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BioC 3.4: CHECK report for AllelicImbalance on morelia

This page was generated on 2017-04-15 16:25:00 -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: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings AllelicImbalance_1.12.0.tar.gz
StartedAt: 2017-04-14 22:29:44 -0700 (Fri, 14 Apr 2017)
EndedAt: 2017-04-14 22:37:37 -0700 (Fri, 14 Apr 2017)
EllapsedTime: 473.6 seconds
RetCode: 0
Status:  OK 
CheckDir: AllelicImbalance.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings AllelicImbalance_1.12.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.4-bioc/meat/AllelicImbalance.Rcheck’
* using R version 3.3.3 (2017-03-06)
* using platform: x86_64-apple-darwin13.4.0 (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 ‘1.12.0’
* 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 sizes of PDF files under ‘inst/doc’ ... 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 69.536  2.417  73.725
import-bam           14.237  0.473  14.722
annotation-wrappers   7.315  0.349   8.100
getAlleleQuality      5.317  0.013   5.334
getAlleleCounts       5.279  0.017   5.300
* 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
  ‘/Users/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-barplot0.1980.0070.205
ASEset-class0.3820.0080.390
ASEset-filters0.4750.0020.477
ASEset-gbarplot0.0240.0010.026
ASEset-glocationplot2.2090.0502.261
ASEset-gviztrack0.5290.0100.539
ASEset-scanForHeterozygotes1.9790.0081.987
ASEset.old0.0010.0000.001
ASEset.sim0.0010.0000.000
ASEsetFromBam0.0030.0010.004
DetectedAI-class0.0950.0020.097
DetectedAI-plot1.4960.0071.504
DetectedAI-summary0.1010.0050.105
GRvariants0.0020.0020.003
GlobalAnalysis-class0.0020.0010.003
LinkVariantAlmlof-class0.0000.0000.001
LinkVariantAlmlof-plot1.2350.0051.246
RegionSummary-class0.0000.0000.001
RiskVariant-class0.0010.0000.001
annotation-wrappers7.3150.3498.100
annotationBarplot0.0000.0000.001
barplot-lattice-support0.2570.0030.260
binom.test0.0490.0040.053
chisq.test0.0540.0040.058
cigar-utilities0.0160.0010.018
countAllelesFromBam0.0030.0010.004
coverageMatrixListFromGAL1.1020.0231.127
decorateWithExons0.0020.0020.004
decorateWithGenes0.0020.0010.003
defaultMapBias0.0400.0020.042
defaultPhase0.0010.0010.001
detectAI0.0720.0050.077
fractionPlotDf0.0350.0020.037
gba0.0010.0010.001
genomatrix0.0010.0000.001
genotype2phase0.0100.0030.013
getAlleleCounts5.2790.0175.300
getAlleleQuality5.3170.0135.334
getAreaFromGeneNames0.5500.0100.561
getDefaultMapBiasExpMean0.0120.0020.013
getSnpIdFromLocation69.536 2.41773.725
histplot0.0010.0010.001
implodeList-old0.0020.0000.002
import-bam-20.0080.0000.008
import-bam14.237 0.47314.722
import-bcf0.6220.0190.641
inferAlleles0.0090.0010.011
inferAltAllele0.0180.0020.018
inferGenotypes0.0290.0010.031
initialize-ASEset0.0410.0000.043
initialize-DetectedAI0.0620.0010.063
initialize-GlobalAnalysis0.0040.0010.005
initialize-RiskVariant0.0020.0010.002
legendBarplot0.0000.0000.001
locationplot0.4240.0030.428
lva1.8010.0621.864
lva.internal0.2820.0030.285
makeMaskedFasta0.7350.0740.810
mapBiasRef0.0140.0010.016
minCountFilt0.0440.0020.046
minFreqFilt0.0440.0020.046
multiAllelicFilt0.0120.0020.014
phase2genotype0.0170.0030.019
phaseArray2phaseMatrix0.0080.0010.010
phaseMatrix2Array0.0050.0010.006
randomRef0.0140.0010.014
reads0.0000.0000.001
refAllele0.0160.0010.016
regionSummary0.4900.0030.494
scanForHeterozygotes-old4.9000.0494.952