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BioC 3.0: CHECK report for AllelicImbalance on zin1

This page was generated on 2015-04-10 09:41:21 -0700 (Fri, 10 Apr 2015).

Package 33/933HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
AllelicImbalance 1.4.2
Jesper R Gadin
Snapshot Date: 2015-04-09 16:20:12 -0700 (Thu, 09 Apr 2015)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_0/madman/Rpacks/AllelicImbalance
Last Changed Rev: 101024 / Revision: 102249
Last Changed Date: 2015-03-23 05:48:25 -0700 (Mon, 23 Mar 2015)
zin1 Linux (Ubuntu 12.04.4 LTS) / x86_64  NotNeeded  OK [ OK ]
moscato1 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  NotNeeded  OK  OK  OK 
perceval Mac OS X Snow Leopard (10.6.8) / x86_64  NotNeeded  OK  OK  OK 
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK  OK  OK 

Summary

Package: AllelicImbalance
Version: 1.4.2
Command: /home/biocbuild/bbs-3.0-bioc/R/bin/R CMD check --no-vignettes --timings AllelicImbalance_1.4.2.tar.gz
StartedAt: 2015-04-09 21:28:06 -0700 (Thu, 09 Apr 2015)
EndedAt: 2015-04-09 21:34:23 -0700 (Thu, 09 Apr 2015)
EllapsedTime: 377.5 seconds
RetCode: 0
Status:  OK 
CheckDir: AllelicImbalance.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.0-bioc/R/bin/R CMD check --no-vignettes --timings AllelicImbalance_1.4.2.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.0-bioc/meat/AllelicImbalance.Rcheck’
* using R version 3.1.3 (2015-03-09)
* using platform: x86_64-unknown-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 ‘1.4.2’
* 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 ... [29s/29s] 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
barplotLatticeCounts: no visible binding for global variable ‘alleles’
barplotLatticeFraction: no visible binding for global variable
  ‘alleles’
getSnpIdFromLocation: no visible global function definition for
  ‘getSNPlocs’
* 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 ... [65s/65s] OK
Examples with CPU or elapsed time > 5s
                       user system elapsed
getSnpIdFromLocation 21.562  0.280  21.942
import-bam            8.344  0.012   8.414
getAlleleCounts       7.520  0.008   7.541
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running ‘test-all.R’ [14s/14s]
 [15s/15s] 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

NOTE: There was 1 note.
See
  ‘/home/biocbuild/bbs-3.0-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 ‘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
* DONE (AllelicImbalance)

AllelicImbalance.Rcheck/AllelicImbalance-Ex.timings:

nameusersystemelapsed
ASEset-barplot0.1560.0000.157
ASEset-class0.0640.0000.061
ASEset-glocationplot2.5410.0122.554
ASEset-gviztrack0.5040.0000.507
ASEset-lbarplot0.1080.0000.108
ASEset-locationplot0.3760.0000.378
ASEset.sim000
GRvariants0.0000.0000.002
ReferenceBias-class0.0720.0000.073
ReferenceBias-show000
annotation-wrappers2.5520.0482.635
barplot-lattice-support0.1800.0000.181
binom.test0.0520.0000.053
boxplot0.0320.0000.030
chisq.test0.0400.0000.041
cigar-utilities0.0320.0000.028
coverageMatrixListFromGAL1.1680.0001.172
decorateWithExons0.0000.0000.002
decorateWithGenes0.0000.0000.001
defaultMapBias0.0480.0000.047
detectAI0.0440.0000.047
genofilters0.0280.0000.028
getAlleleCounts7.5200.0087.541
getAreaFromGeneNames0.4280.0200.445
getDefaultMapBiasExpMean0.0080.0000.011
getSnpIdFromLocation21.562 0.28021.942
histplot000
implodeList0.0040.0000.002
import-bam8.3440.0128.414
import-bcf0.4560.0040.466
inferAlleles0.0080.0000.008
inferGenotypes0.0240.0000.021
initialize-ASEset0.0240.0000.025
initialize-ReferenceBias0.0680.0000.068
reads0.0000.0000.001
refAllele0.0360.0000.035
refFraction0.0240.0000.024
scanForHeterozygotes3.4040.0283.442