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 '/Users/biocbuild/bbs-2.2-bioc/meat/reb.Rcheck'
* using R version 2.7.0 beta (2008-04-07 r45159)
* using session charset: ASCII
* 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 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 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
/Users/biocbuild/bbs-2.2-bioc/meat/reb.Rcheck/00check.log
for details
* Installing *source* package 'reb' ...
** libs
** arch - i386
gcc-4.2 -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -I/usr/local/include -fPIC -g -O2 -march=nocona -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'
gcc-4.2 -arch i386 -std=gnu99 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -o reb.so movbin.o -F/Library/Frameworks/R.framework/.. -framework R -lintl -liconv -lc -Wl,-framework -Wl,CoreFoundation
** arch - ppc
gcc-4.2 -arch ppc -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/ppc -I/usr/local/include -fPIC -g -O2 -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'
gcc-4.2 -arch ppc -std=gnu99 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -o reb.so movbin.o -F/Library/Frameworks/R.framework/.. -framework R -lintl -liconv -lc -Wl,-framework -Wl,CoreFoundation
** arch - x86_64
gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64 -I/usr/local/include -fPIC -g -O2 -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'
gcc-4.2 -arch x86_64 -std=gnu99 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -o reb.so movbin.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
** R
** data
** inst
** help
Note: removing empty section \value
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: removing empty section \note
>>> Building/Updating help pages for package 'reb'
Formats: text html latex example
Hs.arms text html latex
absMax text html latex example
buildChromCytoband text html latex example
buildChromMap text html latex example
cset2band text html latex example
fromRevIsh text html latex example
isAbnormal text html latex example
mcr.eset text html latex example
movbin text html latex example
movt text html latex example
naMean text html latex example
regmap text html latex example
revish text html latex example
rmAmbigMappings text html latex example
smoothByRegion text html latex example
summarizeByRegion text html latex example
tBinomTest text html latex example
writeGFF3 text html latex example
** building package indices ...
* DONE (reb)