edgeR 3.0.8
Mark Robinson , Davis McCarthy , Yunshun Chen , 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/edgeR | | Last Changed Rev: 72255 / Revision: 74773 | | Last Changed Date: 2013-01-02 20:13:26 -0800 (Wed, 02 Jan 2013) |
| lamb1 | Linux (openSUSE 12.1) / x86_64 | OK | [ OK ] | |
| moscato1 | Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 | OK | OK | OK |
| perceval | Mac OS X Leopard (10.5.8) / i386 | OK | OK | OK |
* using log directory ‘/loc/home/biocbuild/bbs-2.11-bioc/meat/edgeR.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 ‘edgeR/DESCRIPTION’ ... OK
* this is package ‘edgeR’ version ‘3.0.8’
* 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 ‘edgeR’ 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 ... 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 ... 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 compilation flags in Makevars ... 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
* checking for unstated dependencies in tests ... OK
* checking tests ...
Running ‘edgeR-Tests.R’
Comparing ‘edgeR-Tests.Rout’ to ‘edgeR-Tests.Rout.save’ ... OK
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 ‘edgeR’ ...
** libs
g++ -I/home/biocbuild/bbs-2.11-bioc/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c cr_adjustment.cpp -o cr_adjustment.o
cr_adjustment.cpp: In function ‘SEXPREC* cr_adjustment(SEXP, SEXP, SEXP)’:
cr_adjustment.cpp:22:33: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
cr_adjustment.cpp:23:33: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
gcc -std=gnu99 -I/home/biocbuild/bbs-2.11-bioc/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c fmm_spline.c -o fmm_spline.o
g++ -I/home/biocbuild/bbs-2.11-bioc/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c lowess_by_col.cpp -o lowess_by_col.o
g++ -I/home/biocbuild/bbs-2.11-bioc/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c maximize_interpolant.cpp -o maximize_interpolant.o
maximize_interpolant.cpp: In function ‘SEXPREC* maximize_interpolant(SEXP, SEXP)’:
maximize_interpolant.cpp:61:22: warning: variable ‘first’ set but not used [-Wunused-but-set-variable]
g++ -I/home/biocbuild/bbs-2.11-bioc/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c mglm_levenberg.cpp -o mglm_levenberg.o
mglm_levenberg.cpp: In function ‘double deviance_nb(const std::deque<double>&, const std::deque<double>&, const double&)’:
mglm_levenberg.cpp:16:28: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
g++ -I/home/biocbuild/bbs-2.11-bioc/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c simple_good_turing.cpp -o simple_good_turing.o
g++ -shared -L/usr/local/lib64 -o edgeR.so cr_adjustment.o fmm_spline.o lowess_by_col.o maximize_interpolant.o mglm_levenberg.o simple_good_turing.o -L/home/biocbuild/bbs-2.11-bioc/R/lib -lRlapack -L/home/biocbuild/bbs-2.11-bioc/R/lib -lRblas -lgfortran -lm -lquadmath -L/home/biocbuild/bbs-2.11-bioc/R/lib -lR
installing to /loc/home/biocbuild/bbs-2.11-bioc/meat/edgeR.Rcheck/edgeR/libs
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
‘edgeR.Rnw’
** testing if installed package can be loaded
* DONE (edgeR)