ReportingTools 1.99.3
Jason A. Hackney , Gabriel Becker
| Snapshot Date: 2013-03-24 17:01:43 -0700 (Sun, 24 Mar 2013) | | URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/ReportingTools | | Last Changed Rev: 74740 / Revision: 74774 | | Last Changed Date: 2013-03-23 06:30:49 -0700 (Sat, 23 Mar 2013) |
| 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 | [ OK ] | OK |
* using log directory '/Users/biocbuild/bbs-2.12-bioc/meat/ReportingTools.Rcheck'
* using R Under development (unstable) (2013-02-26 r62077)
* using platform: i386-apple-darwin9.8.0 (32-bit)
* using session charset: ASCII
* using option '--no-vignettes'
* checking for file 'ReportingTools/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'ReportingTools' version '1.99.3'
* 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 'ReportingTools' can be installed ... [47s/48s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Package 'utils, knitr' is specified in field VignetteBuilder but is in
neither Imports nor Depends.
* 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 ... 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 ... OK
* checking contents of 'data' directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking sizes of PDF files under 'inst/doc' ... OK
* checking installed files from 'inst/doc' ... OK
* checking examples ... [19s/19s] OK
* checking for unstated dependencies in tests ... OK
* checking tests ...
Running 'runTests.R' [114s/118s]
[114s/118s] 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
NOTE: There was 1 note.
See
'/Users/biocbuild/bbs-2.12-bioc/meat/ReportingTools.Rcheck/00check.log'
for details.
* installing *source* package 'ReportingTools' ...
** R
** data
** inst
** byte-compile and prepare package for lazy loading
in method for 'objectToHTML' with signature 'object="trellis"': no definition for class "trellis"
in method for 'objectToHTML' with signature 'object="ggplot"': no definition for class "ggplot"
No methods found in "GenomicRanges" for requests: summary
in method for 'publish' with signature 'object="trellis",publicationType="HTMLReport"': no definition for class "trellis"
Note: no visible binding for '<<-' assignment to '.->.basePath'
Note: no visible binding for '<<-' assignment to '.->.handlers'
Note: no visible binding for '<<-' assignment to '.->.report'
Note: no visible binding for '<<-' assignment to '.->.reportDirectory'
Note: no visible binding for '<<-' assignment to '.->.shortName'
Note: no visible binding for '<<-' assignment to '.->.title'
Note: no visible binding for '<<-' assignment to '.reportDirectory'
Note: no visible binding for '<<-' assignment to '.->.basePath'
Note: no visible binding for '<<-' assignment to '.->.handlers'
Note: no visible binding for '<<-' assignment to '.->.modifyDF'
Note: no visible binding for '<<-' assignment to '.->.report'
Note: no visible binding for '<<-' assignment to '.->.reportDirectory'
Note: no visible binding for '<<-' assignment to '.->.shortName'
Note: no visible binding for '<<-' assignment to '.->.title'
Note: no visible binding for '<<-' assignment to '.->.toDF'
Note: no visible binding for '<<-' assignment to '.->.toHTML'
Note: no visible binding for '<<-' assignment to '.reportDirectory'
** help
*** installing help indices
** building package indices
** installing vignettes
'basicReportingTools.Rnw'
'knitr.Rmd'
processing file: knitr.Rmd
output file: /Users/biocbuild/bbs-2.12-bioc/meat/ReportingTools.Rcheck/ReportingTools/doc/knitr.R
'microarrayAnalysis.Rnw'
'rnaseqAnalysis.Rnw'
'shiny.Rnw'
** testing if installed package can be loaded
No methods found in "GenomicRanges" for requests: summary
* DONE (ReportingTools)