Package: genArise

Version: 1.30.0

Command: /Library/Frameworks/R.framework/Versions/2.14/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch genArise_1.30.0.tar.gz

StartedAt: 2012-03-24 01:11:00 -0700 (Sat, 24 Mar 2012)

EndedAt: 2012-03-24 01:12:01 -0700 (Sat, 24 Mar 2012)

EllapsedTime: 60.9 seconds

RetCode: 0

Status:  OK

CheckDir: genArise.Rcheck

Warnings: 0

* using log directory '/Users/biocbuild/bbs-2.9-bioc/meat/genArise.Rcheck'
* using R version 2.14.2 (2012-02-29)
* using platform: i386-apple-darwin9.8.0 (32-bit)
* using session charset: ASCII
* using option '--no-vignettes'
* checking for file 'genArise/DESCRIPTION' ... OK
* this is package 'genArise' version '1.30.0'
* 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 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 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
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 sizes of PDF files under 'inst/doc' ... OK
* checking examples ... 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

* installing *source* package 'genArise' ...
** R
** data
** inst
** preparing package for lazy loading
locfit 1.5-6 	 2010-01-20 
** help
*** installing help indices
** building package indices ...
*** tangling vignette sources ...
   'genArise.Rnw' 
** testing if installed package can be loaded
locfit 1.5-6 	 2010-01-20 

* DONE (genArise)

name	user	system	elapsed
Simon	0.061	0.008	0.069
WT.dataset	0.066	0.009	0.074
Zscore	0.836	0.026	0.871
Zscore.plot	0.193	0.011	0.207
a.arise	0.009	0.001	0.010
alter.unique	0.242	0.005	0.249
bg.correct	0.009	0.001	0.011
cys.plot	0.148	0.006	0.156
filter.spot	0.154	0.055	0.210
global.norm	0.051	0.006	0.057
grid.norm	0.161	0.006	0.173
i.arise	0.018	0.013	0.030
imageLimma	0.038	0.004	0.042
m.arise	0.009	0.001	0.010
ma.plot	0.079	0.005	0.085
meanUnique	0.292	0.027	0.321
r.arise	0.008	0.001	0.010
ri.plot	0.086	0.005	0.091
spotUnique	0.262	0.038	0.309
trim	0.000	0.000	0.001
write.dataSet	0.038	0.004	0.042
write.spot	0.083	0.005	0.088
write.zscore	0.068	0.009	0.081