Package: ecolitk

Version: 1.25.0

Command: /Library/Frameworks/R.framework/Versions/2.14/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch ecolitk_1.25.0.tar.gz

StartedAt: 2011-07-07 02:45:27 -0700 (Thu, 07 Jul 2011)

EndedAt: 2011-07-07 02:46:38 -0700 (Thu, 07 Jul 2011)

EllapsedTime: 71.2 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: ecolitk.Rcheck

Warnings: 1

* using log directory '/Users/biocbuild/bbs-2.9-bioc/meat/ecolitk.Rcheck'
* using R version 2.14.0 Under development (unstable) (2011-06-22 r56208)
* using platform: i386-apple-darwin9.8.0 (32-bit)
* using session charset: ASCII
* using option '--no-vignettes'
* checking for file 'ecolitk/DESCRIPTION' ... OK
* this is package 'ecolitk' version '1.25.0'
* checking package name space information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking whether package 'ecolitk' can be installed ... OK
* checking installed package size ... OK
* 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 name space can be loaded with stated dependencies ... OK
* checking whether the name space 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 ... NOTE
.buildGENEPRODFUN: possible error in strsplit(line, "\t", extended =
  TRUE): unused argument(s) (extended = TRUE)
* checking Rd files ... NOTE
prepare_Rd: multiFun.Rd:16-18: Dropping empty section \details
prepare_Rd: polar2xy.Rd:28-33: Dropping empty section \value
prepare_Rd: polygonChrom.Rd:59: Dropping empty section \seealso
prepare_Rd: wstringapply.Rd:24-25: Dropping empty section \examples
* 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 ... WARNING
  Warning: large data file(s) saved inefficiently:
                         size ASCII compress
  ecoli.m52.genome.rda  1.3Mb  TRUE     gzip
  ecoligenomeCHRLOC.rda 122Kb  TRUE     gzip
  
  Note: significantly better compression could be obtained
        by using tools::resaveRdaFiles() or R CMD build --resave-data
                                  old_size new_size compress
  ecoli.genome.rda                    22Kb     16Kb       xz
  ecoli.m52.genome.rda               1.3Mb    1.1Mb       xz
  ecoligenome.operon.rda              21Kb     16Kb       xz
  ecoligenomeBNUM.rda                 84Kb     54Kb       xz
  ecoligenomeBNUM2GENBANK.rda         27Kb      9Kb       xz
  ecoligenomeBNUM2GENEPRODUCT.rda     75Kb     46Kb    bzip2
  ecoligenomeBNUM2MULTIFUN.rda        25Kb     15Kb    bzip2
  ecoligenomeBNUM2STRAND.rda          14Kb      5Kb       xz
  ecoligenomeBNUM2SYMBOL.rda          14Kb      8Kb       xz
  ecoligenomeCHRLOC.rda              122Kb     91Kb       xz
  ecoligenomeSTRAND.rda               70Kb     48Kb    bzip2
  ecoligenomeSYMBOL.rda               43Kb     27Kb       xz
  ecoligenomeSYMBOL2AFFY.rda          42Kb     23Kb       xz
  ecoligenomeSYMBOL2BNUM.rda          22Kb     12Kb       xz
  multiFun.rda                        10Kb      8Kb    bzip2
* checking sizes of PDF files under 'inst/doc' ... OK
* checking examples ... OK
* checking for unstated dependencies in vignettes ... NOTE
'library' or 'require' call not declared from: 'affy'
* 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

WARNING: There was 1 warning, see
  '/Users/biocbuild/bbs-2.9-bioc/meat/ecolitk.Rcheck/00check.log'
for details

* installing *source* package 'ecolitk' ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices ...
*** tangling vignette sources ...
   'ecolitk.Rnw' 
** testing if installed package can be loaded

* DONE (ecolitk)

name	user	system	elapsed
ecoli.data	0.855	0.025	1.044
ecoligenome.operon	0.145	0.004	0.153
linkedmultiget	0.321	0.007	0.337
multiFun	0.001	0.000	0.000
pointsCircle	0.058	0.005	0.064
polar2xy	0.004	0.001	0.004
polygonChrom	0.271	0.005	0.276