-RiskVariant0.0020.0020.004
legendBarplot000
locationplot1.9290.0531.986
lva9.7830.0209.862
lva.internal0.3720.0020.375
makeMaskedFasta0.9320.0050.940
mapBiasRef0.0230.0030.026
minCountFilt0.1400.0020.144
minFreqFilt0.1560.0010.158
multiAllelicFilt0.0430.0020.045
phase2genotype0.0530.0050.059
phaseArray2phaseMatrix0.0070.0030.010
phaseMatrix2Array0.0050.0010.007
randomRef0.0450.0010.047
reads000
refAllele0.0180.0030.021
regionSummary0.5980.0040.609
scanForHeterozygotes-old3.9470.0173.991