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 3.1: CHECK report for AllelicImbalance on morelia

This page was generated on 2015-10-09 09:41:17 -0700 (Fri, 09 Oct 2015).

Package 34/1024HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
AllelicImbalance 1.6.2
Jesper R Gadin
Snapshot Date: 2015-10-08 17:20:21 -0700 (Thu, 08 Oct 2015)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_1/madman/Rpacks/AllelicImbalance
Last Changed Rev: 103901 / Revision: 109384
Last Changed Date: 2015-05-16 07:33:48 -0700 (Sat, 16 May 2015)
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
petty Mac OS X Snow Leopard (10.6.8) / x86_64  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: 1.6.2
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings AllelicImbalance_1.6.2.tar.gz
StartedAt: 2015-10-08 23:07:03 -0700 (Thu, 08 Oct 2015)
EndedAt: 2015-10-08 23:12:48 -0700 (Thu, 08 Oct 2015)
EllapsedTime: 344.4 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_1.6.2.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.1-bioc/meat/AllelicImbalance.Rcheck’
* using R version 3.2.2 (2015-08-14)
* 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 ‘1.6.2’
* 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 ... [24s/24s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Packages listed in more than one of Depends, Imports, Suggests, Enhances:
  ‘Gviz’ ‘VariantAnnotation’
A package should be listed in only one of these fields.
* 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 ... NOTE
Namespace in Imports field not imported from: ‘Gviz’
  All declared Imports should be used.
Package in Depends field not imported from: ‘Gviz’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
barplotLatticeCounts: no visible binding for global variable ‘alleles’
barplotLatticeFraction: no visible binding for global variable ‘groups’
ASEDAnnotationTrack,ASEset: no visible global function definition for
  ‘AnnotationTrack’
CoverageDataTrack,ASEset: no visible global function definition for
  ‘DataTrack’
countAllelesFromBam,GRanges : .local: no visible binding for global
  variable ‘UserDir’
getSnpIdFromLocation,GRanges : .local: no visible global function
  definition for ‘getSNPlocs’
glocationplot,ASEset: no visible global function definition for
  ‘GeneRegionTrack’
glocationplot,ASEset: no visible global function definition for
  ‘plotTracks’
* 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 ... [74s/75s] OK
Examples with CPU or elapsed time > 5s
                           user system elapsed
getSnpIdFromLocation     19.633  1.010  20.859
scanForHeterozygotes-old 12.224  0.371  12.665
import-bam                9.299  0.608  10.025
getAlleleCounts           6.258  0.275   6.534
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘test-all.R’ [12s/12s]
 [13s/13s] 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: 3 NOTEs
See
  ‘/Users/biocbuild/bbs-3.1-bioc/meat/AllelicImbalance.Rcheck/00check.log’
for details.


AllelicImbalance.Rcheck/00install.out:

* installing *source* package ‘AllelicImbalance’ ...
** R
** data
*** moving datasets to lazyload DB
Creating a generic function for ‘nchar’ from package ‘base’ in package ‘S4Vectors’
** inst
** preparing package for lazy loading
Creating a generic function for ‘ref’ from ‘VariantAnnotaton’ in package ‘AllelicImbalance’
    (from the saved implicit definition)
Creating a generic function for ‘ref<-’ from ‘VariantAnnotaton’ in package ‘AllelicImbalance’
    (from the saved implicit definition)
Creating a generic function for ‘alt’ from ‘VariantAnnotaton’ in package ‘AllelicImbalance’
    (from the saved implicit definition)
Creating a generic function for ‘alt<-’ from ‘VariantAnnotaton’ in package ‘AllelicImbalance’
    (from the saved implicit definition)
Creating a generic function for ‘binom.test’ from package ‘stats’ in package ‘AllelicImbalance’
Creating a generic function for ‘chisq.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
Creating a generic function for ‘nchar’ from package ‘base’ in package ‘S4Vectors’
* DONE (AllelicImbalance)

AllelicImbalance.Rcheck/AllelicImbalance-Ex.timings:

nameusersystemelapsed
ASEset-barplot0.1490.0030.152
ASEset-class0.0690.0000.070
ASEset-gbarplot0.1380.0010.139
ASEset-glocationplot2.2750.0882.365
ASEset-gviztrack0.4020.0100.412
ASEset-scanForHeterozygotes2.7960.1252.921
ASEset.sim000
ASEsetFromBam0.0020.0000.002
DetectedAI-class0.0560.0000.057
GRvariants0.0010.0010.001
GlobalAnalysis-class0.0010.0000.002
ReferenceBias-class0.050.000.05
ReferenceBias-show0.0010.0000.001
annotation-wrappers2.4120.2752.714
annotationBarplot0.0000.0000.001
barplot-lattice-support0.2010.0320.233
binom.test0.0570.0090.067
boxplot0.0300.0010.031
chisq.test0.0450.0020.046
cigar-utilities0.0310.0070.038
countAllelesFromBam0.0020.0020.003
coverageMatrixListFromGAL1.1840.0961.279
decorateWithExons0.0020.0000.002
decorateWithGenes0.0020.0010.002
defaultMapBias0.0330.0090.041
defaultPhase0.0000.0010.001
detectAI0.0550.0160.071
fractionPlotDf0.0400.0090.049
gba0.0010.0010.001
genofilters0.0250.0080.033
getAlleleCounts6.2580.2756.534
getAreaFromGeneNames0.3860.0080.394
getDefaultMapBiasExpMean0.0100.0000.011
getSnpIdFromLocation19.633 1.01020.859
histplot0.0000.0000.001
implodeList-old0.0020.0000.002
import-bam-20.010.000.01
import-bam 9.299 0.60810.025
import-bcf0.4650.0620.539
inferAlleles0.0080.0000.009
inferAltAllele0.0120.0000.013
inferGenotypes0.0240.0000.025
initialize-ASEset0.0320.0050.037
initialize-DetectedAI0.0770.0010.077
initialize-GlobalAnalysis0.0060.0000.005
initialize-ReferenceBias0.0690.0010.070
legendBarplot000
locationplot0.6450.0330.680
makeMaskedFasta0.4160.0240.441
mapBiasRef0.0090.0000.009
phaseArray2Matrix0.0130.0000.013
phaseMatrix2Array0.0110.0010.012
randomRef0.0290.0000.029
reads0.0010.0010.000
refAllele0.0150.0000.015
refFraction0.0250.0010.026
regionSummary0.1260.0020.128
scanForHeterozygotes-old12.224 0.37112.665