MANOR 1.14.0
Pierre Neuvial
| Bioconductor Changelog | | Snapshot Date: 2009-04-18 11:27:48 -0700 (Sat, 18 Apr 2009) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_3/madman/Rpacks/MANOR | | Last Changed Rev: 34811 / Revision: 38965 | | Last Changed Date: 2008-10-21 15:32:58 -0700 (Tue, 21 Oct 2008) |
| 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 (10.5.6) / i386 | OK | OK | OK |
* checking for working pdflatex ... OK
* using log directory 'E:/biocbld/bbs-2.3-bioc/meat/MANOR.Rcheck'
* using R version 2.8.1 (2008-12-22)
* using session charset: ISO8859-1
* checking for file 'MANOR/DESCRIPTION' ... OK
* this is package 'MANOR' version '1.14.0'
* 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 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 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
* creating MANOR-Ex.R ... OK
* checking examples ... OK
* checking package vignettes in 'inst/doc' ... OK
* creating MANOR-manual.tex ... OK
* checking MANOR-manual.tex using pdflatex ... OK
installing R.css in E:/biocbld/bbs-2.3-bioc/meat/MANOR.Rcheck
---------- Making package MANOR ------------
adding build stamp to DESCRIPTION
making DLL ...
making Rnem_arg.d from Rnem_arg.c
making Rnem_exe.d from Rnem_exe.c
making exememo.d from exememo.c
making lib_io.d from lib_io.c
making nem_alg.d from nem_alg.c
making nem_hlp.d from nem_hlp.c
making nem_mod.d from nem_mod.c
making nem_nei.d from nem_nei.c
making nem_rnd.d from nem_rnd.c
making nem_ver.d from nem_ver.c
gcc -std=gnu99 -Ie:/biocbld/bbs-2.3-bioc/R/include -O3 -Wall -c Rnem_arg.c -o Rnem_arg.o
gcc -std=gnu99 -Ie:/biocbld/bbs-2.3-bioc/R/include -O3 -Wall -c Rnem_exe.c -o Rnem_exe.o
gcc -std=gnu99 -Ie:/biocbld/bbs-2.3-bioc/R/include -O3 -Wall -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 -std=gnu99 -Ie:/biocbld/bbs-2.3-bioc/R/include -O3 -Wall -c lib_io.c -o lib_io.o
lib_io.c: In function 'CountLinesColumns':
lib_io.c:354: warning: 'maxcols' may be used uninitialized in this function
lib_io.c:354: warning: 'mincols' may be used uninitialized in this function
gcc -std=gnu99 -Ie:/biocbld/bbs-2.3-bioc/R/include -O3 -Wall -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
nem_alg.c:1631: warning: 'bestbeta' may be used uninitialized in this function
nem_alg.c:1631: note: 'bestbeta' was declared here
gcc -std=gnu99 -Ie:/biocbld/bbs-2.3-bioc/R/include -O3 -Wall -c nem_hlp.c -o nem_hlp.o
gcc -std=gnu99 -Ie:/biocbld/bbs-2.3-bioc/R/include -O3 -Wall -c nem_mod.c -o nem_mod.o
gcc -std=gnu99 -Ie:/biocbld/bbs-2.3-bioc/R/include -O3 -Wall -c nem_nei.c -o nem_nei.o
gcc -std=gnu99 -Ie:/biocbld/bbs-2.3-bioc/R/include -O3 -Wall -c nem_rnd.c -o nem_rnd.o
gcc -std=gnu99 -Ie:/biocbld/bbs-2.3-bioc/R/include -O3 -Wall -c nem_ver.c -o nem_ver.o
windres --preprocessor="gcc -E -xc -DRC_INVOKED" -I e:/biocbld/bbs-2.3-bioc/R/include -i MANOR_res.rc -o MANOR_res.o
gcc -std=gnu99 -shared -s -o MANOR.dll MANOR.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 MANOR_res.o -Le:/biocbld/bbs-2.3-bioc/R/bin -lR
... DLL made
installing DLL
installing R files
installing inst files
installing data files
preparing package MANOR for lazy loading
Loading required package: GLAD
installing man source files
installing indices
not zipping data
installing help
>>> Building/Updating help pages for package 'MANOR'
Formats: text html latex example chm
MANOR-internal text html latex chm
Note: ignoring empty \keyword entries in file 'arrayTrend.Rd'
Note: ignoring empty \keyword entries in file 'arrayTrend.Rd'
arrayTrend text html latex example chm
Note: ignoring empty \keyword entries in file 'detectSB.Rd'
Note: ignoring empty \keyword entries in file 'detectSB.Rd'
detectSB text html latex example chm
Note: ignoring empty \keyword entries in file 'flag.Rd'
Note: ignoring empty \keyword entries in file 'flag.Rd'
flag text html latex example chm
Note: ignoring empty \keyword entries in file 'flag.arrayCGH.Rd'
Note: ignoring empty \keyword entries in file 'flag.arrayCGH.Rd'
flag.arrayCGH text html latex example chm
Note: ignoring empty \keyword entries in file 'flag.summary.Rd'
Note: ignoring empty \keyword entries in file 'flag.summary.Rd'
flag.summary text html latex example chm
flags text html latex example chm
Note: ignoring empty \keyword entries in file 'genome.plot.Rd'
Note: ignoring empty \keyword entries in file 'genome.plot.Rd'
genome.plot text html latex example chm
Note: ignoring empty \keyword entries in file 'html.report.Rd'
Note: removing empty section \examples in file 'html.report.Rd'
Note: ignoring empty \keyword entries in file 'html.report.Rd'
Note: removing empty section \examples in file 'html.report.Rd'
html.report text html latex chm
Note: ignoring empty \keyword entries in file 'import.Rd'
Note: ignoring empty \keyword entries in file 'import.Rd'
import text html latex example chm
Note: ignoring empty \keyword entries in file 'nem.Rd'
Note: ignoring empty \keyword entries in file 'nem.Rd'
nem text html latex example chm
Note: ignoring empty \keyword entries in file 'norm.arrayCGH.Rd'
Note: ignoring empty \keyword entries in file 'norm.arrayCGH.Rd'
norm.arrayCGH text html latex example chm
Note: ignoring empty \keyword entries in file 'qscore.Rd'
Note: removing empty section \details in file 'qscore.Rd'
Note: removing empty section \examples in file 'qscore.Rd'
Note: ignoring empty \keyword entries in file 'qscore.Rd'
Note: removing empty section \details in file 'qscore.Rd'
Note: removing empty section \examples in file 'qscore.Rd'
qscore text html latex chm
Note: ignoring empty \keyword entries in file 'qscore.arrayCGH.Rd'
Note: ignoring empty \keyword entries in file 'qscore.arrayCGH.Rd'
qscore.arrayCGH text html latex example chm
Note: ignoring empty \keyword entries in file 'qscore.summary.Rd'
Note: ignoring empty \keyword entries in file 'qscore.summary.Rd'
qscore.summary text html latex example chm
qscores text html latex example chm
Note: ignoring empty \keyword entries in file 'report.plot.Rd'
Note: ignoring empty \keyword entries in file 'report.plot.Rd'
report.plot text html latex example chm
Note: ignoring empty \keyword entries in file 'sort.arrayCGH.Rd'
Note: ignoring empty \keyword entries in file 'sort.arrayCGH.Rd'
sort.arrayCGH text html latex example chm
spatial text html latex example chm
Microsoft HTML Help Compiler 4.74.8702
Compiling e:\biocbld\bbs-2.3-bioc\meat\MANOR.Rcheck\00_pkg_src\MANOR\chm\MANOR.chm
Compile time: 0 minutes, 1 second
20 Topics
121 Local links
20 Internet links
1 Graphic
Created e:\biocbld\bbs-2.3-bioc\meat\MANOR.Rcheck\00_pkg_src\MANOR\chm\MANOR.chm, 50,450 bytes
Compression decreased file by 62,403 bytes.
adding MD5 sums
* DONE (MANOR)