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BioC 2.13: CHECK report for ADaCGH2 on zin1

This page was generated on 2014-04-05 09:47:58 -0700 (Sat, 05 Apr 2014).

Package 10/750HostnameOS / ArchBUILDCHECKBUILD BIN
ADaCGH2 2.2.0
Ramon Diaz-Uriarte
Snapshot Date: 2014-04-04 16:20:29 -0700 (Fri, 04 Apr 2014)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_13/madman/Rpacks/ADaCGH2
Last Changed Rev: 81642 / Revision: 88450
Last Changed Date: 2013-10-14 14:29:21 -0700 (Mon, 14 Oct 2013)
zin1 Linux (Ubuntu 12.04.4 LTS) / x86_64  OK [ OK ]
moscato1 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK  OK 
perceval Mac OS X Snow Leopard (10.6.8) / x86_64  OK  OK  OK 

Summary

Package: ADaCGH2
Version: 2.2.0
Command: /home/biocbuild/bbs-2.13-bioc/R/bin/R CMD check --no-vignettes --timings ADaCGH2_2.2.0.tar.gz
StartedAt: 2014-04-04 23:16:36 -0700 (Fri, 04 Apr 2014)
EndedAt: 2014-04-04 23:19:21 -0700 (Fri, 04 Apr 2014)
EllapsedTime: 165.4 seconds
RetCode: 0
Status:  OK 
CheckDir: ADaCGH2.Rcheck
Warnings: 0

Command output

* using log directory ‘/home/biocbuild/bbs-2.13-bioc/meat/ADaCGH2.Rcheck’
* using R version 3.0.3 (2014-03-06)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘ADaCGH2/DESCRIPTION’ ... OK
* this is package ‘ADaCGH2’ version ‘2.2.0’
* 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 for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘ADaCGH2’ can be installed ... [12s/12s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... 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 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 ... OK
* 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 compiled code ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [41s/51s] OK
Examples with CPU or elapsed time > 5s
                     user system elapsed
pChromPlot         10.189  1.268   3.757
pSegment            9.712  1.324  20.645
outputToCGHregions  9.092  1.108   9.819
inputToADaCGH       2.116  0.240   9.347
* 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 vignette outputs ... SKIPPED
* checking PDF version of manual ... OK

ADaCGH2.Rcheck/00install.out:

* installing *source* package ‘ADaCGH2’ ...
** libs
gcc -std=gnu99 -I/home/biocbuild/bbs-2.13-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c r_haarseg.c -o r_haarseg.o
r_haarseg.c: In function ‘ad_HaarConv’:
r_haarseg.c:65:12: warning: unused variable ‘totalNorm’ [-Wunused-variable]
r_haarseg.c: In function ‘ad_FindLocalPeaks’:
r_haarseg.c:152:8: warning: "/*" within comment [-Wcomment]
r_haarseg.c:176:8: warning: "/*" within comment [-Wcomment]
r_haarseg.c:128:9: warning: unused variable ‘j’ [-Wunused-variable]
r_haarseg.c: In function ‘ad_HaarConv’:
r_haarseg.c:97:27: warning: ‘highNonNormed’ may be used uninitialized in this function [-Wuninitialized]
r_haarseg.c:96:26: warning: ‘lowNonNormed’ may be used uninitialized in this function [-Wuninitialized]
r_haarseg.c:99:27: warning: ‘highWeightSum’ may be used uninitialized in this function [-Wuninitialized]
r_haarseg.c:98:26: warning: ‘lowWeightSum’ may be used uninitialized in this function [-Wuninitialized]
gcc -std=gnu99 -shared -L/usr/local/lib -o ADaCGH2.so r_haarseg.o -L/home/biocbuild/bbs-2.13-bioc/R/lib -lR
installing to /home/biocbuild/bbs-2.13-bioc/meat/ADaCGH2.Rcheck/ADaCGH2/libs
** R
** data
** inst
** preparing package for lazy loading
Warning: replacing previous import by ‘ffbase::[.ff’ when loading ‘ADaCGH2’
Warning: replacing previous import by ‘ffbase::[<-.ff’ when loading ‘ADaCGH2’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Warning: replacing previous import by ‘ffbase::[.ff’ when loading ‘ADaCGH2’
Warning: replacing previous import by ‘ffbase::[<-.ff’ when loading ‘ADaCGH2’
* DONE (ADaCGH2)

ADaCGH2.Rcheck/ADaCGH2-Ex.timings:

nameusersystemelapsed
cutFile0.0240.0522.160
inputToADaCGH2.1160.2409.347
outputToCGHregions9.0921.1089.819
pChromPlot10.189 1.268 3.757
pSegment 9.712 1.32420.645