girafe 1.2.0
J. Toedling
| Snapshot Date: 2011-04-06 23:24:01 -0700 (Wed, 06 Apr 2011) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_7/madman/Rpacks/girafe | | Last Changed Rev: 50293 / Revision: 54588 | | Last Changed Date: 2010-10-17 22:34:23 -0700 (Sun, 17 Oct 2010) |
| lamb2 | Linux (openSUSE 11.2) / x86_64 | OK | [ OK ] | |
| liverpool | Windows Server 2003 R2 (32-bit) / x64 | OK | OK | OK |
| gewurz | Windows Server 2008 R2 Enterprise (64-bit) / x64 | OK | OK | OK |
* using log directory ‘/loc/home/biocbuild/bbs-2.7-bioc/meat/girafe.Rcheck’
* using R version 2.12.2 (2011-02-25)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘girafe/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘girafe’ version ‘1.2.0’
* checking package name space information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking whether package ‘girafe’ can be installed ... 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 name space can be loaded with stated dependencies ... OK
* checking whether the name space 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
fracOverlap: no visible binding for global variable ‘fraction1’
fracOverlap: no visible binding for global variable ‘fraction2’
getFeatureCounts: no visible binding for global variable ‘fraction1’
getFeatureCounts: no visible binding for global variable ‘Index1’
intPhred: no visible binding for global variable ‘mclapply’
oldAGIoverlap: no visible binding for global variable ‘mclapply’
reduceOne: no visible binding for global variable ‘fraction1’
reduceOne: no visible binding for global variable ‘fraction2’
* 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 examples ... OK
* checking package vignettes in ‘inst/doc’ ... SKIPPED
* checking PDF version of manual ... OK
* installing *source* package ‘girafe’ ...
** libs
g++ -I/home/biocbuild/bbs-2.7-bioc/R/include -I/usr/local/include -fpic -g -O2 -c coverage.cpp -o coverage.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.7-bioc/R/include -I/usr/local/include -fpic -g -O2 -c girafe_init.c -o girafe_init.o
g++ -shared -L/usr/local/lib64 -o girafe.so coverage.o girafe_init.o -L/home/biocbuild/bbs-2.7-bioc/R/lib -lR
installing to /loc/home/biocbuild/bbs-2.7-bioc/meat/girafe.Rcheck/girafe/libs
** R
** inst
** preparing package for lazy loading
Attaching package: 'IRanges'
The following object(s) are masked from 'package:base':
Map, cbind, eval, mapply, order, paste, pmax, pmax.int, pmin,
pmin.int, rbind, rep.int, table
Loading required package: GenomicRanges
Loading required package: Biostrings
Loading required package: lattice
Attaching package: 'intervals'
The following object(s) are masked from 'package:Biostrings':
type
The following object(s) are masked from 'package:IRanges':
reduce
Loading required package: Biobase
Welcome to Bioconductor
Vignettes contain introductory material. To view, type
'openVignette()'. To cite Bioconductor, see
'citation("Biobase")' and for packages 'citation(pkgname)'.
Attaching package: 'Biobase'
The following object(s) are masked from 'package:IRanges':
updateObject
Attaching package: 'genomeIntervals'
The following object(s) are masked from 'package:GenomicRanges':
strand, strand<-
Creating a new generic function for "plot" in "girafe"
Creating a new generic function for "hist" in "girafe"
Creating a new generic function for "sample" in "girafe"
** help
*** installing help indices
** building package indices ...
** testing if installed package can be loaded
* DONE (girafe)