reb 1.13.0
Karl J. Dykema
| Snapshot Date: 2008-04-09 00:13:10 -0700 (Wed, 09 Apr 2008) | | URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/reb | | Last Changed Rev: 29380 / Revision: 30951 | | Last Changed Date: 2008-01-04 05:00:43 -0800 (Fri, 04 Jan 2008) |
| lamb1 | Linux (SUSE 10.1) / x86_64 | OK | WARNINGS | |
| wilson2 | Linux (openSUSE 10.3) / x86_64 | OK | WARNINGS | |
| wellington | Linux (openSUSE 10.3) / i686 | ERROR | skipped | |
| liverpool | Windows Server 2003 R2 (32-bit) / x64 | OK | [ WARNINGS ] | OK |
| pelham | Mac OS X Leopard (10.5.1) / i386 | OK | WARNINGS | OK |
* checking for working pdflatex ... OK
* using log directory 'E:/biocbld/bbs-2.2-bioc/meat/reb.Rcheck'
* using R version 2.7.0 Under development (unstable) (2008-03-10 r44730)
* using session charset: ISO8859-1
* checking for file 'reb/DESCRIPTION' ... OK
* this is package 'reb' version '1.13.0'
* checking package name space information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking whether package 'reb' 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 cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... WARNING
Codoc mismatches from documentation object 'summarizeByRegion':
cgma
Code: function(eset, genome, chrom = "ALL", ref = NULL, center =
TRUE, aggrfun = NULL, p.value = 0.005, FUN = t.test,
verbose = TRUE, explode = FALSE, ...)
Docs: function(eset, genome, chrom = "ALL", ref = NULL, center =
TRUE, aggrfun = NULL, p.value = 0.005, FUN = t.test,
explode = FALSE, ...)
Argument names in code not in docs:
verbose
Mismatches in argument names:
Position: 9 Code: verbose Docs: explode
Position: 10 Code: explode Docs: ...
* 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 reb-Ex.R ... OK
* checking examples ... OK
* checking package vignettes in 'inst/doc' ... OK
* creating reb-manual.tex ... OK
* checking reb-manual.tex using pdflatex ... OK
WARNING: There was 1 warning, see
E:/biocbld/bbs-2.2-bioc/meat/reb.Rcheck/00check.log
for details
installing R.css in E:/biocbld/bbs-2.2-bioc/meat/reb.Rcheck
---------- Making package reb ------------
adding build stamp to DESCRIPTION
installing NAMESPACE file and metadata
making DLL ...
making movbin.d from movbin.c
gcc -std=gnu99 -Ie:/biocbld/bbs-2.2-bioc/R/include -O3 -Wall -c movbin.c -o movbin.o
movbin.c: In function 'bcount':
movbin.c:37: warning: suggest parentheses around comparison in operand of &
movbin.c: In function 'bscore':
movbin.c:48: warning: implicit declaration of function 'sqrt'
movbin.c:48: warning: incompatible implicit declaration of built-in function 'sqrt'
movbin.c: In function 'mean':
movbin.c:63: warning: suggest parentheses around comparison in operand of &
movbin.c: In function 'mspan_mov_binom_mx':
movbin.c:128: warning: unused variable 'im_mx'
movbin.c: In function 'mspan_mov_binom':
movbin.c:145: warning: unused variable 'c'
movbin.c:145: warning: unused variable 'r'
movbin.c: In function 'main':
movbin.c:168: warning: unused variable 'nr'
movbin.c:166: warning: unused variable 'rlen'
movbin.c:163: warning: unused variable 'range'
movbin.c:162: warning: unused variable 'sum_mx'
movbin.c:162: warning: unused variable 'sum_vec'
movbin.c:161: warning: unused variable 'im_mx'
movbin.c:161: warning: unused variable 'im_vec'
movbin.c:160: warning: unused variable 'gx2'
movbin.c:158: warning: unused variable 'data'
windres --preprocessor="gcc -E -xc -DRC_INVOKED" -I e:/biocbld/bbs-2.2-bioc/R/include -i reb_res.rc -o reb_res.o
gcc -std=gnu99 -shared -s -o reb.dll reb.def movbin.o reb_res.o -Le:/biocbld/bbs-2.2-bioc/R/bin -lR
... DLL made
installing DLL
installing R files
installing inst files
installing data files
installing man source files
installing indices
not zipping data
installing help
Note: removing empty section \value
Note: removing empty section \value
Note: removing empty section \note
Note: removing empty section \note
Note: unmatched right brace in 'regmap' on or after line 15
Note: removing empty section \value
Note: removing empty section \note
Note: removing empty section \references
Note: unmatched right brace in 'regmap.Rd' on or after line 15
Note: removing empty section \value
Note: removing empty section \note
Note: removing empty section \references
Note: removing empty section \note
Note: removing empty section \note
>>> Building/Updating help pages for package 'reb'
Formats: text html latex example chm
Hs.arms text html latex chm
absMax text html latex example chm
buildChromCytoband text html latex example chm
buildChromMap text html latex example chm
cset2band text html latex example chm
fromRevIsh text html latex example chm
isAbnormal text html latex example chm
mcr.eset text html latex example chm
movbin text html latex example chm
movt text html latex example chm
naMean text html latex example chm
regmap text html latex example chm
revish text html latex example chm
rmAmbigMappings text html latex example chm
smoothByRegion text html latex example chm
summarizeByRegion text html latex example chm
tBinomTest text html latex example chm
writeGFF3 text html latex example chm
Microsoft HTML Help Compiler 4.74.8702
Compiling e:\biocbld\bbs-2.2-bioc\meat\reb.Rcheck\00_pkg_src\reb\chm\reb.chm
Compile time: 0 minutes, 0 seconds
19 Topics
51 Local links
0 Internet links
1 Graphic
Created e:\biocbld\bbs-2.2-bioc\meat\reb.Rcheck\00_pkg_src\reb\chm\reb.chm, 39,534 bytes
Compression decreased file by 22,759 bytes.
adding MD5 sums
* DONE (reb)