SAGx 1.13.0
Per Broberg
| Snapshot Date: 2007-12-11 00:09:07 -0800 (Tue, 11 Dec 2007) | | URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/SAGx | | Last Changed Rev: 27716 / Revision: 29143 | | Last Changed Date: 2007-10-02 18:16:39 -0700 (Tue, 02 Oct 2007) |
| lamb1 | Linux (SUSE 10.1) / x86_64 | OK | ERROR | |
| wilson2 | Linux (openSUSE 10.3) / x86_64 | OK | ERROR | |
| wellington | Linux (openSUSE 10.3) / i686 | OK | ERROR | |
| liverpool | Windows Server 2003 R2 (32-bit) / x64 | OK | [ ERROR ] | OK |
| lemming | Windows Server 2003 (32-bit) / x64 | OK | ERROR | OK |
* checking for working latex ... OK
* using log directory 'E:/biocbld/bbs-2.2-bioc/meat/SAGx.Rcheck'
* using R version 2.7.0 Under development (unstable) (2007-11-14 r43455)
* checking for file 'SAGx/DESCRIPTION' ... OK
* this is package 'SAGx' version '1.13.0'
* checking package name space information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking whether package 'SAGx' 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 ... NOTE
clin2mim: no visible binding for global variable 'dbs'
clin2mim: no visible binding for global variable 'clinical'
estimatep0: no visible binding for global variable 'pp'
fetchSignal: no visible global function definition for 'sqlQuery'
fp.fn: no visible binding for global variable 'pvals'
Fstat: no visible binding for global variable 'M'
gap: no visible binding for global variable 'g'
GSEA.mean.t: no visible binding for global variable 'samroc.res'
GSEA.mean.t: no visible binding for global variable 'kegg'
GSEA.mean.t : maxmeanf: no visible binding for global variable
'plustat'
list.experiments: no visible global function definition for 'sqlQuery'
mat2TeX: no visible global function definition for 'errif'
p0.mom: no visible binding for global variable 'pvalues'
pava.fdr: no visible binding for global variable 'pvalues'
R2BASE: no visible binding for global variable 'clingen'
R2BASE: no visible binding for global variable 'AZID'
R2BASE: no visible binding for global variable 'dats'
R2BASE: no visible binding for global variable 'annots'
R2mim: no visible binding for global variable 'inm'
rank.genes: no visible binding for global variable 'indats'
rank.trend: no visible binding for global variable 'x'
rsd.test: no visible binding for global variable 'x'
rsd.test: no visible binding for global variable 'y'
samrocN: no visible binding for global variable 'M'
samrocNboot: no visible binding for global variable 'M'
Xprep: no visible binding for global variable 'M'
Xprep.resid: no visible binding for global variable 'M'
* 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 line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking for portable use of $BLAS_LIBS ... OK
* creating SAGx-Ex.R ... OK
* checking examples ... ERROR
Running examples in 'SAGx-Ex.R' failed.
The error most likely occurred in:
> ### * samrocnboot
>
> flush(stderr()); flush(stdout())
>
> ### Name: samrocNboot
> ### Title: Calculate ROC curve based SAM statistic
> ### Aliases: samrocNboot
> ### Keywords: htest
>
> ### ** Examples
>
> library(multtest)
> #Loading required package: genefilter
> #Loading required package: survival
> #Loading required package: splines
> #Loading required package: reposTools
> data(golub)
> # This makes the expression data from Golub et al available
> # in the matrix golub, and the sample labels in the vector golub.cl
> set.seed(849867)
> samroc.res <- samrocNboot(data = golub, formula = ~as.factor(golub.cl))
> # The proportion of unchanged genes is estimated at
> samroc.res@p0
[1] 0.3849281
> # The fudge factor equals
> samroc.res$s0
Error in samroc.res$s0 : $ operator not defined for this S4 class
Execution halted
installing R.css in E:/biocbld/bbs-2.2-bioc/meat/SAGx.Rcheck
---------- Making package SAGx ------------
adding build stamp to DESCRIPTION
installing NAMESPACE file and metadata
making DLL ...
making minigsea.d from minigsea.c
making newboot.d from newboot.c
making samrocNboot.d from samrocNboot.c
gcc-sjlj -std=gnu99 -Ie:/biocbld/bbs-2.2-bioc/R/include -O3 -Wall -c minigsea.c -o minigsea.o
gcc-sjlj -std=gnu99 -Ie:/biocbld/bbs-2.2-bioc/R/include -O3 -Wall -c newboot.c -o newboot.o
gcc-sjlj -std=gnu99 -Ie:/biocbld/bbs-2.2-bioc/R/include -O3 -Wall -c samrocNboot.c -o samrocNboot.o
windres --preprocessor="gcc-sjlj -E -xc -DRC_INVOKED" -I e:/biocbld/bbs-2.2-bioc/R/include -i SAGx_res.rc -o SAGx_res.o
gcc-sjlj -std=gnu99 -shared -s -o SAGx.dll SAGx.def minigsea.o newboot.o samrocNboot.o SAGx_res.o -Le:/biocbld/bbs-2.2-bioc/R/bin -lR
... DLL made
installing DLL
installing R files
installing inst files
preparing package SAGx for lazy loading
Loading required package: multtest
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: survival
Loading required package: splines
installing man source files
installing indices
installing help
>>> Building/Updating help pages for package 'SAGx'
Formats: text html latex example chm
Fstat text html latex example chm
GSEA.mean.t text html latex chm
JT.test text html latex example chm
R2BASE text html latex chm
R2mim text html latex chm
Xprep text html latex chm
Xprep.resid text html latex chm
clin2mim text html latex chm
cluster.q text html latex chm
estimatep0 text html latex chm
fetchSignal text html latex example chm
firstpass text html latex example chm
fom text html latex chm
fp.fn text html latex chm
gap text html latex example chm
list.experiments text html latex example chm
list.intersection.p text html latex chm
mat2TeX text html latex chm
myclus text html latex example chm
normalise text html latex chm
one.probeset.per.gene text html latex chm
outlier text html latex example chm
p0.mom text html latex chm
pava.fdr text html latex chm
pava text html latex example chm
rank.genes text html latex chm
rank.trend text html latex example chm
rsd.test text html latex chm
samroc.result-class text html latex chm
samrocn text html latex chm
samrocnboot text html latex example chm
union.of.pways text html latex example chm
Microsoft HTML Help Compiler 4.74.8702
Compiling e:\biocbld\bbs-2.2-bioc\meat\SAGx.Rcheck\00_pkg_src\SAGx\chm\SAGx.chm
Compile time: 0 minutes, 0 seconds
33 Topics
68 Local links
6 Internet links
1 Graphic
Created e:\biocbld\bbs-2.2-bioc\meat\SAGx.Rcheck\00_pkg_src\SAGx\chm\SAGx.chm, 53,515 bytes
Compression decreased file by 38,867 bytes.
adding MD5 sums
* DONE (SAGx)