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Package 79/419HostnameOS / ArchBUILDCHECKBUILD BIN
chipseq 1.0.0
Biocore Team c/o BioC user list
Snapshot Date: 2011-03-30 23:22:56 -0700 (Wed, 30 Mar 2011)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_7/madman/Rpacks/chipseq
Last Changed Rev: 50293 / Revision: 54281
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 
pelham Mac OS X Leopard (10.5.8) / i386  OK  OK  OK 

Summary

Package: chipseq
Version: 1.0.0
Command: E:\biocbld\bbs-2.7-bioc\R\bin\R.exe CMD check --no-vignettes --timings chipseq_1.0.0.tar.gz
StartedAt: 2011-03-31 05:57:54 -0700 (Thu, 31 Mar 2011)
EndedAt: 2011-03-31 06:01:08 -0700 (Thu, 31 Mar 2011)
EllapsedTime: 194.5 seconds
RetCode: 0
Status:  OK  
CheckDir: chipseq.Rcheck
Warnings: 0

Command output

* using log directory 'E:/biocbld/bbs-2.7-bioc/meat/chipseq.Rcheck'
* using R version 2.12.2 (2011-02-25)
* using platform: i386-pc-mingw32 (32-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'chipseq/DESCRIPTION' ... OK
* this is package 'chipseq' version '1.0.0'
* checking package name space information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking whether package 'chipseq' can be installed ... 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
correlation.estimate: no visible binding for global variable 'mu'
correlation.estimate: no visible binding for global variable 'corr'
coverage.estimate: no visible binding for global variable 'mu'
coverage.estimate: no visible binding for global variable 'covered'
diffPeakSummaryRef: no visible global function definition for
  'laneCoverage'
islandDepthPlot: no visible binding for global variable 'depth'
* 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 data for non-ASCII characters ... 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

chipseq.Rcheck/00install.out:

* installing *source* package 'chipseq' ...
** libs
gcc -I"E:/biocbld/BBS-2˜1.7-B/R/include"         -O3 -Wall  -std=gnu99 -c rlesumprod.c -o rlesumprod.o
rlesumprod.c: In function 'rle_sum_prod':
rlesumprod.c:24:16: warning: operation on 'i1' may be undefined
rlesumprod.c:25:16: warning: operation on 'i2' may be undefined
rlesumprod.c:27:44: warning: operation on 'i1' may be undefined
rlesumprod.c:28:44: warning: operation on 'i2' may be undefined
rlesumprod.c:34:37: warning: operation on 'i1' may be undefined
rlesumprod.c:35:37: warning: operation on 'i2' may be undefined
rlesumprod.c: In function 'rle_sum_any':
rlesumprod.c:61:33: warning: operation on 'i1' may be undefined
rlesumprod.c:62:33: warning: operation on 'i2' may be undefined
gcc -shared -s -static-libgcc -o chipseq.dll tmp.def rlesumprod.o -LE:/biocbld/BBS-2˜1.7-B/R/bin/i386 -lR
installing to E:/biocbld/bbs-2.7-bioc/meat/chipseq.Rcheck/chipseq/libs/i386
** R
** data
** 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: Biostrings
Loading required package: lattice
Loading required package: Rsamtools
** help
*** installing help indices
** building package indices ...
** testing if installed package can be loaded

* DONE (chipseq)

chipseq.Rcheck/chipseq-Ex.timings:

nameusersystemelapsed
chipseqFilter1.360.642.15
combineLanes11.78 0.2112.06
copyIRangesbyChr0.010.000.02
coverageplot0.210.000.20
cstest0.400.010.42
diffPeakSummary10.10 0.2810.58
estimate.mean.fraglen5.140.055.19
extendReads1.860.172.03
islandDepthPlot4.200.094.33
peakCutoff4.140.044.23
readReads000
subsetSummary3.590.013.61