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Package 76/233HostnameOS / ArchBUILDCHECKBUILD BIN
genArise 1.14.0
IFC Development Team
Snapshot Date: 2008-04-09 12:13:20 -0700 (Wed, 09 Apr 2008)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_1/madman/Rpacks/genArise
Last Changed Rev: 27709 / Revision: 30966
Last Changed Date: 2007-10-02 17:41:09 -0700 (Tue, 02 Oct 2007)
lamb1 Linux (SUSE 10.1) / x86_64  OK  OK 
wilson2 Linux (openSUSE 10.3) / x86_64  OK  OK 
wellington Linux (openSUSE 10.3) / i686  OK  OK 
liverpool Windows Server 2003 R2 (32-bit) / x64  OK  OK  OK 
lemming Windows Server 2003 (32-bit) / x64  OK [ OK ] OK 
pitt Mac OS X Tiger (10.4.11) / i386  OK  OK  OK 
Package: genArise
Version: 1.14.0
Command: D:\biocbld\bbs-2.1-bioc\R\bin\R.exe CMD check genArise_1.14.0.tar.gz
StartedAt: 2008-04-09 19:19:16 -0700 (Wed, 09 Apr 2008)
EndedAt: 2008-04-09 19:21:59 -0700 (Wed, 09 Apr 2008)
EllapsedTime: 163.8 seconds
RetCode: 0
Status: OK
CheckDir: genArise.Rcheck
Warnings: 0

Command output

* checking for working latex ... OK
* using log directory 'D:/biocbld/bbs-2.1-bioc/meat/genArise.Rcheck'
* using R version 2.6.2 (2008-02-08)
* checking for file 'genArise/DESCRIPTION' ... OK
* this is package 'genArise' version '1.14.0'
* 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 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
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)
Zscore.points : <anonymous>: possible error in pdf(paste(name, ".pdf",
  sep = ""), horiz = FALSE, height = 8, width = 8, title = name):
  unused argument(s) (horiz = FALSE)
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 ... OK

genArise.Rcheck/00install.out:

installing R.css in D:/biocbld/bbs-2.1-bioc/meat/genArise.Rcheck


---------- Making package genArise ------------
  adding build stamp to DESCRIPTION
  installing R files
  installing inst files
  installing data files
  installing man source files
  installing indices
  not zipping data
  installing help
 >>> Building/Updating help pages for package 'genArise'
     Formats: text html latex example chm 
  DataSet-class                     text    html    latex           chm
  Simon                             text    html    latex   example chm
  Spot-class                        text    html    latex           chm
  WT.dataset                        text    html    latex   example chm
  Zscore                            text    html    latex   example chm
  Zscore.plot                       text    html    latex   example chm
  Zscore.points                     text    html    latex           chm
  a.arise                           text    html    latex   example chm
  alter.unique                      text    html    latex   example chm
  analysis.window                   text    html    latex           chm
  annotations                       text    html    latex           chm
  back.gui                          text    html    latex           chm
  bg.correct                        text    html    latex   example chm
  classes                           text    html    latex           chm
  create.project                    text    html    latex           chm
  cys.plot                          text    html    latex   example chm
  filter.spot                       text    html    latex   example chm
  genArise                          text    html    latex           chm
  genArise.init                     text    html    latex           chm
  genMerge                          text    html    latex           chm
  get.Zscore                        text    html    latex           chm
  get.values                        text    html    latex           chm
  global.norm                       text    html    latex   example chm
  graphic.choose                    text    html    latex           chm
  grid.norm                         text    html    latex   example chm
  help                              text    html    latex           chm
  i.arise                           text    html    latex   example chm
  imageLimma                        text    html    latex   example chm
  m.arise                           text    html    latex   example chm
  ma.plot                           text    html    latex   example chm
  make.swap                         text    html    latex           chm
  meanUnique                        text    html    latex   example chm
  note                              text    html    latex           chm
  old.project                       text    html    latex           chm
  post.analysis                     text    html    latex           chm
  principal                         text    html    latex           chm
  projects.select                   text    html    latex           chm
  r.arise                           text    html    latex   example chm
  read.dataset                      text    html    latex           chm
  read.spot                         text    html    latex           chm
  reset.history                     text    html    latex           chm
  ri.plot                           text    html    latex   example chm
  set.grid.properties               text    html    latex           chm
  set.history.project               text    html    latex           chm
  set.path.project                  text    html    latex           chm
  set.project.properties            text    html    latex           chm
  single.norm                       text    html    latex           chm
  spotUnique                        text    html    latex   example chm
  swap.select                       text    html    latex           chm
  trim                              text    html    latex   example chm
  write.dataSet                     text    html    latex   example chm
  write.spot                        text    html    latex   example chm
  write.zscore                      text    html    latex   example chm
HHC5012: Error: Cannot create a temporary file in your TEMP path.
HHC4016: Warning: Cannot open "Files\Affymetrix\GDAC NetAffx;c:\gs\gs8.51\bin;c:\Program Files\Java\jdk1.5.0_06\bin;c:\program files\imagemagick-6.3.2-q16;c:\Program Files\MySQL\MySQL Server 5.0\bin;c:\Program Files\ggobi".
Microsoft HTML Help Compiler 4.74.8702

Compiling d:\biocbld\bbs-2.1-bioc\meat\genArise.Rcheck\00_pkg_src\genArise\chm\genArise.chm

HHC4016: Warning: Cannot open "Files\Affymetrix\GDAC NetAffx;c:\gs\gs8.51\bin;c:\Program Files\Java\jdk1.5.0_06\bin;c:\program files\imagemagick-6.3.2-q16;c:\Program Files\MySQL\MySQL Server 5.0\bin;c:\Program Files\ggobi".


The following files were not compiled:
  preparing package genArise for lazy loading
Loading required package: locfit
Loading required package: akima
Loading required package: lattice
Loading required package: tkrplot
Loading required package: tcltk
Loading Tcl/Tk interface ... done
Loading required package: xtable
  adding MD5 sums

* DONE (genArise)