Package: SLGI

Version: 1.14.0

Command: /Library/Frameworks/R.framework/Versions/2.14/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch SLGI_1.14.0.tar.gz

StartedAt: 2012-03-24 04:18:17 -0700 (Sat, 24 Mar 2012)

EndedAt: 2012-03-24 04:34:46 -0700 (Sat, 24 Mar 2012)

EllapsedTime: 989.3 seconds

RetCode: 0

Status:  OK

CheckDir: SLGI.Rcheck

Warnings: 0

* using log directory '/Users/biocbuild/bbs-2.9-bioc/meat/SLGI.Rcheck'
* using R version 2.14.2 (2012-02-29)
* using platform: i386-apple-darwin9.8.0 (32-bit)
* using session charset: ASCII
* 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 25.4Mb
  sub-directories of 1Mb or more:
    data     13.7Mb
    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 sizes of PDF files under 'inst/doc' ... OK
* 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

* 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)

name	user	system	elapsed
Atong	0.040	0.003	0.043
AtongFnDomain	8.818	0.131	8.998
AtongPair	1.069	0.022	1.098
SDL	0.009	0.001	0.010
SGA	0.010	0.002	0.012
SGD.SL	0.182	0.011	0.195
TFmat	0.238	0.013	0.261
byComplex	1.394	0.119	1.547
comemberIn	1.936	0.134	2.098
compare	42.711	33.517	79.635
congruence	0.005	0.000	0.005
createSquareMatrix	0.512	0.076	0.597
domainDist	4.382	0.058	4.479
essglist	0.009	0.007	0.016
getFASTAname	5.905	0.058	6.009
getInteraction	0.003	0.000	0.004
getSharedDomains	0.210	0.010	0.228
getSharedInteraction	0.002	0.000	0.003
getTestedPairs	0.019	0.002	0.021
getUniquePairs	0.032	0.001	0.033
gi2005	0.092	0.005	0.099
gi2007	0.298	0.015	0.322
gi2Interactome	0.001	0.000	0.001
hyperG	0.008	0.001	0.009
iSummary	50.422	19.169	72.606
modelSLGI	52.217	34.742	88.205
normInteraction	21.149	18.749	42.479
plot	54.501	32.539	90.385
seqMatcherAlign	0.000	0.000	0.001
sharedBy	5.718	0.071	5.897
sharedInt	0.005	0.000	0.006
siResult-class	54.772	34.304	93.145
test2Interact	0.005	0.000	0.005
topInteraction	29.844	18.370	49.948
twoWayTable	14.796	0.245	15.163
withinComplex	1.758	0.117	1.892