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Package 305/353HostnameOS / ArchBUILDCHECKBUILD BIN
SAGx 1.20.0
Per Broberg,
Snapshot Date: 2010-04-02 23:28:25 -0700 (Fri, 02 Apr 2010)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_5/madman/Rpacks/SAGx
Last Changed Rev: 42684 / Revision: 45705
Last Changed Date: 2009-10-27 16:33:29 -0700 (Tue, 27 Oct 2009)
wilson2 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 
Package: SAGx
Version: 1.20.0
Command: E:\biocbld\bbs-2.5-bioc\R\bin\R.exe CMD check --no-vignettes SAGx_1.20.0.tar.gz
StartedAt: 2010-04-03 06:22:44 -0700 (Sat, 03 Apr 2010)
EndedAt: 2010-04-03 06:23:41 -0700 (Sat, 03 Apr 2010)
EllapsedTime: 57.4 seconds
RetCode: 0
Status: OK
CheckDir: SAGx.Rcheck
Warnings: 0

Command output

* checking for working pdflatex ... OK
* using log directory 'E:/biocbld/bbs-2.5-bioc/meat/SAGx.Rcheck'
* using R version 2.10.1 (2009-12-14)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'SAGx/DESCRIPTION' ... OK
* this is package 'SAGx' version '1.20.0'
* 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 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 line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking for portable use of $BLAS_LIBS ... OK
* checking examples ... OK
* checking package vignettes in 'inst/doc' ... SKIPPED
* checking PDF version of manual ... OK

SAGx.Rcheck/00install.out:

* install options are ' --no-html'

* installing *source* package 'SAGx' ...
** libs
  making DLL ...
gcc -I"e:/biocbld/bbs-2.5-bioc/R/include"        -O3 -Wall  -std=gnu99 -c minigsea.c -o minigsea.o
gcc -I"e:/biocbld/bbs-2.5-bioc/R/include"        -O3 -Wall  -std=gnu99 -c newboot.c -o newboot.o
gcc -I"e:/biocbld/bbs-2.5-bioc/R/include"        -O3 -Wall  -std=gnu99 -c samrocNboot.c -o samrocNboot.o
gcc -shared -s -o SAGx.dll tmp.def minigsea.o newboot.o samrocNboot.o -Le:/biocbld/bbs-2.5-bioc/R/bin -lR
  ... done
** R
** inst
** preparing package for lazy loading
Loading required package: Biobase

Welcome to Bioconductor

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

** help
*** installing help indices
** building package indices ...
** MD5 sums
* DONE (SAGx)