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Package 31/658HostnameOS / ArchBUILDCHECKBUILD BIN
AgiMicroRna 2.9.0
Pedro Lopez-Romero
Snapshot Date: 2013-03-24 17:01:43 -0700 (Sun, 24 Mar 2013)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/AgiMicroRna
Last Changed Rev: 70052 / Revision: 74774
Last Changed Date: 2012-10-01 15:43:56 -0700 (Mon, 01 Oct 2012)
george2 Linux (Ubuntu 12.04.1 LTS) / x86_64  OK [ OK ]
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK  OK 
petty Mac OS X Leopard (10.5.8) / i386  OK  WARNINGS  OK 

Summary

Package: AgiMicroRna
Version: 2.9.0
Command: /home/biocbuild/bbs-2.12-bioc/R/bin/R CMD check --no-vignettes --timings AgiMicroRna_2.9.0.tar.gz
StartedAt: 2013-03-24 23:55:04 -0700 (Sun, 24 Mar 2013)
EndedAt: 2013-03-25 00:10:15 -0700 (Mon, 25 Mar 2013)
EllapsedTime: 911.3 seconds
RetCode: 0
Status:  OK 
CheckDir: AgiMicroRna.Rcheck
Warnings: 0

Command output

* using log directory ‘/home/biocbuild/bbs-2.12-bioc/meat/AgiMicroRna.Rcheck’
* using R version 3.0.0 beta (2013-03-19 r62328)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘AgiMicroRna/DESCRIPTION’ ... OK
* this is package ‘AgiMicroRna’ version ‘2.9.0’
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘AgiMicroRna’ can be installed ... [66s/69s] OK
* checking installed package size ... OK
* checking package 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 for unstated dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... NOTE
Foreign function call with ‘PACKAGE’ argument in a different package:
  .Call("rma_c_complete_copy", ..., PACKAGE = "affy")
See the chapter ‘System and foreign language interfaces’ of the
‘Writing R Extensions’ manual.
* checking R code for possible problems ... NOTE
HeatMapMicroRna: warning in heatmap.2(DD.s, labCol = samples, labRow =
  names, scale = "none", col = rbg, margin = c(10, 10), tracecol =
  "cyan"): partial argument match of 'margin' to 'margins'
* 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 examples ... [328s/336s] OK
Examples with CPU or elapsed time > 5s
               user system elapsed
rmaMicroRna 261.637  0.972 270.191
mvaMicroRna  19.685  0.148  19.874
* 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 vignettes ... SKIPPED
* checking PDF version of manual ... OK

NOTE: There were 2 notes.
See
  ‘/home/biocbuild/bbs-2.12-bioc/meat/AgiMicroRna.Rcheck/00check.log’
for details.

AgiMicroRna.Rcheck/00install.out:

* installing *source* package ‘AgiMicroRna’ ...
** R
** data
** inst
** preparing package for lazy loading
No methods found in "GenomicRanges" for requests: summary
** help
*** installing help indices
** building package indices
** installing vignettes
   ‘AgiMicroRna.Rnw’ using ‘latin1’ 
** testing if installed package can be loaded
No methods found in "GenomicRanges" for requests: summary
* DONE (AgiMicroRna)

AgiMicroRna.Rcheck/AgiMicroRna-Ex.timings:

nameusersystemelapsed
HeatMapMicroRna0.9360.2361.185
PCAplotMicroRna0.1920.0080.203
RleMicroRna4.4170.0844.584
basicLimma0.0360.0000.036
boxplotMicroRna1.1640.0041.168
cvArray0.0120.0000.011
filterMicroRna3.5760.0243.605
getDecideTests0.0360.0000.035
hierclusMicroRna0.0440.0040.050
mvaBASIC1.8360.1001.955
mvaMicroRna19.685 0.14819.874
plotDensityMicroRna0.2880.0160.307
pvalHistogram0.9360.0040.939
qcPlots0.0160.0000.018
readMicroRnaAFE0.0000.0040.007
rmaMicroRna261.637 0.972270.191
significantMicroRna0.9960.0121.157
tgsMicroRna2.5640.0322.606
tgsNormalization0.0080.0000.006
uRNAList0.0080.0000.006
writeEset0.0160.0040.019