Back to the "Multiple platform build/check report" A  B  C  D  E  F  G  H  I  J  K  L [M] N  O  P  Q  R  S  T  U  V  W  X  Y  Z 

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: E:\biocbld\bbs-2.7-bioc\R\bin\R.exe CMD check --no-vignettes --timings MANOR_1.22.0.tar.gz
StartedAt: 2011-04-07 07:47:16 -0700 (Thu, 07 Apr 2011)
EndedAt: 2011-04-07 07:48:21 -0700 (Thu, 07 Apr 2011)
EllapsedTime: 65.2 seconds
RetCode: 0
Status:  OK  
CheckDir: MANOR.Rcheck
Warnings: 0

Command output

* using log directory 'E:/biocbld/bbs-2.7-bioc/meat/MANOR.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 '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 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 -I"E:/biocbld/BBS-2˜1.7-B/R/include"         -O3 -Wall  -std=gnu99 -c Rnem_arg.c -o Rnem_arg.o
gcc -I"E:/biocbld/BBS-2˜1.7-B/R/include"         -O3 -Wall  -std=gnu99 -c Rnem_exe.c -o Rnem_exe.o
gcc -I"E:/biocbld/BBS-2˜1.7-B/R/include"         -O3 -Wall  -std=gnu99 -c exememo.c -o exememo.o
exememo.c: In function 'GenAlloc':
exememo.c:39:6: warning: format '%ld' expects type 'long int', but argument 5 has type 'size_t'
exememo.c:39:6: warning: format '%ld' expects type 'long int', but argument 6 has type 'size_t'
gcc -I"E:/biocbld/BBS-2˜1.7-B/R/include"         -O3 -Wall  -std=gnu99 -c lib_io.c -o lib_io.o
lib_io.c: In function 'CountLinesColumns':
lib_io.c:354:13: warning: 'mincols' may be used uninitialized in this function
gcc -I"E:/biocbld/BBS-2˜1.7-B/R/include"         -O3 -Wall  -std=gnu99 -c nem_alg.c -o nem_alg.o
gcc -I"E:/biocbld/BBS-2˜1.7-B/R/include"         -O3 -Wall  -std=gnu99 -c nem_hlp.c -o nem_hlp.o
gcc -I"E:/biocbld/BBS-2˜1.7-B/R/include"         -O3 -Wall  -std=gnu99 -c nem_mod.c -o nem_mod.o
gcc -I"E:/biocbld/BBS-2˜1.7-B/R/include"         -O3 -Wall  -std=gnu99 -c nem_nei.c -o nem_nei.o
gcc -I"E:/biocbld/BBS-2˜1.7-B/R/include"         -O3 -Wall  -std=gnu99 -c nem_rnd.c -o nem_rnd.o
gcc -I"E:/biocbld/BBS-2˜1.7-B/R/include"         -O3 -Wall  -std=gnu99 -c nem_ver.c -o nem_ver.o
gcc -shared -s -static-libgcc -o MANOR.dll tmp.def 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 -LE:/biocbld/BBS-2˜1.7-B/R/bin/i386 -lR
installing to E:/biocbld/bbs-2.7-bioc/meat/MANOR.Rcheck/MANOR/libs/i386
** 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
arrayTrend0.960.021.00
detectSB1.250.001.25
flag.arrayCGH3.360.013.38
flag.summary0.190.000.18
flags0.200.000.21
genome.plot1.130.001.12
import1.020.001.02
nem4.850.004.90
norm4.610.034.69
qscore.arrayCGH0.220.020.24
qscore.summary1.720.001.71
qscores1.810.011.83
report.plot4.550.004.55
sort0.940.020.97
spatial1.860.031.90
to.flag0.970.000.97