BioC 2.9: CHECK report for limma on moscato1

Package: limma

Version: 3.10.3

Command: rm -rf limma.buildbin-libdir && mkdir limma.buildbin-libdir && D:\biocbld\bbs-2.9-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=limma.buildbin-libdir limma_3.10.3.tar.gz >limma-install.out 2>&1 && D:\biocbld\bbs-2.9-bioc\R\bin\R.exe CMD check --library=limma.buildbin-libdir --install="check:limma-install.out" --force-multiarch --no-vignettes --timings limma_3.10.3.tar.gz && mv limma.buildbin-libdir/* limma.Rcheck/ && rmdir limma.buildbin-libdir

StartedAt: 2012-03-24 01:55:33 -0700 (Sat, 24 Mar 2012)

EndedAt: 2012-03-24 01:57:52 -0700 (Sat, 24 Mar 2012)

EllapsedTime: 138.6 seconds

RetCode: 0

Status: WARNINGS

CheckDir: limma.Rcheck

Warnings: 1

* using log directory 'D:/biocbld/bbs-2.9-bioc/meat/limma.Rcheck'
* using R version 2.14.2 (2012-02-29)
* using platform: i386-pc-mingw32 (32-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'limma/DESCRIPTION' ... OK
* this is package 'limma' version '3.10.3'
* 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 'limma' can be installed ... OK
* checking installed package size ... 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... WARNING
Codoc mismatches from documentation object 'normalizeCyclicLoess':
normalizeCyclicLoess
  Code: function(x, weights = NULL, span = 0.7, iterations = 3, method
                 = "fast")
  Docs: function(x, weights = NULL, span = 0.7, iterations = 3, method
                 = "pairs")
  Mismatches in argument default values:
    Name: 'method' Code: "fast" Docs: "pairs"

Codoc mismatches from documentation object 'normalizeBetweenArrays':
normalizeBetweenArrays
  Code: function(object, method = NULL, targets = NULL, cyclic.method =
                 "fast", ...)
  Docs: function(object, method = NULL, targets = NULL, cyclic.method =
                 "pairs", ...)
  Mismatches in argument default values:
    Name: 'cyclic.method' Code: "fast" Docs: "pairs"

* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... NOTE
'library' or 'require' call not declared from: 'sma'
* 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 ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
** running examples for arch 'x64' ... OK
* checking for unstated dependencies in tests ... NOTE
'library' or 'require' call not declared from: 'marray'
* checking tests ...
** running tests for arch 'i386'
  Running 'limma-Tests.R'
  Comparing 'limma-Tests.Rout' to 'limma-Tests.Rout.save' ... OK
 OK
** running tests for arch 'x64'
  Running 'limma-Tests.R'
  Comparing 'limma-Tests.Rout' to 'limma-Tests.Rout.save' ...920,921c920,921
< mu+alpha    0.3333333 3.333333e-01  5.551115e-17
< mu+beta    -0.3333333 5.551115e-17  3.333333e-01
---
> mu+alpha    0.3333333 3.333333e-01  9.280771e-17
> mu+beta    -0.3333333 9.280771e-17  3.333333e-01
 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

WARNING: There was 1 warning, see
  'D:/biocbld/bbs-2.9-bioc/meat/limma.Rcheck/00check.log'
for details


install for i386

* installing *source* package 'limma' ...
** libs
gcc  -I"D:/biocbld/BBS-2˜1.9-B/R/include"          -O3 -Wall  -std=gnu99 -mtune=core2 -c normexp.c -o normexp.o
normexp.c: In function 'normexp_m2loglik_saddle':
normexp.c:49:10: warning: variable 'maxDeviation' set but not used [-Wunused-but-set-variable]
normexp.c: In function 'fit_saddle_nelder_mead':
normexp.c:153:3: warning: floating constant exceeds range of 'double' [-Woverflow]
gcc -shared -s -static-libgcc -o limma.dll tmp.def normexp.o -LD:/biocbld/BBS-2˜1.9-B/R/bin/i386 -lR
installing to D:/biocbld/bbs-2.9-bioc/meat/limma.buildbin-libdir/limma/libs/i386
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices ...
*** tangling vignette sources ...
   'limma.Rnw' 
** testing if installed package can be loaded

add DLL for x64

* installing *source* package 'limma' ...
** libs
gcc -m64 -I"D:/biocbld/BBS-2˜1.9-B/R/include"     -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c normexp.c -o normexp.o
normexp.c: In function 'normexp_m2loglik_saddle':
normexp.c:49:10: warning: variable 'maxDeviation' set but not used [-Wunused-but-set-variable]
normexp.c: In function 'fit_saddle_nelder_mead':
normexp.c:153:3: warning: floating constant exceeds range of 'double' [-Woverflow]
gcc -m64 -shared -s -static-libgcc -o limma.dll tmp.def normexp.o -Ld:/RCompile/CRANpkg/extralibs64/local/lib/x64 -Ld:/RCompile/CRANpkg/extralibs64/local/lib -LD:/biocbld/BBS-2˜1.9-B/R/bin/x64 -lR
installing to D:/biocbld/bbs-2.9-bioc/meat/limma.buildbin-libdir/limma/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'limma' as limma_3.10.3.zip

* DONE (limma)

Summary

Command output