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BioC 3.0: CHECK report for genArise on perceval

This page was generated on 2015-04-10 09:52:19 -0700 (Fri, 10 Apr 2015).

Package 342/933HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
genArise 1.42.0
IFC Development Team
Snapshot Date: 2015-04-09 16:20:12 -0700 (Thu, 09 Apr 2015)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_0/madman/Rpacks/genArise
Last Changed Rev: 95439 / Revision: 102249
Last Changed Date: 2014-10-13 14:38:33 -0700 (Mon, 13 Oct 2014)
zin1 Linux (Ubuntu 12.04.4 LTS) / x86_64  NotNeeded  OK  OK 
moscato1 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  NotNeeded  OK  OK  OK 
perceval Mac OS X Snow Leopard (10.6.8) / x86_64  NotNeeded  OK [ OK ] OK 
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK  OK  OK 

Summary

Package: genArise
Version: 1.42.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch genArise_1.42.0.tar.gz
StartedAt: 2015-04-10 01:49:41 -0700 (Fri, 10 Apr 2015)
EndedAt: 2015-04-10 01:50:42 -0700 (Fri, 10 Apr 2015)
EllapsedTime: 61.1 seconds
RetCode: 0
Status:  OK 
CheckDir: genArise.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch genArise_1.42.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.0-bioc/meat/genArise.Rcheck’
* using R version 3.1.3 (2015-03-09)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘genArise/DESCRIPTION’ ... OK
* this is package ‘genArise’ version ‘1.42.0’
* 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 for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘genArise’ can be installed ... [3s/4s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Package listed in more than one of Depends, Imports, Suggests, Enhances:
  ‘methods’
A package should be listed in only one of these fields.
* 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
* 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 loading without being on the library search path ... OK
* checking dependencies in R code ... NOTE
Packages in Depends field not imported from:
  ‘locfit’ ‘tkrplot’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
* 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'
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 : normalized.gui: no visible global function definition
  for ‘tkrreplot’
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 : filter.gui: no visible global function definition for
  ‘tkrreplot’
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 : remove.duplicates.gui: no visible global function
  definition for ‘tkrreplot’
analysis.window : <anonymous>: no visible global function definition
  for ‘tkrreplot’
analysis.window : cys.plot: no visible global function definition for
  ‘tkrreplot’
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 (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
  (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
  (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 (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
  (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
  (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 (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 (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 (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 (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 (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 (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 (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 (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 (horiz = F)
analysis.window: no visible global function definition for ‘tkrplot’
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’
global.norm: no visible global function definition for ‘locfit’
global.norm: no visible global function definition for ‘rbox’
grid.norm: no visible global function definition for ‘locfit’
grid.norm: no visible global function definition for ‘rbox’
old.project : selected.zscore: no visible global function definition
  for ‘tkrreplot’
old.project : save.pdf: possible error in pdf(name, horiz = F, height =
  8, width = 8, title = paste(name, sep = "_")): unused argument (horiz
  = F)
old.project : imageLimma.plot: no visible global function definition
  for ‘tkrreplot’
old.project : otra.funcion: no visible global function definition for
  ‘tkrreplot’
old.project: no visible global function definition for ‘tkrplot’
old.project : <anonymous>: no visible global function definition for
  ‘tkrreplot’
old.project : <anonymous>: possible error in pdf(paste(name, ".pdf",
  sep = ""), horiz = FALSE, height = 8, width = 8, title = name):
  unused argument (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 (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 (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 (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 (horiz = F)
principal: no visible global function definition for ‘tkrplot’
principal : <anonymous>: no visible global function definition for
  ‘tkrreplot’
Zscore.points : <anonymous>: no visible global function definition for
  ‘tkrreplot’
Zscore.points : <anonymous>: possible error in pdf(paste(name, ".pdf",
  sep = ""), horiz = FALSE, height = 8, width = 8, title = name):
  unused argument (horiz = FALSE)
Zscore.points: no visible global function definition for ‘tkrplot’
* 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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [3s/4s] 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 vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

NOTE: There were 3 notes.
See
  ‘/Users/biocbuild/bbs-3.0-bioc/meat/genArise.Rcheck/00check.log’
for details.

genArise.Rcheck/00install.out:

* installing *source* package ‘genArise’ ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (genArise)

genArise.Rcheck/genArise-Ex.timings:

nameusersystemelapsed
Simon0.0830.0070.089
WT.dataset0.0400.0060.052
Zscore0.6620.0980.749
Zscore.plot0.1180.0050.142
a.arise0.0050.0010.005
alter.unique0.1590.0230.177
bg.correct0.0040.0010.005
cys.plot0.0960.0050.473
filter.spot0.1130.0570.166
global.norm0.0270.0020.029
grid.norm0.0730.0090.079
i.arise0.0130.0120.025
imageLimma0.0230.0020.036
m.arise0.0050.0010.005
ma.plot0.0320.0030.043
meanUnique0.2240.0380.257
r.arise0.0040.0010.005
ri.plot0.0370.0030.048
spotUnique0.2210.0470.262
trim0.0000.0000.001
write.dataSet0.0220.0030.025
write.spot0.0980.0040.101
write.zscore0.0600.0030.063