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Package 220/514HostnameOS / ArchBUILDCHECKBUILD BIN
GlobalAncova 3.22.0
Manuela Hummel
Snapshot Date: 2012-03-23 18:21:46 -0700 (Fri, 23 Mar 2012)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_9/madman/Rpacks/GlobalAncova
Last Changed Rev: 59920 / Revision: 64395
Last Changed Date: 2011-10-31 15:59:03 -0700 (Mon, 31 Oct 2011)
wilson2 Linux (openSUSE 11.4) / x86_64  OK  OK 
moscato1 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK  OK 
pitt Mac OS X Leopard (10.5.8) / i386  OK [ OK ] OK 

Summary

Package: GlobalAncova
Version: 3.22.0
Command: /Library/Frameworks/R.framework/Versions/2.14/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch GlobalAncova_3.22.0.tar.gz
StartedAt: 2012-03-24 01:33:19 -0700 (Sat, 24 Mar 2012)
EndedAt: 2012-03-24 01:35:56 -0700 (Sat, 24 Mar 2012)
EllapsedTime: 157.4 seconds
RetCode: 0
Status:  OK 
CheckDir: GlobalAncova.Rcheck
Warnings: 0

Command output

* using log directory '/Users/biocbuild/bbs-2.9-bioc/meat/GlobalAncova.Rcheck'
* using R version 2.14.2 (2012-02-29)
* using platform: i386-apple-darwin9.8.0 (32-bit)
* using session charset: ASCII
* using option '--no-vignettes'
* checking for file 'GlobalAncova/DESCRIPTION' ... OK
* this is package 'GlobalAncova' version '3.22.0'
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking whether package 'GlobalAncova' 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 namespace can be loaded with stated dependencies ... OK
* checking whether the namespace 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
File 'GlobalAncova/R/zzz.r':
  .onLoad calls:
    require(methods)

Package startup functions should not change the search path.
See section 'Good practice' in ?.onAttach.

* 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 ... OK
* checking contents of 'data' directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* 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 compiled code ... NOTE
File '/Users/biocbuild/bbs-2.9-bioc/meat/GlobalAncova.Rcheck/GlobalAncova/libs/i386/GlobalAncova.so':
  Found '_putchar', possibly from 'putchar' (C)

Compiled code should not call functions which might terminate R nor
write to stdout/stderr instead of to the console.  The detected symbols
are linked into the code but might come from libraries and not actually
be called.

See 'Writing portable packages' in the 'Writing R Extensions' manual.
* checking sizes of PDF files under 'inst/doc' ... 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

GlobalAncova.Rcheck/00install.out:

* installing *source* package 'GlobalAncova' ...
** libs
*** arch - i386
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386  -I/usr/local/include    -fPIC  -g -O2 -Wall -pedantic -c GlobalAncova.c -o GlobalAncova.o
GlobalAncova.c: In function 'permut':
GlobalAncova.c:268: warning: 'ord_perm' may be used uninitialized in this function
GlobalAncova.c: In function 'permut_withFperm':
GlobalAncova.c:166: warning: 'ord_perm' may be used uninitialized in this function
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386  -I/usr/local/include    -fPIC  -g -O2 -Wall -pedantic -c ludcmp.c -o ludcmp.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386  -I/usr/local/include    -fPIC  -g -O2 -Wall -pedantic -c matrix.c -o matrix.o
gcc -arch i386 -std=gnu99 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -o GlobalAncova.so GlobalAncova.o ludcmp.o matrix.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-2.9-bioc/meat/GlobalAncova.Rcheck/GlobalAncova/libs/i386
** R
** data
** inst
** preparing package for lazy loading
Warning in .simpleDuplicateClass(def, prev) :
  A specification for class "data.frameOrNULL" in package 'globaltest' seems equivalent to one from package 'Biobase' and is not turning on duplicate class definitions for this class
** help
*** installing help indices
** building package indices ...
*** tangling vignette sources ...
   'GlobalAncova.rnw' 
   'GlobalAncovaDecomp.rnw' 
** testing if installed package can be loaded

* DONE (GlobalAncova)

GlobalAncova.Rcheck/GlobalAncova-Ex.timings:

nameusersystemelapsed
GlobalAncova2.5920.1472.753
GlobalAncova.decomp0.5720.0790.656
Plot.all0.1450.0200.167
Plot.genes0.6210.0280.657
Plot.sequential0.0860.0100.098
Plot.subjects0.4300.0210.453
colon.normal0.0160.0010.023
colon.pheno0.0010.0000.003
colon.tumour0.0150.0010.017
genesettesting0.0010.0000.000
pair.compare6.2591.7808.133
pathways0.0030.0000.004
phenodata0.0020.0000.002
vantVeer0.0400.0020.042