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Package 204/479HostnameOS / ArchBUILDCHECKBUILD BIN
girafe 1.5.2
J. Toedling
Snapshot Date: 2011-07-06 19:21:50 -0700 (Wed, 06 Jul 2011)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/girafe
Last Changed Rev: 56583 / Revision: 56603
Last Changed Date: 2011-07-06 01:47:14 -0700 (Wed, 06 Jul 2011)
wilson2 Linux (openSUSE 11.4) / 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 
moscato1 Windows Server 2008 R2 Enterprise (64-bit) / x64  OK  OK  OK 
pitt Mac OS X Leopard (10.5.8) / i386  OK  OK  OK 

Summary

Package: girafe
Version: 1.5.2
Command: D:\biocbld\bbs-2.9-bioc\R\bin\R.exe CMD check --no-vignettes --timings --no-multiarch girafe_1.5.2.tar.gz
StartedAt: 2011-07-07 04:22:11 -0700 (Thu, 07 Jul 2011)
EndedAt: 2011-07-07 04:26:38 -0700 (Thu, 07 Jul 2011)
EllapsedTime: 267.2 seconds
RetCode: 0
Status:  OK  
CheckDir: girafe.Rcheck
Warnings: 0

Command output

* using log directory 'D:/biocbld/bbs-2.9-bioc/meat/girafe.Rcheck'
* using R version 2.14.0 Under development (unstable) (2011-06-03 r56036)
* using platform: x86_64-pc-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'girafe/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'girafe' version '1.5.2'
* 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 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
* 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
agiFromBam: no visible binding for global variable 'mclapply'
countReadsAnnotated: no visible binding for global variable 'mclapply'
countReadsAnnotated: no visible binding for global variable 'fraction1'
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'
windowCountAndGC: no visible binding for global variable 'n.reads'
* 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 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

girafe.Rcheck/00install.out:

* installing *source* package 'girafe' ...
** libs
x86_64-w64-mingw32-g++  -I"D:/biocbld/BBS-2˜1.9-B/R/include"          -O2 -Wall  -c coverage.cpp -o coverage.o
x86_64-w64-mingw32-gcc  -I"D:/biocbld/BBS-2˜1.9-B/R/include"          -O2 -Wall  -std=gnu99 -c girafe_init.c -o girafe_init.o
x86_64-w64-mingw32-g++ -shared -s -static-libgcc -o girafe.dll tmp.def coverage.o girafe_init.o -LD:/biocbld/BBS-2˜1.9-B/R/bin/x64 -lR
installing to D:/biocbld/bbs-2.9-bioc/meat/girafe.Rcheck/girafe/libs/x64
** R
** inst
** preparing package for lazy loading

Attaching package: 'IRanges'

The following object(s) are masked from 'package:base':

    Map, cbind, eval, intersect, mapply, order, paste, pmax, pmax.int,
    pmin, pmin.int, rbind, rep.int, setdiff, table, union

Loading required package: GenomicRanges
Loading required package: Biostrings
Loading required package: lattice
Loading required package: latticeExtra
Loading required package: RColorBrewer

Attaching package: 'intervals'

The following object(s) are masked from 'package:Biostrings':

    type

The following object(s) are masked from 'package:IRanges':

    reduce


Attaching package: 'genomeIntervals'

The following object(s) are masked from 'package:GenomicRanges':

    strand, strand<-

Creating a generic function for "plot" from package "graphics" in package "girafe"
Creating a generic function for "hist" from package "graphics" in package "girafe"
Creating a generic function for "sample" from package "base" in package "girafe"
** help
*** installing help indices
** building package indices ...
*** tangling vignette sources ...
   'girafe.Rnw' 
** testing if installed package can be loaded

* DONE (girafe)

girafe.Rcheck/girafe-Ex.timings:

nameusersystemelapsed
AlignedGenomeIntervals-class6.380.286.70
agiFromBam0.600.020.61
countReadsAnnotated0.210.000.21
fracOverlap0.150.000.15
intPhred0.190.340.53
medianByPosition1.360.261.63
negbinomsig18.76 0.2218.98
perWindow19.11 0.3319.55
plotAligned0.070.000.06
trimAdapter0.320.380.74
weightedConsensusMatrix0.020.000.01
whichNearestMethods0.730.361.10