ScISI 1.12.0
Tony Chiang
| Snapshot Date: 2008-08-08 00:12:03 -0700 (Fri, 08 Aug 2008) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_2/madman/Rpacks/ScISI | | Last Changed Rev: 31430 / Revision: 33132 | | Last Changed Date: 2008-04-29 16:50:18 -0700 (Tue, 29 Apr 2008) |
| lamb1 | Linux (SUSE 10.1) / x86_64 | OK | [ OK ] | |
| wilson2 | Linux (openSUSE 10.3) / x86_64 | OK | OK | |
| wellington | Linux (openSUSE 10.3) / i686 | 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 |
* checking for working pdflatex ... OK
* using log directory '/home/biocbuild/bbs-2.2-bioc/meat/ScISI.Rcheck'
* using R version 2.7.1 (2008-06-23)
* using session charset: ISO8859-1
* checking for file 'ScISI/DESCRIPTION' ... OK
* this is package 'ScISI' version '1.12.0'
* checking package name space information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking whether package 'ScISI' can be installed ... 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 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 ... NOTE
checkComplex: no visible binding for global variable 'ScISI'
getAPMSData: no visible binding for global variable 'yNameTAP'
getAPMSData: no visible binding for global variable 'MBMEcHMSPCI'
getAPMSData: no visible binding for global variable 'MBMEcKrogan'
getGOInfo: no visible binding for global variable 'xtraGO'
getGOInfo: no visible binding for global variable 'unwanted'
getMipsInfo: no visible binding for global variable 'nonGenes'
* checking Rd files ... 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
* creating ScISI-Ex.R ... OK
* checking examples ... OK
* checking package vignettes in 'inst/doc' ... OK
* creating ScISI-manual.tex ... OK
* checking ScISI-manual.tex using pdflatex ... OK
* Installing *source* package 'ScISI' ...
** R
** data
** inst
** preparing package for lazy loading
Loading required package: apComplex
Loading required package: graph
Loading required package: RBGL
Loading required package: Rgraphviz
Loading required package: grid
Loading required package: YEAST
******* Deprecation warning *******:
The package 'YEAST' is deprecated and will not be supported in the future.
Instead we strongly reccomend that you should start using the 'org.Sc.sgd.db' package.
We hope you will enjoy these new packages. If you still have questions, you can search
(http://dir.gmane.org/gmane.science.biology.informatics.conductor) or ask the mailing list
(http://bioconductor.org/docs/mailList.html).
Loading required package: GO
******* Deprecation warning *******:
The package 'GO' is deprecated and will not be supported in the future.
Instead we strongly reccomend that you should start using the 'GO.db' package.
We hope you will enjoy these new packages. If you still have questions, you can search
(http://dir.gmane.org/gmane.science.biology.informatics.conductor) or ask the mailing list
(http://bioconductor.org/docs/mailList.html).
Loading required package: GOstats
Loading required package: GO.db
Loading required package: AnnotationDbi
Loading required package: Biobase
Loading required package: tools
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: DBI
Loading required package: RSQLite
Attaching package: 'GO.db'
The following object(s) are masked from package:GO :
GO,
GOBPANCESTOR,
GOBPCHILDREN,
GOBPOFFSPRING,
GOBPPARENTS,
GOCCANCESTOR,
GOCCCHILDREN,
GOCCOFFSPRING,
GOCCPARENTS,
GOMAPCOUNTS,
GOMFANCESTOR,
GOMFCHILDREN,
GOMFOFFSPRING,
GOMFPARENTS,
GOOBSOLETE,
GOSYNONYM,
GOTERM
Loading required package: annotate
Loading required package: xtable
Attaching package: 'annotate'
The following object(s) are masked from package:Rgraphviz :
toFile
Loading required package: Category
Loading required package: genefilter
Loading required package: survival
Loading required package: splines
Loading required package: Rintact
Loading required package: XML
Attaching package: 'XML'
The following object(s) are masked from package:graph :
addNode
Loading required package: hypergraph
Attaching package: 'hypergraph'
The following object(s) are masked from package:xtable :
label,
label<-
The following object(s) are masked from package:AnnotationDbi :
head,
tail
The following object(s) are masked from package:Rgraphviz :
head,
tail
The following object(s) are masked from package:utils :
head,
tail
** help
Note: removing empty section \details
Note: removing empty section \references
Note: removing empty section \examples
Note: removing empty section \examples
Note: removing empty section \note
Note: removing empty section \examples
Note: removing empty section \examples
Note: removing empty section \examples
Note: removing empty section \examples
Note: removing empty section \details
Note: removing empty section \examples
Note: removing empty section \examples
Note: removing empty section \details
Note: removing empty section \examples
Note: removing empty section \details
Note: removing empty section \examples
Note: removing empty section \examples
Note: removing empty section \details
Note: removing empty section \details
Note: removing empty section \details
Note: removing empty section \examples
>>> Building/Updating help pages for package 'ScISI'
Formats: text html latex example
Desc-methods text html latex
ID-methods text html latex
JaccardCoef text html latex example
ScISI text html latex example
ScISI2html text html latex example
arp23 text html latex example
arp23G text html latex example
arp23Orf text html latex example
arp23Y2HG text html latex example
calcGraphStats text html latex
cfia text html latex example
cfiaOrf text html latex example
checkComplex text html latex
checkSGN text html latex
compBijection text html latex
compareComplex text html latex
createGODataFrame text html latex example
createGOMatrix text html latex example
createMipsDataFrame text html latex
createMipsMatrix text html latex example
createYeastDataObj text html latex example
dataS text html latex example
eAt text html latex example
eAt2 text html latex example
edgeProp text html latex
egEBI16112 text html latex example
expStats text html latex example
findSubComp text html latex example
gavin2mergeMG text html latex example
getAPMSData text html latex example
getGOInfo text html latex example
getLocOrfs text html latex
getMipsInfo text html latex example
getURL-methods text html latex
graphSumStats text html latex
ho2mergeMGG text html latex example
krogan2mergeMGGH text html latex example
locScISI text html latex example
mapping2SysG text html latex example
mappingsG text html latex example
maximizeSimilarity text html latex example
meanDeg text html latex
mergeBGMat text html latex example
mips2go text html latex example
nAt text html latex
nAtMap text html latex example
nonGenes text html latex example
nucComp text html latex example
recCompSize text html latex example
redundantM text html latex example
rmByEvi text html latex
runAlignment text html latex example
runCompareComplex text html latex example
subCompM text html latex example
sumStats text html latex example
unWantedComp text html latex example
unwanted text html latex example
xtraGO text html latex example
xtraGONodes text html latex
yeastData-class text html latex example
** building package indices ...
* DONE (ScISI)