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BioC 3.2: CHECK report for AllelicImbalance on oaxaca

This page was generated on 2016-04-23 10:27:08 -0700 (Sat, 23 Apr 2016).

Package 36/1103HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
AllelicImbalance 1.8.3
Jesper R Gadin
Snapshot Date: 2016-04-22 16:20:12 -0700 (Fri, 22 Apr 2016)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_2/madman/Rpacks/AllelicImbalance
Last Changed Rev: 115705 / Revision: 116712
Last Changed Date: 2016-04-03 12:42:11 -0700 (Sun, 03 Apr 2016)
zin1 Linux (Ubuntu 14.04.2 LTS) / x86_64  NotNeeded  OK  OK UNNEEDED, same version exists in internal repository
moscato1 Windows Server 2008 R2 Standard (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: 1.8.3
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings AllelicImbalance_1.8.3.tar.gz
StartedAt: 2016-04-22 21:45:02 -0700 (Fri, 22 Apr 2016)
EndedAt: 2016-04-22 21:52:38 -0700 (Fri, 22 Apr 2016)
EllapsedTime: 456.1 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_1.8.3.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.2-bioc/meat/AllelicImbalance.Rcheck’
* using R version 3.2.4 (2016-03-10)
* 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 ‘1.8.3’
* 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 ... [33s/33s] 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
countAllelesFromBam,GRanges : .local: no visible binding for global
  variable ‘UserDir’
detectAI,ASEset : .local: no visible binding for global variable
  ‘tf.keep1’
detectAI,ASEset : .local: no visible binding for global variable
  ‘tf.keep2’
detectedAI_vs_threshold_variable_multigraph_plot,DetectedAI : .local:
  no visible binding for global variable ‘grid.arrange’
detectedAI_vs_threshold_variable_plot,DetectedAI : .local :
  <anonymous>: no visible global function definition for
  ‘panel.smoothScatter’
detectedAI_vs_threshold_variable_plot,DetectedAI : .local :
  <anonymous>: no visible global function definition for
  ‘panel.linejoin’
detectedAI_vs_threshold_variable_plot,DetectedAI : .local: no visible
  global function definition for ‘doubleYScale’
frequency_vs_threshold_variable_multigraph_plot,DetectedAI : .local: no
  visible binding for global variable ‘grid.arrange’
frequency_vs_threshold_variable_plot,DetectedAI : .local : <anonymous>:
  no visible global function definition for ‘panel.smoothScatter’
frequency_vs_threshold_variable_plot,DetectedAI : .local : <anonymous>:
  no visible global function definition for ‘panel.linejoin’
frequency_vs_threshold_variable_plot,DetectedAI : .local: no visible
  global function definition for ‘doubleYScale’
getSnpIdFromLocation,GRanges : .local: no visible global function
  definition for ‘getSNPlocs’
reference_frequency_density_vs_threshold_variable_multigraph_plot,DetectedAI
  : .local: no visible binding for global variable ‘grid.arrange’
reference_frequency_density_vs_threshold_variable_plot,DetectedAI :
  .local: no visible global function definition for ‘levelplot’
* 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 ... NOTE
  Error in nrow(x@elementMetadata) : 
    no slot of name "elementMetadata" for this object of class "ASEset"
  Calls: <Anonymous> ... withCallingHandlers -> check_one -> length -> length -> nrow
  Execution halted
* 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 ... [104s/107s] OK
Examples with CPU or elapsed time > 5s
                           user system elapsed
getSnpIdFromLocation     21.806  0.541  23.651
import-bam               12.676  0.256  12.959
scanForHeterozygotes-old 12.391  0.044  12.446
getAlleleQuality          8.199  0.018   8.232
annotation-wrappers       6.988  0.377   9.080
getAlleleCounts           7.112  0.021   7.139
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘test-all.R’ [16s/16s]
 [17s/17s] 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: 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.2-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-barplot0.2150.0050.220
ASEset-class0.4180.0080.426
ASEset-gbarplot0.1550.0030.171
ASEset-glocationplot2.1700.0102.182
ASEset-gviztrack0.6300.0040.635
ASEset-scanForHeterozygotes3.7190.0623.785
ASEset.old0.0000.0000.001
ASEset.sim000
ASEsetFromBam0.0030.0010.004
DetectedAI-class0.0690.0020.071
DetectedAI-plot1.5750.0091.586
DetectedAI-summary0.0890.0050.094
GRvariants0.0020.0010.004
GlobalAnalysis-class0.0020.0010.004
LinkVariantAlmlof-class0.0010.0000.001
LinkVariantAlmlof-plot1.4120.0071.421
RegionSummary-class0.0010.0010.001
RiskVariant-class0.0010.0000.001
annotation-wrappers6.9880.3779.080
annotationBarplot0.0010.0000.000
barplot-lattice-support0.1870.0010.190
binom.test0.0370.0020.038
chisq.test0.0490.0020.050
cigar-utilities0.0190.0000.019
countAllelesFromBam0.0030.0010.004
coverageMatrixListFromGAL1.2960.0171.314
decorateWithExons0.0010.0010.002
decorateWithGenes0.0010.0010.003
defaultMapBias0.0370.0020.038
defaultPhase0.0020.0000.002
detectAI0.0550.0020.056
fractionPlotDf0.0370.0010.038
gba0.0000.0000.001
genofilters0.0380.0020.040
genomatrix0.0010.0000.000
genotype2phase0.0090.0030.012
getAlleleCounts7.1120.0217.139
getAlleleQuality8.1990.0188.232
getAreaFromGeneNames0.4660.0070.474
getDefaultMapBiasExpMean0.0100.0020.011
getSnpIdFromLocation21.806 0.54123.651
histplot0.0010.0010.001
implodeList-old0.0020.0000.003
import-bam-20.0110.0000.012
import-bam12.676 0.25612.959
import-bcf0.6120.0280.641
inferAlleles0.0120.0010.013
inferAltAllele0.0170.0020.018
inferGenotypes0.0270.0010.029
initialize-ASEset0.0460.0010.047
initialize-DetectedAI0.0700.0020.072
initialize-GlobalAnalysis0.0070.0010.008
initialize-RiskVariant0.0030.0020.003
legendBarplot0.0000.0000.001
locationplot0.5630.0100.607
lva1.7780.0411.820
lva.internal0.2750.0020.277
makeMaskedFasta0.5500.0250.575
mapBiasRef0.0110.0020.012
phase2genotype0.0180.0020.020
phaseArray2phaseMatrix0.0090.0020.010
phaseMatrix2Array0.0080.0010.009
randomRef0.0140.0010.015
reads000
refAllele0.0200.0020.022
regionSummary0.6880.0080.697
scanForHeterozygotes-old12.391 0.04412.446