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Package 460/514HostnameOS / ArchBUILDCHECKBUILD BIN
SLGI 1.14.0
Nolwenn Le Meur
Snapshot Date: 2012-03-23 18:21:46 -0700 (Fri, 23 Mar 2012)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_9/madman/Rpacks/SLGI
Last Changed Rev: 59920 / Revision: 64395
Last Changed Date: 2011-10-31 15:59:03 -0700 (Mon, 31 Oct 2011)
wilson2 Linux (openSUSE 11.4) / x86_64  OK [ OK ]
moscato1 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK  OK 
pitt Mac OS X Leopard (10.5.8) / i386  OK  OK  OK 

Summary

Package: SLGI
Version: 1.14.0
Command: /home/biocbuild/bbs-2.9-bioc/R/bin/R CMD check --no-vignettes --timings SLGI_1.14.0.tar.gz
StartedAt: 2012-03-24 02:46:57 -0700 (Sat, 24 Mar 2012)
EndedAt: 2012-03-24 02:57:23 -0700 (Sat, 24 Mar 2012)
EllapsedTime: 626.2 seconds
RetCode: 0
Status:  OK 
CheckDir: SLGI.Rcheck
Warnings: 0

Command output

* using log directory ‘/loc/home/biocbuild/bbs-2.9-bioc/meat/SLGI.Rcheck’
* using R version 2.14.2 (2012-02-29)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘SLGI/DESCRIPTION’ ... OK
* this is package ‘SLGI’ version ‘1.14.0’
* 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 whether package ‘SLGI’ can be installed ... OK
* checking installed package size ... NOTE
  installed size is 25.5Mb
  sub-directories of 1Mb or more:
    data     13.8Mb
    extdata  11.3Mb
* checking package directory ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level 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 ... 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 ... NOTE
‘library’ or ‘require’ call not declared from: ‘YEAST’
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... NOTE
  
  Note: significantly better compression could be obtained
        by using R CMD build --resave-data
                          old_size new_size compress
  Atong.rda                   13Kb      6Kb    bzip2
  AtongFnDomain.rda          6.3Mb    181Kb       xz
  AtongPair.rda               57Kb     20Kb       xz
  Boeke2006raw.rda            24Kb     15Kb       xz
  SGA.rda                     14Kb      9Kb    bzip2
  SGAraw.rda                  13Kb      9Kb       xz
  SGD.SL.rda                 895Kb    499Kb       xz
  SGD.SynGrowthDefect.rda    869Kb    488Kb       xz
  SGD.SynRescue.rda          851Kb    486Kb       xz
  TFmat.rda                 1008Kb    625Kb       xz
  dSLAM.GPL1444.rda          335Kb    138Kb       xz
  dSLAM.rda                   30Kb      5Kb       xz
  gi2005.rda                 768Kb    456Kb       xz
  gi2007.rda                 2.6Mb    1.2Mb       xz
  tong2004raw.RData           44Kb     28Kb       xz
* checking examples ... 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 vignettes ... SKIPPED
* checking PDF version of manual ... OK

SLGI.Rcheck/00install.out:

* installing *source* package ‘SLGI’ ...
** R
** data
** inst
** preparing package for lazy loading
Warning in .simpleDuplicateClass(def, prev) :
  A specification for S3 class “connection” in package ‘graph’ seems equivalent to one from package ‘IRanges’ and is not turning on duplicate class definitions for this class
Warning in .simpleDuplicateClass(def, prev) :
  A specification for S3 class “file” in package ‘graph’ seems equivalent to one from package ‘IRanges’ and is not turning on duplicate class definitions for this class
Creating a generic function for ‘plot’ from package ‘graphics’ in package ‘SLGI’
** help
*** installing help indices
** building package indices ...
*** tangling vignette sources ...
   ‘SLGI.Rnw’ 
** testing if installed package can be loaded

* DONE (SLGI)

SLGI.Rcheck/SLGI-Ex.timings:

nameusersystemelapsed
Atong0.0160.0040.022
AtongFnDomain8.2000.1489.703
AtongPair1.0130.0121.027
SDL0.0080.0000.008
SGA0.0040.0040.009
SGD.SL0.0960.0040.101
TFmat0.1000.0080.109
byComplex1.0480.0081.058
comemberIn1.8880.0481.942
compare39.466 0.02440.654
congruence0.0040.0000.004
createSquareMatrix0.2320.0160.250
domainDist3.5520.0123.570
essglist0.0080.0040.010
getFASTAname4.2450.0244.289
getInteraction0.0040.0000.003
getSharedDomains0.1360.0080.258
getSharedInteraction0.0000.0000.002
getTestedPairs0.0160.0000.013
getUniquePairs0.0240.0000.023
gi20050.0400.0040.042
gi20070.1120.0000.128
gi2Interactome0.0000.0000.001
hyperG0.0040.0000.005
iSummary41.750 0.32443.405
modelSLGI42.567 0.13243.936
normInteraction17.721 0.00417.751
plot43.855 0.00844.006
seqMatcherAlign000
sharedBy3.1960.0163.214
sharedInt0.0040.0000.004
siResult-class49.663 0.01649.740
test2Interact0.0040.0000.004
topInteraction26.514 0.00426.542
twoWayTable16.377 0.08016.507
withinComplex1.5000.0081.515