* using log directory 'D:/biocbld/bbs-2.11-bioc/meat/genArise.Rcheck'
* using R version 2.15.3 (2013-03-01)
* using platform: i386-w64-mingw32 (32-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'genArise/DESCRIPTION' ... OK
* this is package 'genArise' version '1.34.0'
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking whether package 'genArise' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking for portable file names ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over 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
* loading checks for arch 'i386'
** checking whether the package can be loaded ... OK
** checking whether the package can be loaded with stated dependencies ... OK
** checking whether the package can be unloaded cleanly ... OK
** checking whether the namespace can be loaded with stated dependencies ... OK
** checking whether the namespace can be unloaded cleanly ... OK
* loading checks for arch 'x64'
** checking whether the package can be loaded ... OK
** checking whether the package can be loaded with stated dependencies ... OK
** checking whether the package can be unloaded cleanly ... OK
** checking whether the namespace can be loaded with stated dependencies ... OK
** checking whether the namespace can be unloaded cleanly ... 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
genMerge: warning in assign(gene.association.file$V1[i], list(GO =
gene.association.file$V2[i]), env = GMRGgenomehash): partial argument
match of 'env' to 'envir'
genMerge: warning in assign(des.file$V1[i], list(Description =
des.file$V2[i]), env = descriptionHash): partial argument match of
'env' to 'envir'
genMerge: warning in ls(env = GMRGgenomehash): partial argument match
of 'env' to 'envir'
genMerge: warning in get(population.file$V1[i], env = GMRGgenomehash):
partial argument match of 'env' to 'envir'
genMerge: warning in assign(unique.list$values[i], list(count =
unique.list$lengths[i], frequence =
unique.list$lengths[i]/total.no.detected.genes), env = output.hash):
partial argument match of 'env' to 'envir'
genMerge: warning in get(study.genes.file$V1[i], env = GMRGgenomehash):
partial argument match of 'env' to 'envir'
genMerge: warning in get(updownGMRGs[k], env = id.hash): partial
argument match of 'env' to 'envir'
genMerge: warning in assign(updownGMRGs[k], unique.list, env =
id.hash): partial argument match of 'env' to 'envir'
genMerge: warning in assign(updownGMRGs[k], study.genes.file$V1[i], env
= id.hash): partial argument match of 'env' to 'envir'
genMerge: warning in get(output2$uniqueUpDownGMRGIDs[i], env =
output.hash): partial argument match of 'env' to 'envir'
genMerge: warning in get(output2$uniqueUpDownGMRGIDs[k], env =
descriptionHash): partial argument match of 'env' to 'envir'
genMerge: warning in get(output2$uniqueUpDownGMRGIDs[k], env =
id.hash): partial argument match of 'env' to 'envir'
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)
* 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 Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of 'data' directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking installed files from 'inst/doc' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
** running examples for arch 'x64' ... OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in 'inst/doc' ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignettes ... SKIPPED
* checking PDF version of manual ... OK
NOTE: There was 1 note.
See
'D:/biocbld/bbs-2.11-bioc/meat/genArise.Rcheck/00check.log'
for details.