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Package 242/419HostnameOS / ArchBUILDCHECKBUILD BIN
MANOR 1.22.0
Pierre Neuvial
Snapshot Date: 2011-04-06 23:24:01 -0700 (Wed, 06 Apr 2011)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_7/madman/Rpacks/MANOR
Last Changed Rev: 50293 / Revision: 54588
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 

Summary

Package: MANOR
Version: 1.22.0
Command: /home/biocbuild/bbs-2.7-bioc/R/bin/R CMD check --no-vignettes --timings MANOR_1.22.0.tar.gz
StartedAt: 2011-04-07 07:31:08 -0700 (Thu, 07 Apr 2011)
EndedAt: 2011-04-07 07:31:40 -0700 (Thu, 07 Apr 2011)
EllapsedTime: 32.5 seconds
RetCode: 0
Status:  OK 
CheckDir: MANOR.Rcheck
Warnings: 0

Command output

* using log directory ‘/loc/home/biocbuild/bbs-2.7-bioc/meat/MANOR.Rcheck’
* using R version 2.12.2 (2011-02-25)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘MANOR/DESCRIPTION’ ... OK
* this is package ‘MANOR’ version ‘1.22.0’
* checking package name space information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking whether package ‘MANOR’ can be installed ... 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 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 ... 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 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

MANOR.Rcheck/00install.out:

* installing *source* package ‘MANOR’ ...
** libs
gcc -std=gnu99 -I/home/biocbuild/bbs-2.7-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -c Rnem_arg.c -o Rnem_arg.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.7-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -c Rnem_exe.c -o Rnem_exe.o
Rnem_exe.c: In function ‘MakeErrinfo’:
Rnem_exe.c:216: warning: cast from pointer to integer of different size
gcc -std=gnu99 -I/home/biocbuild/bbs-2.7-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -c exememo.c -o exememo.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.7-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -c lib_io.c -o lib_io.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.7-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -c nem_alg.c -o nem_alg.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.7-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -c nem_hlp.c -o nem_hlp.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.7-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -c nem_mod.c -o nem_mod.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.7-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -c nem_nei.c -o nem_nei.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.7-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -c nem_rnd.c -o nem_rnd.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.7-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -c nem_ver.c -o nem_ver.o
gcc -std=gnu99 -shared -L/usr/local/lib64 -o MANOR.so Rnem_arg.o Rnem_exe.o exememo.o lib_io.o nem_alg.o nem_hlp.o nem_mod.o nem_nei.o nem_rnd.o nem_ver.o -L/home/biocbuild/bbs-2.7-bioc/R/lib -lR
installing to /loc/home/biocbuild/bbs-2.7-bioc/meat/MANOR.Rcheck/MANOR/libs
** R
** data
** inst
** preparing package for lazy loading


######################################################################################



Have fun with GLAD



For smoothing it is possible to use either

the AWS algorithm (Polzehl and Spokoiny, 2002)

or the HaarSeg algorithm (Ben-Yaacov and Eldar, Bioinformatics,  2008)



If you use the package with AWS, please cite:

Hupe et al. (Bioinformatics, 2004) and Polzehl and Spokoiny (2002)



If you use the package with HaarSeg, please cite:

Hupe et al. (Bioinformatics, 2004) and (Ben-Yaacov and Eldar, Bioinformatics, 2008)



For fast computation it is recommanded to use

the daglad function with smoothfunc=haarseg



######################################################################################



New options are available in daglad: see help for details.


** help
*** installing help indices
** building package indices ...
** testing if installed package can be loaded

* DONE (MANOR)

MANOR.Rcheck/MANOR-Ex.timings:

nameusersystemelapsed
arrayTrend0.6120.0120.626
detectSB0.5160.0000.515
flag.arrayCGH2.0440.0082.055
flag.summary0.1000.0000.102
flags0.1040.0000.104
genome.plot0.6200.0080.628
import0.3320.0000.334
nem2.3000.0042.307
norm1.3760.0201.398
qscore.arrayCGH0.0960.0000.100
qscore.summary0.9280.0000.929
qscores0.9360.0000.936
report.plot1.3920.0201.408
sort0.2160.0000.218
spatial0.2760.0120.290
to.flag0.5880.0040.589