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BioC 2.13: CHECK report for AllelicImbalance on moscato1

This page was generated on 2014-04-05 09:51:31 -0700 (Sat, 05 Apr 2014).

Package 32/750HostnameOS / ArchBUILDCHECKBUILD BIN
AllelicImbalance 1.0.0
Jesper R Gadin
Snapshot Date: 2014-04-04 16:20:29 -0700 (Fri, 04 Apr 2014)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_13/madman/Rpacks/AllelicImbalance
Last Changed Rev: 81642 / Revision: 88450
Last Changed Date: 2013-10-14 14:29:21 -0700 (Mon, 14 Oct 2013)
zin1 Linux (Ubuntu 12.04.4 LTS) / x86_64  OK  OK 
moscato1 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK [ OK ] OK 
perceval Mac OS X Snow Leopard (10.6.8) / x86_64  OK  OK  OK 

Summary

Package: AllelicImbalance
Version: 1.0.0
Command: rm -rf AllelicImbalance.buildbin-libdir && mkdir AllelicImbalance.buildbin-libdir && D:\biocbld\bbs-2.13-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=AllelicImbalance.buildbin-libdir AllelicImbalance_1.0.0.tar.gz >AllelicImbalance-install.out 2>&1 && D:\biocbld\bbs-2.13-bioc\R\bin\R.exe CMD check --library=AllelicImbalance.buildbin-libdir --install="check:AllelicImbalance-install.out" --force-multiarch --no-vignettes --timings AllelicImbalance_1.0.0.tar.gz && mv AllelicImbalance.buildbin-libdir/* AllelicImbalance.Rcheck/ && rmdir AllelicImbalance.buildbin-libdir
StartedAt: 2014-04-05 02:07:23 -0700 (Sat, 05 Apr 2014)
EndedAt: 2014-04-05 02:17:19 -0700 (Sat, 05 Apr 2014)
EllapsedTime: 596.7 seconds
RetCode: 0
Status:  OK  
CheckDir: AllelicImbalance.Rcheck
Warnings: 0

Command output

* using log directory 'D:/biocbld/bbs-2.13-bioc/meat/AllelicImbalance.Rcheck'
* using R version 3.0.3 (2014-03-06)
* using platform: i386-w64-mingw32 (32-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'AllelicImbalance/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'AllelicImbalance' version '1.0.0'
* 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 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 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 ... OK
* 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 ...
** running examples for arch 'i386' ... [148s] OK
Examples with CPU or elapsed time > 5s
                         user system elapsed
getAlleleCount          64.04   0.00   64.05
getSnpIdFromLocation    27.91   0.39   28.30
import-bam-functions    19.61   0.07   19.69
scanForHeterozygotes    18.29   0.02   18.30
getAnnotation-functions  5.58   0.17    5.75
** running examples for arch 'x64' ... [163s] OK
Examples with CPU or elapsed time > 5s
                      user system elapsed
getAlleleCount       67.53   0.03   67.61
getSnpIdFromLocation 30.75   0.51   31.27
import-bam-functions 24.85   0.09   24.95
scanForHeterozygotes 21.67   0.02   21.68
* checking for unstated dependencies in tests ... OK
* checking tests ...
** running tests for arch 'i386'
  Running 'runTests.R' [9s]
 [9s] OK
** running tests for arch 'x64'
  Running 'runTests.R' [11s]
 [11s] 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

AllelicImbalance.Rcheck/00install.out:


install for i386

* installing *source* package 'AllelicImbalance' ...
** R
** data
*** moving datasets to lazyload DB
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded

install for x64

* installing *source* package 'AllelicImbalance' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'AllelicImbalance' as AllelicImbalance_1.0.0.zip
* DONE (AllelicImbalance)

AllelicImbalance.Rcheck/examples_i386/AllelicImbalance-Ex.timings:

nameusersystemelapsed
ASEset-barplot0.160.000.15
ASEset-locationplot0.70.00.7
ASEset0.110.000.11
GRvariants0.020.000.01
binom.test0.110.000.11
chisq.test0.100.000.09
cigar-utilities0.060.000.06
decorateWithExons0.020.000.02
decorateWithGenes000
getAlleleCount64.04 0.0064.05
getAnnotation-functions5.580.175.75
getAreaFromGeneNames0.700.050.75
getDefaultMapBiasExpMean0.030.000.03
getSnpIdFromLocation27.91 0.3928.30
import-bam-functions19.61 0.0719.69
import-bcf-functions0.380.020.39
initialize-ASEset0.030.000.03
reads000
scanForHeterozygotes18.29 0.0218.30

AllelicImbalance.Rcheck/examples_x64/AllelicImbalance-Ex.timings:

nameusersystemelapsed
ASEset-barplot0.420.000.44
ASEset-locationplot0.70.00.7
ASEset0.110.000.11
GRvariants000
binom.test0.140.000.14
chisq.test0.110.000.11
cigar-utilities0.100.000.09
decorateWithExons000
decorateWithGenes000
getAlleleCount67.53 0.0367.61
getAnnotation-functions4.410.054.77
getAreaFromGeneNames0.650.001.06
getDefaultMapBiasExpMean0.030.000.03
getSnpIdFromLocation30.75 0.5131.27
import-bam-functions24.85 0.0924.95
import-bcf-functions0.620.020.66
initialize-ASEset0.060.000.06
reads000
scanForHeterozygotes21.67 0.0221.68