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Package 80/444HostnameOS / ArchBUILDCHECKBUILD BIN
chipseq 1.1.2
Biocore Team c/o BioC user list
Snapshot Date: 2011-03-17 11:16:30 -0700 (Thu, 17 Mar 2011)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/chipseq
Last Changed Rev: 51113 / Revision: 53825
Last Changed Date: 2010-11-29 13:21:02 -0800 (Mon, 29 Nov 2010)
lamb1 Linux (openSUSE 11.3) / 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 
petty Mac OS X Snow Leopard (10.6.6) / i386  OK [ OK ] OK 

Summary

Package: chipseq
Version: 1.1.2
Command: /Library/Frameworks/R.framework/Versions/2.13/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch chipseq_1.1.2.tar.gz
StartedAt: 2011-03-17 15:56:48 -0700 (Thu, 17 Mar 2011)
EndedAt: 2011-03-17 15:59:58 -0700 (Thu, 17 Mar 2011)
EllapsedTime: 189.9 seconds
RetCode: 0
Status:  OK 
CheckDir: chipseq.Rcheck
Warnings: 0

Command output

* using log directory '/Users/biocbuild/bbs-2.8-bioc/meat/chipseq.Rcheck'
* using R version 2.13.0 Under development (unstable) (2011-03-06 r54683)
* using platform: i386-apple-darwin9.8.0 (32-bit)
* using session charset: ASCII
* using option '--no-vignettes'
* checking for file 'chipseq/DESCRIPTION' ... OK
* this is package 'chipseq' version '1.1.2'
* 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 installed package size ... NOTE
  installed size is  5.0Mb
  sub-directories of 1Mb or more:
    data   2.2Mb
    doc    1.9Mb
* 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
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 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 package vignettes in 'inst/doc' ... SKIPPED
* checking PDF version of manual ... OK

chipseq.Rcheck/00install.out:

* installing *source* package 'chipseq' ...
** libs
*** arch - i386
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include/i386  -I/usr/local/include    -fPIC  -g -O2 -Wall -pedantic -c rlesumprod.c -o rlesumprod.o
rlesumprod.c: In function 'rle_sum_prod':
rlesumprod.c:24: warning: operation on 'i1' may be undefined
rlesumprod.c:25: warning: operation on 'i2' may be undefined
rlesumprod.c:27: warning: operation on 'i1' may be undefined
rlesumprod.c:28: warning: operation on 'i2' may be undefined
rlesumprod.c:34: warning: operation on 'i1' may be undefined
rlesumprod.c:35: warning: operation on 'i2' may be undefined
rlesumprod.c: In function 'rle_sum_any':
rlesumprod.c:61: warning: operation on 'i1' may be undefined
rlesumprod.c:62: warning: operation on 'i2' may be undefined
gcc -arch i386 -std=gnu99 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -o chipseq.so rlesumprod.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-2.8-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, intersect, mapply, order, paste, pmax, pmax.int,
    pmin, pmin.int, rbind, rep.int, setdiff, table, union

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
chipseqFilter0.7120.0080.749
combineLanes9.1520.5569.709
copyIRangesbyChr0.0170.0000.018
coverageplot0.1350.0010.135
cstest0.3710.0290.400
diffPeakSummary 9.275 1.23810.512
estimate.mean.fraglen2.2270.4922.719
extendReads1.2760.2341.510
islandDepthPlot2.5240.4672.991
peakCutoff3.0860.4453.531
readReads0.0000.0000.001
subsetSummary3.0420.3783.419