altcdfenvs 2.6.0
Laurent Gautier
| Bioconductor Changelog | | Snapshot Date: 2009-10-20 11:27:33 -0700 (Tue, 20 Oct 2009) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_4/madman/Rpacks/altcdfenvs | | Last Changed Rev: 39013 / Revision: 42512 | | Last Changed Date: 2009-04-20 16:24:12 -0700 (Mon, 20 Apr 2009) |
| wilson1 | Linux (openSUSE 11.1) / x86_64 | OK | OK | |
| liverpool | Windows Server 2003 R2 (32-bit) / x64 | OK | [ OK ] | OK |
| pitt | Mac OS X Tiger (10.4.11) / i386 | OK | OK | OK |
| pelham | Mac OS X Leopard (10.5.8) / i386 | OK | OK | OK |
* checking for working pdflatex ... OK
* using log directory 'E:/biocbld/bbs-2.4-bioc/meat/altcdfenvs.Rcheck'
* using R version 2.9.2 (2009-08-24)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'altcdfenvs/DESCRIPTION' ... OK
* this is package 'altcdfenvs' version '2.6.0'
* checking package name space information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking whether package 'altcdfenvs' can be installed ... OK
* checking package directory ... OK
* checking for portable file names ... 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 name space can be loaded with stated dependencies ... 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 files against version 2 parser ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking data for non-ASCII characters ... OK
* checking examples ... OK
* checking package vignettes in 'inst/doc' ... SKIPPED
* checking PDF version of manual ... OK
* Installing *source* package 'altcdfenvs' ...
** R
** data
** inst
** preparing package for lazy loading
Welcome to Bioconductor
Vignettes contain introductory material. To view, type
'openVignette()'. To cite Bioconductor, see
'citation("Biobase")' and for packages 'citation(pkgname)'.
Loading required package: AnnotationDbi
Loading required package: Biostrings
Loading required package: IRanges
Attaching package: 'IRanges'
The following object(s) are masked from package:base :
cbind,
duplicated,
order,
pmax,
pmax.int,
pmin,
pmin.int,
rank,
rbind,
rep.int,
sapply,
sort,
table,
unique
*** Deprecation warning ***
The matchprobes package is deprecated and will not be supported
anymore starting with Bioconductor 2.4. Please switch to using the
Biostrings package for efficient string manipulations. If you need
to build a probe package, please see the makeProbePackage vignette
in the AnnotationDbi package.
Loading required package: affyio
Loading required package: graph
Attaching package: 'graph'
The following object(s) are masked from package:Biostrings :
complement
Attaching package: 'hypergraph'
The following object(s) are masked from package:IRanges :
head,
tail
The following object(s) are masked from package:AnnotationDbi :
head,
tail
The following object(s) are masked from package:utils :
head,
tail
NOTE: arguments in definition for validity method for class 'AffyProbesMatch' changed from (obj) to (object)
Warning in matchSignature(signature, fdef, where) :
in the method signature for function "toHypergraph" no definition for class: "CdfEnvAffy"
Creating a new generic function for "plot" in "altcdfenvs"
** help
*** installing help indices
>>> Building/Updating help pages for package 'altcdfenvs'
Formats: text html latex example chm
AffyProbesMatch-class text html latex example chm
CdfEnvAffy-class text html latex example chm
appendCdfEnvAffy text html latex example chm
buildCdfEnv.biostrings text html latex chm
cdfenv text html latex example chm
cdfenvEx text html latex example chm
copyCdfEnvAffy text html latex chm
Note: removing empty section \details in file 'countduplicated.Rd'
Note: removing empty section \examples in file 'countduplicated.Rd'
Note: removing empty section \details in file 'countduplicated.Rd'
Note: removing empty section \examples in file 'countduplicated.Rd'
countduplicated text html latex chm
geneNames text html latex chm
getxy.probeseq text html latex example chm
Note: removing empty section \details in file 'index2xy.Rd'
Note: removing empty section \section{Warning} in file 'index2xy.Rd'
Note: removing empty section \details in file 'index2xy.Rd'
Note: removing empty section \section{Warning} in file 'index2xy.Rd'
index2xy text html latex example chm
Note: removing empty section \examples in file 'indexProbes.CdfEnvAffy.Rd'
Note: removing empty section \examples in file 'indexProbes.CdfEnvAffy.Rd'
indexProbes.CdfEnvAffy text html latex chm
Note: removing empty section \note in file 'matchAffyProbes.Rd'
Note: removing empty section \note in file 'matchAffyProbes.Rd'
matchAffyProbes text html latex example chm
plot.CdfEnvAffy text html latex example chm
removeIndex text html latex example chm
toHypergraph text html latex chm
unique.CdfEnvAffy text html latex example chm
utils.FASTA text html latex example chm
Note: removing empty section \value in file 'validAffyBatch.Rd'
Note: removing empty section \value in file 'validAffyBatch.Rd'
validAffyBatch text html latex example chm
Microsoft HTML Help Compiler 4.74.8702
Compiling e:\biocbld\BBS-2~1.4-B\meat\ALTCDF~1.RCH\00_PKG~1\ALTCDF~1\chm\altcdfenvs.chm
Compile time: 0 minutes, 1 second
20 Topics
83 Local links
0 Internet links
1 Graphic
Created e:\biocbld\BBS-2~1.4-B\meat\ALTCDF~1.RCH\00_PKG~1\ALTCDF~1\chm\altcdfenvs.chm, 36,263 bytes
Compression decreased file by 35,631 bytes.
** building package indices ...
** MD5 sums
* DONE (altcdfenvs)