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 

BioC 3.3: CHECK report for AllelicImbalance on zin2

This page was generated on 2016-10-13 12:44:12 -0700 (Thu, 13 Oct 2016).

Package 36/1210HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
AllelicImbalance 1.10.2
Jesper R Gadin
Snapshot Date: 2016-10-12 17:20:15 -0700 (Wed, 12 Oct 2016)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_3/madman/Rpacks/AllelicImbalance
Last Changed Rev: 117513 / Revision: 122332
Last Changed Date: 2016-05-15 13:18:19 -0700 (Sun, 15 May 2016)
zin2 Linux (Ubuntu 14.04.2 LTS) / x86_64  NotNeeded  OK [ OK ]UNNEEDED, same version exists in internal repository
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: AllelicImbalance
Version: 1.10.2
Command: /home/biocbuild/bbs-3.3-bioc/R/bin/R CMD check --no-vignettes --timings AllelicImbalance_1.10.2.tar.gz
StartedAt: 2016-10-12 23:22:08 -0700 (Wed, 12 Oct 2016)
EndedAt: 2016-10-12 23:28:18 -0700 (Wed, 12 Oct 2016)
EllapsedTime: 370.2 seconds
RetCode: 0
Status:  OK 
CheckDir: AllelicImbalance.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.3-bioc/R/bin/R CMD check --no-vignettes --timings AllelicImbalance_1.10.2.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.3-bioc/meat/AllelicImbalance.Rcheck’
* using R version 3.3.1 (2016-06-21)
* 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 ‘1.10.2’
* 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 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 67.401  0.887  68.417
import-bam           11.338  0.032  11.383
annotation-wrappers   5.962  0.056   6.020
getAlleleQuality      5.319  0.000   5.323
getAlleleCounts       5.180  0.004   5.193
* 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-3.3-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'
Creating a generic function for 'hist' from package 'graphics' 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-barplot0.5070.0000.507
ASEset-class0.2520.0160.267
ASEset-filters0.0300.0080.038
ASEset-gbarplot0.0260.0000.026
ASEset-glocationplot1.5180.0081.524
ASEset-gviztrack0.8080.0040.812
ASEset-scanForHeterozygotes2.3430.0362.379
ASEset.old0.0010.0000.001
ASEset.sim000
ASEsetFromBam0.0020.0000.003
DetectedAI-class0.0570.0000.057
DetectedAI-plot1.1470.0001.149
DetectedAI-summary0.0700.0000.071
GRvariants0.0020.0000.002
GlobalAnalysis-class0.0020.0000.002
LinkVariantAlmlof-class000
LinkVariantAlmlof-plot0.8990.0080.906
RegionSummary-class0.0000.0000.001
RiskVariant-class000
annotation-wrappers5.9620.0566.020
annotationBarplot0.0010.0000.000
barplot-lattice-support0.1380.0000.140
binom.test0.0280.0000.027
chisq.test0.0340.0000.034
cigar-utilities0.0090.0040.013
countAllelesFromBam0.0020.0000.003
coverageMatrixListFromGAL0.8010.0040.805
decorateWithExons0.0020.0000.002
decorateWithGenes0.0020.0000.002
defaultMapBias0.0310.0000.031
defaultPhase0.0010.0000.001
detectAI0.0510.0000.051
fractionPlotDf0.0220.0000.024
gba0.0000.0000.001
genomatrix000
genotype2phase0.0060.0000.007
getAlleleCounts5.1800.0045.193
getAlleleQuality5.3190.0005.323
getAreaFromGeneNames0.3470.0000.347
getDefaultMapBiasExpMean0.0110.0000.011
getSnpIdFromLocation67.401 0.88768.417
histplot0.0000.0000.001
implodeList-old0.0010.0040.001
import-bam-20.0050.0000.007
import-bam11.338 0.03211.383
import-bcf0.5130.0040.527
inferAlleles0.0090.0000.009
inferAltAllele0.0080.0040.012
inferGenotypes0.020.000.02
initialize-ASEset0.0260.0000.027
initialize-DetectedAI0.0470.0000.046
initialize-GlobalAnalysis0.0040.0000.005
initialize-RiskVariant0.0010.0000.002
legendBarplot0.0010.0000.000
locationplot0.3160.0000.316
lva1.2250.0001.225
lva.internal0.1780.0000.178
makeMaskedFasta0.5590.0000.559
mapBiasRef0.0090.0000.009
minCountFilt0.0280.0000.028
minFreqFilt0.0280.0000.028
multiAllelicFilt0.0050.0040.009
phase2genotype0.0150.0000.015
phaseArray2phaseMatrix0.0070.0000.007
phaseMatrix2Array0.0050.0000.005
randomRef0.0110.0000.011
reads0.0010.0000.001
refAllele0.0130.0000.013
regionSummary0.3410.0000.341
scanForHeterozygotes-old4.1550.0044.161