Back to Multiple platform build/check report for BioC 3.6
ABCDEF[G]HIJKLMNOPQRSTUVWXYZ

CHECK report for genArise on tokay1

This page was generated on 2018-04-12 13:17:38 -0400 (Thu, 12 Apr 2018).

Package 528/1472HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
genArise 1.54.0
IFC Development Team
Snapshot Date: 2018-04-11 16:45:18 -0400 (Wed, 11 Apr 2018)
URL: https://git.bioconductor.org/packages/genArise
Branch: RELEASE_3_6
Last Commit: 8733844
Last Changed Date: 2017-10-30 12:39:03 -0400 (Mon, 30 Oct 2017)
malbec1 Linux (Ubuntu 16.04.1 LTS) / x86_64  NotNeeded  OK  OK UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  NotNeeded  OK [ OK ] OK UNNEEDED, same version exists in internal repository
veracruz1 OS X 10.11.6 El Capitan / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: genArise
Version: 1.54.0
Command: rm -rf genArise.buildbin-libdir genArise.Rcheck && mkdir genArise.buildbin-libdir genArise.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=genArise.buildbin-libdir genArise_1.54.0.tar.gz >genArise.Rcheck\00install.out 2>&1 && cp genArise.Rcheck\00install.out genArise-install.out && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=genArise.buildbin-libdir --install="check:genArise-install.out" --force-multiarch --no-vignettes --timings genArise_1.54.0.tar.gz
StartedAt: 2018-04-12 00:10:31 -0400 (Thu, 12 Apr 2018)
EndedAt: 2018-04-12 00:12:10 -0400 (Thu, 12 Apr 2018)
EllapsedTime: 99.4 seconds
RetCode: 0
Status:  OK  
CheckDir: genArise.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf genArise.buildbin-libdir genArise.Rcheck && mkdir genArise.buildbin-libdir genArise.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=genArise.buildbin-libdir genArise_1.54.0.tar.gz >genArise.Rcheck\00install.out 2>&1 && cp genArise.Rcheck\00install.out genArise-install.out  &&  C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=genArise.buildbin-libdir --install="check:genArise-install.out" --force-multiarch --no-vignettes --timings genArise_1.54.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.6-bioc/meat/genArise.Rcheck'
* using R version 3.4.4 (2018-03-15)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'genArise/DESCRIPTION' ... OK
* this is package 'genArise' version '1.54.0'
* 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 whether package 'genArise' can be installed ... 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
* 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
** checking loading without being on the library search path ... 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 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'
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'
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'
Undefined global functions or variables:
  locfit op.counter print.xtable rbox select.experiments tkrplot
  tkrreplot
* 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 files in 'vignettes' ... 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 vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 3 NOTEs
See
  'C:/Users/biocbuild/bbs-3.6-bioc/meat/genArise.Rcheck/00check.log'
for details.



Installation output

genArise.Rcheck/00install.out


install for i386

* installing *source* package 'genArise' ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
  converting help for package 'genArise'
    finding HTML links ... done
    DataSet-class                           html  
    Simon                                   html  
    Spot-class                              html  
    WT.dataset                              html  
    Zscore                                  html  
    Zscore.plot                             html  
    Zscore.points                           html  
    a.arise                                 html  
    alter.unique                            html  
    analysis.window                         html  
    annotations                             html  
    back.gui                                html  
    bg.correct                              html  
    classes                                 html  
    create.project                          html  
    cys.plot                                html  
    filter.spot                             html  
    genArise                                html  
    genArise.init                           html  
    genMerge                                html  
    get.Zscore                              html  
    get.values                              html  
    global.norm                             html  
    graphic.choose                          html  
    grid.norm                               html  
    help                                    html  
    i.arise                                 html  
    imageLimma                              html  
    m.arise                                 html  
    ma.plot                                 html  
    make.swap                               html  
    meanUnique                              html  
    note                                    html  
    old.project                             html  
    post.analysis                           html  
    principal                               html  
    projects.select                         html  
    r.arise                                 html  
    read.dataset                            html  
    read.spot                               html  
    reset.history                           html  
    ri.plot                                 html  
    set.grid.properties                     html  
    set.history.project                     html  
    set.path.project                        html  
    set.project.properties                  html  
    single.norm                             html  
    spotUnique                              html  
    swap.select                             html  
    trim                                    html  
    write.dataSet                           html  
    write.spot                              html  
    write.zscore                            html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL

install for x64

* installing *source* package 'genArise' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'genArise' as genArise_1.54.0.zip
* DONE (genArise)
In R CMD INSTALL
In R CMD INSTALL

Tests output


Example timings

genArise.Rcheck/examples_i386/genArise-Ex.timings

nameusersystemelapsed
Simon0.040.000.03
WT.dataset0.110.020.12
Zscore0.560.000.56
Zscore.plot0.180.000.17
a.arise0.000.020.02
alter.unique0.120.000.13
bg.correct000
cys.plot0.070.000.07
filter.spot0.140.020.16
global.norm0.030.000.03
grid.norm0.050.000.04
i.arise0.010.000.02
imageLimma0.070.000.06
m.arise0.010.000.02
ma.plot0.030.000.03
meanUnique0.180.000.17
r.arise000
ri.plot0.030.000.03
spotUnique0.150.010.17
trim000
write.dataSet0.030.000.04
write.spot0.050.000.04
write.zscore0.050.000.05

genArise.Rcheck/examples_x64/genArise-Ex.timings

nameusersystemelapsed
Simon0.030.010.05
WT.dataset0.060.020.08
Zscore0.70.00.7
Zscore.plot0.160.010.18
a.arise000
alter.unique0.170.000.17
bg.correct0.020.000.02
cys.plot0.080.020.09
filter.spot0.140.020.16
global.norm0.030.000.03
grid.norm0.050.000.05
i.arise0.010.000.01
imageLimma0.110.000.11
m.arise0.000.010.02
ma.plot0.030.000.03
meanUnique0.170.000.17
r.arise000
ri.plot0.030.000.03
spotUnique0.20.00.2
trim0.020.000.02
write.dataSet0.010.000.01
write.spot0.040.020.05
write.zscore0.040.000.05