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Package 371/479HostnameOS / ArchBUILDCHECKBUILD BIN
R453Plus1Toolbox 1.3.1
Hans-Ulrich Klein
Snapshot Date: 2011-07-06 19:21:50 -0700 (Wed, 06 Jul 2011)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/R453Plus1Toolbox
Last Changed Rev: 56470 / Revision: 56603
Last Changed Date: 2011-06-30 08:14:07 -0700 (Thu, 30 Jun 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: R453Plus1Toolbox
Version: 1.3.1
Command: E:\biocbld\bbs-2.9-bioc\R\bin\R.exe CMD check --no-vignettes --timings --no-multiarch R453Plus1Toolbox_1.3.1.tar.gz
StartedAt: 2011-07-07 03:14:43 -0700 (Thu, 07 Jul 2011)
EndedAt: 2011-07-07 03:18:47 -0700 (Thu, 07 Jul 2011)
EllapsedTime: 243.5 seconds
RetCode: 0
Status:  OK  
CheckDir: R453Plus1Toolbox.Rcheck
Warnings: 0

Command output

* using log directory 'E:/biocbld/bbs-2.9-bioc/meat/R453Plus1Toolbox.Rcheck'
* using R version 2.14.0 Under development (unstable) (2011-06-03 r56036)
* using platform: i386-pc-mingw32 (32-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'R453Plus1Toolbox/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'R453Plus1Toolbox' version '1.3.1'
* checking package name space information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking whether package 'R453Plus1Toolbox' 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
.getMutations: no visible binding for global variable 'PatternStart'
.getMutations: no visible binding for global variable 'PatternEnd'
.htmlReport: no visible binding for global variable 'VarFreqForward'
.htmlReport: no visible binding for global variable 'VarFreqReverse'
* 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 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

R453Plus1Toolbox.Rcheck/00install.out:

* installing *source* package 'R453Plus1Toolbox' ...
** libs
gcc  -I"E:/biocbld/BBS-2˜1.9-B/R/include"          -O3 -Wall  -std=gnu99 -c readSFF.c -o readSFF.o
gcc -shared -s -static-libgcc -o R453Plus1Toolbox.dll tmp.def readSFF.o -LE:/biocbld/BBS-2˜1.9-B/R/bin/i386 -lR
installing to E:/biocbld/bbs-2.9-bioc/meat/R453Plus1Toolbox.Rcheck/R453Plus1Toolbox/libs/i386
** R
** data
** inst
** preparing package for lazy loading

Welcome to Bioconductor

  Vignettes contain introductory material. To view, type
  'browseVignettes()'. To cite Bioconductor, see
  'citation("Biobase")' and for packages 'citation("pkgname")'.

Loading required package: IRanges

Attaching package: 'IRanges'

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

    updateObject

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: BSgenome
Loading required package: GenomicRanges
Creating a new generic function for "name" in package "R453Plus1Toolbox"
** help
*** installing help indices
** building package indices ...
*** tangling vignette sources ...
   'vignette.Rnw' 
** testing if installed package can be loaded
Warning message:
multiple methods tables found for 'name' 

* DONE (R453Plus1Toolbox)

R453Plus1Toolbox.Rcheck/R453Plus1Toolbox-Ex.timings:

nameusersystemelapsed
AVASet-class0.080.010.09
AVASet0.030.000.04
AnnotatedVariants-class000
MapperSet-class0.030.020.04
MapperSet0.020.000.02
SFFContainer-class000
SFFRead-class000
alignShortReads0.970.001.06
annotateVariants000
assayDataAmp0.010.000.02
avaSetExample0.020.020.03
avaSetFiltered0.050.000.04
avaSetFiltered_annot000
breakpoints0.000.010.02
calculateTiTv0.010.000.02
captureArray0.000.020.01
coverageOnTarget0.630.010.69
demultiplexReads0.110.000.11
detectBreakpoints0.510.000.59
fDataAmp0.020.000.02
featureDataAmp0.030.000.03
filterChimericReads1.840.021.87
genomeSequencerMIDs0.040.000.05
getAlignedReads0.160.010.17
getVariantPercentages0.050.000.05
htmlReport4.250.305.07
mapperSetExample000
mergeBreakpoints7.610.227.92
plotAmpliconCoverage000
plotChimericReads4.910.004.92
plotVariants000
plotVariationFrequency000
readSFF000
readsOnTarget0.590.010.61
referenceSequences0.020.000.02
removeLinker0.010.020.03
sequenceCaptureLinkers000
setVariantFilter0.110.000.11
transcriptdf000