* checking for working pdflatex ... OK
* using log directory '/Users/biocbuild/bbs-2.3-bioc/meat/genArise.Rcheck'
* using R version 2.8.1 Patched (2009-03-18 r48200)
* using session charset: ASCII
* checking for file 'genArise/DESCRIPTION' ... OK
* this is package 'genArise' version '1.18.0'
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking whether package 'genArise' 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 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 ... NOTE
Zscore.points : <anonymous>: possible error in pdf(paste(name, ".pdf",
sep = ""), horiz = FALSE, height = 8, width = 8, title = name):
unused argument(s) (horiz = FALSE)
analysis.window : bg.question: no visible binding for '<<-' assignment
to 'op.counter'
analysis.window : bg.question: no visible binding for global variable
'op.counter'
analysis.window : normalized.gui: no visible binding for '<<-'
assignment to 'op.counter'
analysis.window : normalized.gui: no visible binding for global
variable 'op.counter'
analysis.window : filter.gui: no visible binding for '<<-' assignment
to 'op.counter'
analysis.window : filter.gui: no visible binding for global variable
'op.counter'
analysis.window : remove.duplicates.gui: no visible binding for '<<-'
assignment to 'op.counter'
analysis.window : remove.duplicates.gui: no visible binding for global
variable 'op.counter'
analysis.window : <anonymous>: possible error in pdf(paste(name,
"OriginalCy3vsCy5.pdf", sep = "_"), horiz = F, height = 8, width = 8,
title = paste(name, "OriginalCy3vsCy5.pdf", sep = "_")): unused
argument(s) (horiz = F)
analysis.window : <anonymous>: possible error in pdf(paste(name,
"OriginalRvsI.pdf", sep = "_"), horiz = F, height = 8, width = 8,
title = paste(name, "OriginalRvsI.pdf", sep = "_")): unused
argument(s) (horiz = F)
analysis.window : <anonymous>: possible error in pdf(paste(name,
"OriginalMvsA.pdf", sep = "_"), horiz = F, height = 8, width = 8,
title = paste(name, "OriginalMvsA.pdf", sep = "_")): unused
argument(s) (horiz = F)
analysis.window : <anonymous>: possible error in pdf(paste(name,
"CorrectedCy3vsCy5.pdf", sep = "_"), horiz = F, height = 8, width =
8, title = paste(name, "CorrectedCy3vsCy5.pdf", sep = "_")): unused
argument(s) (horiz = F)
analysis.window : <anonymous>: possible error in pdf(paste(name,
"CorrectedRvsI.pdf", sep = "_"), horiz = F, height = 8, width = 8,
title = paste(name, "CorrectedRvsI.pdf", sep = "_")): unused
argument(s) (horiz = F)
analysis.window : <anonymous>: possible error in pdf(paste(name,
"CorrectedMvsA.pdf", sep = "_"), horiz = F, height = 8, width = 8,
title = paste(name, "CorrectedMvsA.pdf", sep = "_")): unused
argument(s) (horiz = F)
analysis.window : <anonymous>: possible error in pdf(paste(name,
"NormalCy3vsCy5.pdf", sep = "_"), horiz = F, height = 8, width = 8,
title = paste(name, "NormalCy3vsCy5.pdf", sep = "_")): unused
argument(s) (horiz = F)
analysis.window : <anonymous>: possible error in pdf(paste(name,
"NormalRvsI.pdf", sep = "_"), horiz = F, height = 8, width = 8, title
= paste(name, "NormalRvsI.pdf", sep = "_")): unused argument(s)
(horiz = F)
analysis.window : <anonymous>: possible error in pdf(paste(name,
"NormalMvsA.pdf", sep = "_"), horiz = F, height = 8, width = 8, title
= paste(name, "NormalMvsA.pdf", sep = "_")): unused argument(s)
(horiz = F)
analysis.window : <anonymous>: possible error in pdf(paste(name,
"FilterCy3vsCy5.pdf", sep = "_"), horiz = F, height = 8, width = 8,
title = paste(name, "FilterCy3vsCy5.pdf", sep = "_")): unused
argument(s) (horiz = F)
analysis.window : <anonymous>: possible error in pdf(paste(name,
"FilterRvsI.pdf", sep = "_"), horiz = F, height = 8, width = 8, title
= paste(name, "FilterRvsI.pdf", sep = "_")): unused argument(s)
(horiz = F)
analysis.window : <anonymous>: possible error in pdf(paste(name,
"FilterMvsA.pdf", sep = "_"), horiz = F, height = 8, width = 8, title
= paste(name, "FilterMvsA.pdf", sep = "_")): unused argument(s)
(horiz = F)
analysis.window : <anonymous>: possible error in pdf(paste(name,
"NoDuplicatesCy3vsCy5.pdf", sep = "_"), horiz = F, height = 8, width
= 8, title = paste(name, "NoDuplicatesCy3vsCy5.pdf", sep = "_")):
unused argument(s) (horiz = F)
analysis.window : <anonymous>: possible error in pdf(paste(name,
"NoDuplicatesRvsI.pdf", sep = "_"), horiz = F, height = 8, width = 8,
title = paste(name, "NoDuplicatesRvsI.pdf", sep = "_")): unused
argument(s) (horiz = F)
analysis.window : <anonymous>: possible error in pdf(paste(name,
"NoDuplicatesMvsA.pdf", sep = "_"), horiz = F, height = 8, width = 8,
title = paste(name, "NoDuplicatesMvsA.pdf", sep = "_")): unused
argument(s) (horiz = F)
analysis.window: no visible binding for '<<-' assignment to
'op.counter'
analysis.window: no visible binding for global variable 'op.counter'
annotations: no visible global function definition for 'print.xtable'
genArise.init: no visible binding for '<<-' assignment to 'op.counter'
genArise.init : nuevo.project: no visible global function definition
for 'select.experiments'
old.project : save.pdf: possible error in pdf(name, horiz = F, height =
8, width = 8, title = paste(name, sep = "_")): unused argument(s)
(horiz = F)
old.project : <anonymous>: possible error in pdf(paste(name, ".pdf",
sep = ""), horiz = FALSE, height = 8, width = 8, title = name):
unused argument(s) (horiz = FALSE)
principal : save.as.pdf: possible error in pdf(paste(name, "R&G.pdf",
sep = "_"), horiz = F, height = 8, width = 8, title = paste(name,
"R&G.pdf", sep = "_")): unused argument(s) (horiz = F)
principal : save.as.pdf: possible error in pdf(paste(name, "BgCy5.pdf",
sep = "_"), horiz = F, height = 8, width = 8, title = paste(name,
"BgCy5.pdf", sep = "_")): unused argument(s) (horiz = F)
principal : save.as.pdf: possible error in pdf(paste(name, "BgCy3.pdf",
sep = "_"), horiz = F, height = 8, width = 8, title = paste(name,
"BgCy3.pdf", sep = "_")): unused argument(s) (horiz = F)
principal : save.as.pdf: possible error in pdf(paste(name, "Swap.pdf",
sep = "_"), horiz = F, height = 8, width = 8, title = paste(name,
"Swap.pdf", sep = "_")): unused argument(s) (horiz = F)
Found possibly global 'T' or 'F' in the following functions:
analysis.window old.project principal
* 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
* creating genArise-Ex.R ... OK
* checking examples ... OK
* checking package vignettes in 'inst/doc' ... OK
* creating genArise-manual.tex ... OK
* checking genArise-manual.tex using pdflatex ... OK