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Package 401/462HostnameOS / ArchBUILDCHECKBUILD BIN
SAGx 1.27.0
Per Broberg,
Snapshot Date: 2011-05-09 07:20:56 -0700 (Mon, 09 May 2011)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/SAGx
Last Changed Rev: 54802 / Revision: 55359
Last Changed Date: 2011-04-13 15:36:43 -0700 (Wed, 13 Apr 2011)
wilson2 Linux (openSUSE 11.4) / x86_64  OK [ OK ]
liverpool Windows Server 2003 R2 (32-bit) / x64  OK  OK  OK 
gewurz Windows Server 2008 R2 Enterprise (64-bit) / x64  OK  OK  OK 
pelham Mac OS X Leopard (10.5.8) / i386  OK  OK  OK 

Summary

Package: SAGx
Version: 1.27.0
Command: /home/biocbuild/bbs-2.9-bioc/R/bin/R CMD check --no-vignettes --timings SAGx_1.27.0.tar.gz
StartedAt: 2011-05-09 14:11:08 -0700 (Mon, 09 May 2011)
EndedAt: 2011-05-09 14:11:55 -0700 (Mon, 09 May 2011)
EllapsedTime: 47.9 seconds
RetCode: 0
Status:  OK 
CheckDir: SAGx.Rcheck
Warnings: 0

Command output

* using log directory ‘/loc/home/biocbuild/bbs-2.9-bioc/meat/SAGx.Rcheck’
* using R version 2.14.0 Under development (unstable) (2011-04-18 r55504)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘SAGx/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘SAGx’ version ‘1.27.0’
* 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 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 ... NOTE
Fstat: no visible binding for global variable ‘M’
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’
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’
Xprep: no visible binding for global variable ‘M’
Xprep.resid: no visible binding for global variable ‘M’
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’
gap: no visible binding for global variable ‘g’
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’
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’
* 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 ... NOTE
‘library’ or ‘require’ call not declared from: ‘MASS’
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking examples ... 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

SAGx.Rcheck/00install.out:

* installing *source* package ‘SAGx’ ...
** libs
gcc -std=gnu99 -I/home/biocbuild/bbs-2.9-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -Wall -c minigsea.c -o minigsea.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.9-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -Wall -c newboot.c -o newboot.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.9-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -Wall -c samrocNboot.c -o samrocNboot.o
gcc -std=gnu99 -shared -L/usr/local/lib64 -o SAGx.so minigsea.o newboot.o samrocNboot.o -L/home/biocbuild/bbs-2.9-bioc/R/lib -lR
installing to /loc/home/biocbuild/bbs-2.9-bioc/meat/SAGx.Rcheck/SAGx/libs
** R
** inst
** preparing package for lazy loading
Loading required package: Biobase

Welcome to Bioconductor

  Vignettes contain introductory material. To view, type
  'browseVignettes()'. To cite Bioconductor, see
  'citation("Biobase")' and for packages 'citation("pkgname")'.

** help
*** installing help indices
** building package indices ...
*** tangling vignette sources ...
   ‘samroc-ex.Rnw’ 
** testing if installed package can be loaded

* DONE (SAGx)

SAGx.Rcheck/SAGx-Ex.timings:

nameusersystemelapsed
Fstat0.0240.0000.026
JT.test0.0720.0000.073
fetchSignal000
firstpass000
gap2.8080.0082.816
list.experiments0.0000.0000.001
myclus2.7720.0042.775
outlier000
pava0.0000.0000.001
rank.trend0.0000.0000.002
samrocnboot7.0880.1047.198
union.of.pways0.0040.0000.001