limma 3.14.4
Gordon Smyth
| Snapshot Date: 2013-03-24 16:21:20 -0700 (Sun, 24 Mar 2013) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_11/madman/Rpacks/limma | | Last Changed Rev: 72572 / Revision: 74773 | | Last Changed Date: 2013-01-15 16:40:12 -0800 (Tue, 15 Jan 2013) |
| lamb1 | Linux (openSUSE 12.1) / x86_64 | OK | [ WARNINGS ] | |
| moscato1 | Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 | OK | WARNINGS | OK |
| perceval | Mac OS X Leopard (10.5.8) / i386 | OK | WARNINGS | OK |
* using log directory ‘/loc/home/biocbuild/bbs-2.11-bioc/meat/limma.Rcheck’
* using R version 2.15.3 (2013-03-01)
* 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 ‘3.14.4’
* 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 for sufficient/correct file permissions ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over 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 ... WARNING
Foreign function calls with ‘PACKAGE’ argument in a base package:
.C("loess_raw", ..., PACKAGE = "stats")
.C("lowess", ..., PACKAGE = "stats")
.Fortran("lowesw", ..., PACKAGE = "stats")
Packages should not make .C/.Call/.Fortran calls to base packages. They
are not part of the API, for use only by R itself and subject to change
without notice.
* 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 ... 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 ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
alias2Symbol 5.724 0.1 6.147
* checking for unstated dependencies in tests ... OK
* checking tests ...
Running ‘limma-Tests.R’
Comparing ‘limma-Tests.Rout’ to ‘limma-Tests.Rout.save’ ...588,592c588,592
< 0% -0.78835384 -0.788312144 -0.79410956 -2.04434053 -2.0438088 -10.9766130
< 25% -0.18340154 -0.183595325 -0.17340349 -0.59321065 -0.5863777 -0.7816385
< 50% -0.11492924 -0.123303508 -0.04476096 0.05874864 0.0827054 -0.2577724
< 75% 0.01507921 -0.006825877 0.14015263 0.56010750 0.5606874 0.4406875
< 100% 0.21653837 0.193234186 11.47140874 2.57936026 2.5816432 2.5397022
---
> 0% -0.78835384 -0.78097895 -0.78367166 -2.04434053 -2.04315267 -11.5610680
> 25% -0.18340154 -0.18907787 -0.15525721 -0.59321065 -0.59309327 -0.8249477
> 50% -0.11492924 -0.12136183 -0.03316003 0.05874864 0.08898459 -0.2466309
> 75% 0.01507921 -0.01000344 0.13229151 0.56010750 0.56606786 0.4502908
> 100% 0.21653837 0.21604173 11.69912073 2.57936026 2.56259812 2.5149556
630,635c630,635
< Min. :-5.88044 Min. :-5.66985
< 1st Qu.:-1.18483 1st Qu.:-1.57014
< Median :-0.21632 Median : 0.04823
< Mean : 0.03487 Mean :-0.05481
< 3rd Qu.: 1.49669 3rd Qu.: 1.45113
< Max. : 7.07324 Max. : 6.19744
---
> Min. :-5.85163 Min. :-5.69877
> 1st Qu.:-1.18482 1st Qu.:-1.55421
> Median :-0.21631 Median : 0.06267
> Mean : 0.03613 Mean :-0.05369
> 3rd Qu.: 1.49673 3rd Qu.: 1.41900
> Max. : 7.07528 Max. : 6.28902
646,650c646,650
< [1,] -1.1689588 4.5558123
< [2,] 0.8971363 0.3296544
< [3,] 2.8247439 1.4249960
< [4,] -1.8533240 0.4804851
< [5,] 1.9158459 -5.5087631
---
> [1,] -1.1623390 4.5343276
> [2,] 0.8971391 0.3495635
> [3,] 2.8247455 1.4459533
> [4,] -1.8533288 0.4894799
> [5,] 1.9158416 -5.5363732
661,665c661,665
< [1,] -1.1689588 4.5558123
< [2,] 0.8971363 0.3296544
< [3,] 2.8247439 1.4249960
< [4,] -1.8533240 0.4804851
< [5,] 1.9158459 -5.5087631
---
> [1,] -1.1623390 4.5343276
> [2,] 0.8971391 0.3495635
> [3,] 2.8247455 1.4459533
> [4,] -1.8533288 0.4894799
> [5,] 1.9158416 -5.5363732
906c906
< 'rlm' failed to converge in 20 steps
---
> rlm failed to converge in 20 steps
981,982c981,982
< 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
‘/loc/home/biocbuild/bbs-2.11-bioc/meat/limma.Rcheck/00check.log’
for details.
* installing *source* package ‘limma’ ...
** libs
gcc -std=gnu99 -I/home/biocbuild/bbs-2.11-bioc/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -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 -std=gnu99 -shared -L/usr/local/lib64 -o limma.so normexp.o -L/home/biocbuild/bbs-2.11-bioc/R/lib -lR
installing to /loc/home/biocbuild/bbs-2.11-bioc/meat/limma.Rcheck/limma/libs
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
‘limma.Rnw’
** testing if installed package can be loaded
* DONE (limma)