limma 3.8.3
Gordon Smyth
| Snapshot Date: 2011-10-20 07:20:33 -0700 (Thu, 20 Oct 2011) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_8/madman/Rpacks/limma | | Last Changed Rev: 57246 / Revision: 59457 | | Last Changed Date: 2011-08-05 00:08:17 -0700 (Fri, 05 Aug 2011) |
| lamb1 | Linux (openSUSE 11.3) / x86_64 | OK | [ OK ] | |
| liverpool | Windows Server 2003 R2 (32-bit) / x64 | OK | OK | OK |
| gewurz | Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 | OK | WARNINGS | OK |
| pelham | Mac OS X Leopard (10.5.8) / i386 | OK | OK | OK |
* using log directory ‘/loc/home/biocbuild/bbs-2.8-bioc/meat/limma.Rcheck’
* using R version 2.13.2 (2011-09-30)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘limma/DESCRIPTION’ ... OK
* this is package ‘limma’ version ‘3.8.3’
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... 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 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 ... 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 ... OK
* 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 examples ... OK
* checking for unstated dependencies in tests ... NOTE
'library' or 'require' call not declared from: marray
* checking tests ...
Running ‘limma-Tests.R’
Comparing ‘limma-Tests.Rout’ to ‘limma-Tests.Rout.save’ ...826,830c826,830
< [1,] 1.025680641 0.04440632
< [2,] -0.008931391 -0.04446419
< [3,] 0.069383171 -0.03407404
< [4,] -0.029375980 0.11198606
< [5,] -0.276173422 0.21529287
---
> [1,] 1.02568064 0.04440632
> [2,] -0.00893139 -0.04446419
> [3,] 0.06938317 -0.03407404
> [4,] -0.02937598 0.11198606
> [5,] -0.27617342 0.21529287
871,872c871,872
< [1] 0.07551649 0.14100247 0.30870247 0.13909601 0.32893352 0.17192613
< [7] 0.42951263 0.11976975 0.39067059 0.22671154
---
> [1] 0.0755165 0.1410025 0.3087025 0.1390960 0.3289335 0.1719261 0.4295126
> [8] 0.1197697 0.3906706 0.2267115
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
* installing *source* package ‘limma’ ...
** libs
gcc -std=gnu99 -I/home/biocbuild/bbs-2.8-bioc/R/include -I/usr/local/include -fpic -g -O2 -c normexp.c -o normexp.o
normexp.c: In function ‘fit_saddle_nelder_mead’:
normexp.c:153:3: warning: floating constant exceeds range of ‘double’
gcc -std=gnu99 -shared -L/usr/local/lib64 -o limma.so normexp.o -L/home/biocbuild/bbs-2.8-bioc/R/lib -lR
installing to /loc/home/biocbuild/bbs-2.8-bioc/meat/limma.Rcheck/limma/libs
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices ...
** testing if installed package can be loaded
* DONE (limma)