Repitools 0.99.17
Mark Robinson
| Snapshot Date: 2011-07-06 19:21:50 -0700 (Wed, 06 Jul 2011) | | URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/Repitools | | Last Changed Rev: 56483 / Revision: 56603 | | Last Changed Date: 2011-06-30 23:52:57 -0700 (Thu, 30 Jun 2011) |
| wilson2 | Linux (openSUSE 11.4) / x86_64 | OK | WARNINGS | |
| liverpool | Windows Server 2003 R2 (32-bit) / x64 | OK | WARNINGS | OK |
| gewurz | Windows Server 2008 R2 Enterprise (64-bit) / x64 | OK | WARNINGS | OK |
| moscato1 | Windows Server 2008 R2 Enterprise (64-bit) / x64 | OK | WARNINGS | OK |
| pitt | Mac OS X Leopard (10.5.8) / i386 | OK | [ WARNINGS ] | OK |
* using log directory '/Users/biocbuild/bbs-2.9-bioc/meat/Repitools.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 'Repitools/DESCRIPTION' ... OK
* this is package 'Repitools' version '0.99.17'
* checking package name space information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking whether package 'Repitools' 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 ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... WARNING
Undocumented S4 classes:
'AffymetrixCdfFile'
All user-level objects in a package (including S4 classes and methods)
should have documentation entries.
See the chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
* 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 ... NOTE
Note: significantly better compression could be obtained
by using tools::resaveRdaFiles() or R CMD build --resave-data
old_size new_size compress
samplesList.RData 2.0Mb 1007Kb xz
* checking sizes of PDF files under 'inst/doc' ... NOTE
'qpdf' made some significant size reductions:
compacted 'Repitools_vignette.pdf' from 468Kb to 360Kb
consider running tools::compactPDF() on these files
* checking examples ... OK
* checking for unstated dependencies in tests ... OK
* checking tests ...
Running 'tests.R'
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
WARNING: There was 1 warning, see
'/Users/biocbuild/bbs-2.9-bioc/meat/Repitools.Rcheck/00check.log'
for details
* installing *source* package 'Repitools' ...
** R
** data
** inst
** preparing package for lazy loading
in method for 'GCadjustCopy' with signature '"GRanges","matrix","GCAdjustParams"': no definition for class "GCAdjustParams"
in method for 'GCadjustCopy' with signature '"data.frame","matrix","GCAdjustParams"': no definition for class "GCAdjustParams"
in method for 'GCbiasPlots' with signature '"CopyEstimate"': no definition for class "CopyEstimate"
in method for 'absoluteCN' with signature '"GRanges","matrix","GCAdjustParams"': no definition for class "GCAdjustParams"
in method for 'absoluteCN' with signature '"data.frame","matrix","GCAdjustParams"': no definition for class "GCAdjustParams"
in method for 'binPlots' with signature '"ScoresList"': no definition for class "ScoresList"
in method for '.blocksStats' with signature '"AffymetrixCelSet","GRanges"': no definition for class "AffymetrixCelSet"
in method for 'chromosomeCNplots' with signature '"CopyEstimate"': no definition for class "CopyEstimate"
in method for 'cpgBoxplots' with signature '"AffymetrixCelSet"': no definition for class "AffymetrixCelSet"
in method for '.featureScores' with signature '"AffymetrixCelSet","GRanges"': no definition for class "AffymetrixCelSet"
in method for 'regionStats' with signature '"AffymetrixCelSet"': no definition for class "AffymetrixCelSet"
in method for 'writeWig' with signature '"AffymetrixCelSet"': no definition for class "AffymetrixCelSet"
** help
*** installing help indices
** building package indices ...
*** tangling vignette sources ...
'Repitools_vignette.Rnw' using 'UTF-8'
** testing if installed package can be loaded
* DONE (Repitools)