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BioC 3.4: CHECK report for AllelicImbalance on malbec1

This page was generated on 2017-04-15 16:11:42 -0400 (Sat, 15 Apr 2017).

Package 35/1296HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
AllelicImbalance 1.12.0
Jesper R Gadin
Snapshot Date: 2017-04-14 17:17:13 -0400 (Fri, 14 Apr 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_4/madman/Rpacks/AllelicImbalance
Last Changed Rev: 122710 / Revision: 128728
Last Changed Date: 2016-10-17 14:45:06 -0400 (Mon, 17 Oct 2016)
malbec1 Linux (Ubuntu 16.04.1 LTS) / x86_64  NotNeeded  OK [ OK ]UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository
morelia Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: AllelicImbalance
Version: 1.12.0
Command: /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings AllelicImbalance_1.12.0.tar.gz
StartedAt: 2017-04-14 20:54:15 -0400 (Fri, 14 Apr 2017)
EndedAt: 2017-04-14 21:00:45 -0400 (Fri, 14 Apr 2017)
EllapsedTime: 390.1 seconds
RetCode: 0
Status:  OK 
CheckDir: AllelicImbalance.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings AllelicImbalance_1.12.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.4-bioc/meat/AllelicImbalance.Rcheck’
* using R version 3.3.3 (2017-03-06)
* using platform: x86_64-pc-linux-gnu (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 ‘1.12.0’
* 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 loading without being on the library search path ... 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 ... NOTE
.array2MatrixList: no visible global function definition for 'setNames'
.lvaRegressionPvalue : <anonymous>: no visible global function
  definition for 'lm'
.lvaRegressionReturnCommonParamMatrix : <anonymous>: no visible global
  function definition for 'lm'
.lvaRegressionReturnCommonParamMatrixTxSNPspecific: no visible global
  function definition for 'lm'
decorateWithExons: no visible global function definition for 'lines'
decorateWithExons: no visible global function definition for 'text'
decorateWithGenes: no visible global function definition for 'lines'
decorateWithGenes: no visible global function definition for 'text'
legendBarplot: no visible global function definition for 'symbols'
legendBarplot: no visible global function definition for 'text'
barplot,ASEset: no visible global function definition for
  'plot.default'
barplot,ASEset: no visible global function definition for 'symbols'
barplot,ASEset: no visible global function definition for 'lines'
barplot,ASEset : <anonymous>: no visible global function definition for
  'lines'
barplot,ASEset: no visible global function definition for 'text'
barplot,ASEset: no visible global function definition for 'title'
barplot,ASEset: no visible global function definition for 'dist'
locationplot,ASEset: no visible global function definition for
  'plot.default'
locationplot,ASEset: no visible global function definition for 'lines'
locationplot,ASEset: no visible global function definition for 'points'
locationplot,ASEset: no visible global function definition for 'abline'
plot,LinkVariantAlmlof-ANY: no visible global function definition for
  'abline'
plot,LinkVariantAlmlof-ANY: no visible global function definition for
  'mtext'
reference_frequency_density_vs_threshold_variable_plot,DetectedAI: no
  visible global function definition for 'heat.colors'
Undefined global functions or variables:
  abline dist heat.colors lines lm mtext plot.default points setNames
  symbols text title
Consider adding
  importFrom("grDevices", "heat.colors")
  importFrom("graphics", "abline", "lines", "mtext", "plot.default",
             "points", "symbols", "text", "title")
  importFrom("stats", "dist", "lm", "setNames")
to your NAMESPACE file.
* 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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                       user system elapsed
getSnpIdFromLocation 63.444  1.440  65.053
import-bam           13.892  0.036  13.936
annotation-wrappers   5.516  0.092   5.804
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘test-all.R’
 OK
* 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 NOTE
See
  ‘/home/biocbuild/bbs-3.4-bioc/meat/AllelicImbalance.Rcheck/00check.log’
for details.


AllelicImbalance.Rcheck/00install.out:

* installing *source* package ‘AllelicImbalance’ ...
** R
** data
*** moving datasets to lazyload DB
** inst
** preparing 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)

AllelicImbalance.Rcheck/AllelicImbalance-Ex.timings:

nameusersystemelapsed
ASEset-barplot0.6320.0040.637
ASEset-class0.2080.0040.212
ASEset-filters0.0240.0000.027
ASEset-gbarplot0.0200.0040.024
ASEset-glocationplot1.4600.0121.475
ASEset-gviztrack0.3640.0040.371
ASEset-scanForHeterozygotes1.6080.0041.616
ASEset.old0.0000.0000.001
ASEset.sim0.0000.0000.001
ASEsetFromBam0.0040.0000.002
DetectedAI-class0.0480.0000.049
DetectedAI-plot1.0080.0001.005
DetectedAI-summary0.0600.0000.061
GRvariants0.0040.0000.002
GlobalAnalysis-class0.0000.0000.001
LinkVariantAlmlof-class0.0000.0000.001
LinkVariantAlmlof-plot0.9240.0000.925
RegionSummary-class000
RiskVariant-class000
annotation-wrappers5.5160.0925.804
annotationBarplot000
barplot-lattice-support0.1560.0000.157
binom.test0.0240.0000.026
chisq.test0.0320.0000.032
cigar-utilities0.0080.0000.010
countAllelesFromBam0.0000.0000.002
coverageMatrixListFromGAL0.6040.0080.614
decorateWithExons0.0000.0000.001
decorateWithGenes0.0040.0000.001
defaultMapBias0.0280.0000.029
defaultPhase0.0040.0000.001
detectAI0.0440.0000.045
fractionPlotDf0.0240.0000.022
gba000
genomatrix000
genotype2phase0.0080.0000.006
getAlleleCounts3.5160.0003.519
getAlleleQuality3.6320.0003.636
getAreaFromGeneNames0.3080.0000.306
getDefaultMapBiasExpMean0.0080.0000.008
getSnpIdFromLocation63.444 1.44065.053
histplot000
implodeList-old0.0000.0000.001
import-bam-20.0040.0000.006
import-bam13.892 0.03613.936
import-bcf0.6640.0000.664
inferAlleles0.0080.0000.008
inferAltAllele0.0080.0000.012
inferGenotypes0.0160.0000.019
initialize-ASEset0.0240.0000.025
initialize-DetectedAI0.040.000.04
initialize-GlobalAnalysis0.0040.0000.004
initialize-RiskVariant0.0000.0000.001
legendBarplot000
locationplot0.2920.0040.295
lva1.440.001.44
lva.internal0.1680.0000.170
makeMaskedFasta0.6800.0000.682
mapBiasRef0.0120.0000.009
minCountFilt0.0280.0000.029
minFreqFilt0.0280.0000.028
multiAllelicFilt0.0120.0000.009
phase2genotype0.0160.0000.015
phaseArray2phaseMatrix0.0080.0000.010
phaseMatrix2Array0.0080.0000.009
randomRef0.0160.0000.016
reads0.0000.0000.001
refAllele0.0160.0040.020
regionSummary0.3840.0000.385
scanForHeterozygotes-old3.3960.0003.402