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 203/353HostnameOS / ArchBUILDCHECKBUILD BIN
MANOR 1.18.0
Pierre Neuvial
Snapshot Date: 2010-04-02 23:28:25 -0700 (Fri, 02 Apr 2010)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_5/madman/Rpacks/MANOR
Last Changed Rev: 42684 / Revision: 45705
Last Changed Date: 2009-10-27 16:33:29 -0700 (Tue, 27 Oct 2009)
wilson2 Linux (openSUSE 11.1) / x86_64  OK  OK 
liverpool Windows Server 2003 R2 (32-bit) / x64  OK [ OK ] OK 
pitt Mac OS X Tiger (10.4.11) / i386  OK  OK  OK 
pelham Mac OS X Leopard (10.5.8) / i386  OK  OK  OK 
Package: MANOR
Version: 1.18.0
Command: E:\biocbld\bbs-2.5-bioc\R\bin\R.exe CMD check --no-vignettes MANOR_1.18.0.tar.gz
StartedAt: 2010-04-03 05:24:56 -0700 (Sat, 03 Apr 2010)
EndedAt: 2010-04-03 05:25:47 -0700 (Sat, 03 Apr 2010)
EllapsedTime: 50.6 seconds
RetCode: 0
Status: OK
CheckDir: MANOR.Rcheck
Warnings: 0

Command output

* checking for working pdflatex ... OK
* using log directory 'E:/biocbld/bbs-2.5-bioc/meat/MANOR.Rcheck'
* using R version 2.10.1 (2009-12-14)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'MANOR/DESCRIPTION' ... OK
* this is package 'MANOR' version '1.18.0'
* 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 name space can be loaded with stated dependencies ... 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 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 ... OK
* checking examples ... OK
* checking package vignettes in 'inst/doc' ... SKIPPED
* checking PDF version of manual ... OK

MANOR.Rcheck/00install.out:

* install options are ' --no-html'

* installing *source* package 'MANOR' ...
** libs
  making DLL ...
gcc -I"e:/biocbld/bbs-2.5-bioc/R/include"        -O3 -Wall  -std=gnu99 -c Rnem_arg.c -o Rnem_arg.o
gcc -I"e:/biocbld/bbs-2.5-bioc/R/include"        -O3 -Wall  -std=gnu99 -c Rnem_exe.c -o Rnem_exe.o
gcc -I"e:/biocbld/bbs-2.5-bioc/R/include"        -O3 -Wall  -std=gnu99 -c exememo.c -o exememo.o
exememo.c: In function 'GenAlloc':
exememo.c:39: warning: format '%ld' expects type 'long int', but argument 5 has type 'size_t'
exememo.c:39: warning: format '%ld' expects type 'long int', but argument 6 has type 'size_t'
gcc -I"e:/biocbld/bbs-2.5-bioc/R/include"        -O3 -Wall  -std=gnu99 -c lib_io.c -o lib_io.o
lib_io.c: In function 'CountLinesColumns':
lib_io.c:354: warning: 'mincols' may be used uninitialized in this function
gcc -I"e:/biocbld/bbs-2.5-bioc/R/include"        -O3 -Wall  -std=gnu99 -c nem_alg.c -o nem_alg.o
nem_alg.c: In function 'ClassifyByNemOneBeta':
nem_alg.c:1626: warning: 'bestCritS.Errcur.Errorrate' may be used uninitialized in this function
nem_alg.c:1626: note: 'bestCritS.Errcur.Errorrate' was declared here
nem_alg.c:1626: warning: 'bestCritS.Errcur.Ibestpermut' may be used uninitialized in this function
nem_alg.c:1626: note: 'bestCritS.Errcur.Ibestpermut' was declared here
nem_alg.c:1626: warning: 'bestCritS.Errcur.Loclas_N_Kc' may be used uninitialized in this function
nem_alg.c:1626: note: 'bestCritS.Errcur.Loclas_N_Kc' was declared here
nem_alg.c:1626: warning: 'bestCritS.Errcur.Agree_Km_Km' may be used uninitialized in this function
nem_alg.c:1626: note: 'bestCritS.Errcur.Agree_Km_Km' was declared here
nem_alg.c:1626: warning: 'bestCritS.Errinfo.Perm_Kmfac_Km' may be used uninitialized in this function
nem_alg.c:1626: note: 'bestCritS.Errinfo.Perm_Kmfac_Km' was declared here
nem_alg.c:1626: warning: 'bestCritS.Errinfo.Refclas_N_Kr' may be used uninitialized in this function
nem_alg.c:1626: note: 'bestCritS.Errinfo.Refclas_N_Kr' was declared here
nem_alg.c:1626: warning: 'bestCritS.Errinfo.TieRule' may be used uninitialized in this function
nem_alg.c:1626: note: 'bestCritS.Errinfo.TieRule' was declared here
nem_alg.c:1626: warning: 'bestCritS.Errinfo.Kmfac' may be used uninitialized in this function
nem_alg.c:1626: note: 'bestCritS.Errinfo.Kmfac' was declared here
nem_alg.c:1626: warning: 'bestCritS.Errinfo.Km' may be used uninitialized in this function
nem_alg.c:1626: note: 'bestCritS.Errinfo.Km' was declared here
nem_alg.c:1626: warning: 'bestCritS.Errinfo.Kr' may be used uninitialized in this function
nem_alg.c:1626: note: 'bestCritS.Errinfo.Kr' was declared here
nem_alg.c:1626: warning: 'bestCritS.Errinfo.Kc' may be used uninitialized in this function
nem_alg.c:1626: note: 'bestCritS.Errinfo.Kc' was declared here
nem_alg.c:1626: warning: 'bestCritS.Z' may be used uninitialized in this function
nem_alg.c:1626: note: 'bestCritS.Z' was declared here
nem_alg.c:1626: warning: 'bestCritS.G' may be used uninitialized in this function
nem_alg.c:1626: note: 'bestCritS.G' was declared here
nem_alg.c:1626: warning: 'bestCritS.U' may be used uninitialized in this function
nem_alg.c:1626: note: 'bestCritS.U' was declared here
nem_alg.c:1626: warning: 'bestCritS.M' may be used uninitialized in this function
nem_alg.c:1626: note: 'bestCritS.M' was declared here
nem_alg.c:1626: warning: 'bestCritS.D' may be used uninitialized in this function
nem_alg.c:1626: note: 'bestCritS.D' was declared here
nem_alg.c:1626: warning: 'bestCritS.L' may be used uninitialized in this function
nem_alg.c:1626: note: 'bestCritS.L' was declared here
gcc -I"e:/biocbld/bbs-2.5-bioc/R/include"        -O3 -Wall  -std=gnu99 -c nem_hlp.c -o nem_hlp.o
gcc -I"e:/biocbld/bbs-2.5-bioc/R/include"        -O3 -Wall  -std=gnu99 -c nem_mod.c -o nem_mod.o
gcc -I"e:/biocbld/bbs-2.5-bioc/R/include"        -O3 -Wall  -std=gnu99 -c nem_nei.c -o nem_nei.o
gcc -I"e:/biocbld/bbs-2.5-bioc/R/include"        -O3 -Wall  -std=gnu99 -c nem_rnd.c -o nem_rnd.o
gcc -I"e:/biocbld/bbs-2.5-bioc/R/include"        -O3 -Wall  -std=gnu99 -c nem_ver.c -o nem_ver.o
gcc -shared -s -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-2.5-bioc/R/bin -lR
  ... done
** 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 ...
** MD5 sums
* DONE (MANOR)