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Package 108/609HostnameOS / ArchBUILDCHECKBUILD BIN
ChIPseqR 1.12.0
Peter Humburg
Snapshot Date: 2013-03-24 16:21:20 -0700 (Sun, 24 Mar 2013)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_11/madman/Rpacks/ChIPseqR
Last Changed Rev: 70050 / Revision: 74773
Last Changed Date: 2012-10-01 15:16:24 -0700 (Mon, 01 Oct 2012)
lamb1 Linux (openSUSE 12.1) / x86_64  OK [ OK ]
moscato1 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK  OK 
perceval Mac OS X Leopard (10.5.8) / i386  OK  OK  OK 

Summary

Package: ChIPseqR
Version: 1.12.0
Command: /home/biocbuild/bbs-2.11-bioc/R/bin/R CMD check --no-vignettes --timings ChIPseqR_1.12.0.tar.gz
StartedAt: 2013-03-25 00:05:07 -0700 (Mon, 25 Mar 2013)
EndedAt: 2013-03-25 00:11:14 -0700 (Mon, 25 Mar 2013)
EllapsedTime: 367.7 seconds
RetCode: 0
Status:  OK 
CheckDir: ChIPseqR.Rcheck
Warnings: 0

Command output

* using log directory ‘/loc/home/biocbuild/bbs-2.11-bioc/meat/ChIPseqR.Rcheck’
* using R version 2.15.3 (2013-03-01)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘ChIPseqR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘ChIPseqR’ version ‘1.12.0’
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking whether package ‘ChIPseqR’ can be installed ... OK
* checking installed package size ... 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 for left-over 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 namespace can be loaded with stated dependencies ... OK
* checking whether the namespace 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
getCutoff : nllk: warning in pnorm(cutoff, sd = sd, log = FALSE):
  partial argument match of 'log' to 'log.p'
getCutoff : nllk: warning in pnorm(0, sd = sd, log = FALSE): partial
  argument match of 'log' to 'log.p'
* checking Rd files ... NOTE
prepare_Rd: startScore.Rd:38: Dropping empty section \references
* 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 compiled code ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                     user system elapsed
alignFeature       33.238  0.064  33.802
BindScore          27.786  0.136  28.194
simpleNucCall      19.329  0.036  19.614
callBindingSites   15.969  0.084  16.698
RLEBindScore-class 14.461  0.044  14.600
* 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

NOTE: There were 2 notes.
See
  ‘/loc/home/biocbuild/bbs-2.11-bioc/meat/ChIPseqR.Rcheck/00check.log’
for details.

ChIPseqR.Rcheck/00install.out:

* installing *source* package ‘ChIPseqR’ ...
** libs
gcc -std=gnu99 -I/home/biocbuild/bbs-2.11-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c startScore.c -o startScore.o
startScore.c: In function ‘_ratioStat_pois’:
startScore.c:66:15: warning: unused variable ‘tmp_stat’ [-Wunused-variable]
gcc -std=gnu99 -shared -L/usr/local/lib64 -o ChIPseqR.so startScore.o -L/home/biocbuild/bbs-2.11-bioc/R/lib -lR
installing to /loc/home/biocbuild/bbs-2.11-bioc/meat/ChIPseqR.Rcheck/ChIPseqR/libs
** R
** inst
** preparing package for lazy loading
Warning: replacing previous import ‘image’ when loading ‘graphics’
** help
*** installing help indices
** building package indices
** installing vignettes
   ‘Introduction.Rnw’ 
** testing if installed package can be loaded
Warning: replacing previous import ‘image’ when loading ‘graphics’

* DONE (ChIPseqR)

ChIPseqR.Rcheck/ChIPseqR-Ex.timings:

nameusersystemelapsed
BindScore27.786 0.13628.194
ChIPseqR-package000
RLEBindScore-class14.461 0.04414.600
RLEReadCounts-class0.0120.0040.016
ReadCounts0.020.000.02
alignFeature33.238 0.06433.802
callBindingSites15.969 0.08416.698
pos2gff0.0080.0000.008
simpleNucCall19.329 0.03619.614
strandPileup0.0160.0000.014
windowCounts0.0480.0000.051