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CHECK report for explorase on tokay2

This page was generated on 2019-04-09 11:55:54 -0400 (Tue, 09 Apr 2019).

Package 521/1703HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
explorase 1.47.0
Michael Lawrence
Snapshot Date: 2019-04-08 17:01:18 -0400 (Mon, 08 Apr 2019)
URL: https://git.bioconductor.org/packages/explorase
Branch: master
Last Commit: 5552cea
Last Changed Date: 2018-10-30 11:54:27 -0400 (Tue, 30 Oct 2018)
malbec2 Linux (Ubuntu 18.04.2 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository
celaya2 OS X 10.11.6 El Capitan / x86_64 ...NOT SUPPORTED...
merida2 OS X 10.11.6 El Capitan / x86_64 ...NOT SUPPORTED...

Summary

Package: explorase
Version: 1.47.0
Command: C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe --arch i386 CMD check --no-multiarch --install=check:explorase.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings explorase_1.47.0.tar.gz
StartedAt: 2019-04-09 02:39:16 -0400 (Tue, 09 Apr 2019)
EndedAt: 2019-04-09 02:40:09 -0400 (Tue, 09 Apr 2019)
EllapsedTime: 53.3 seconds
RetCode: 0
Status:  OK  
CheckDir: explorase.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe --arch i386 CMD check --no-multiarch --install=check:explorase.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings explorase_1.47.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.9-bioc/meat/explorase.Rcheck'
* using R Under development (unstable) (2019-03-09 r76216)
* using platform: i386-w64-mingw32 (32-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'explorase/DESCRIPTION' ... OK
* this is package 'explorase' version '1.47.0'
* 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 ... NOTE
Found the following hidden files and directories:
  .BBSoptions
These were most likely included in error. See section 'Package
structure' in the 'Writing R Extensions' manual.
* checking for portable file names ... OK
* checking whether package 'explorase' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Description field: should contain one or more complete sentences.
* 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 dependencies in R code ... NOTE
'library' or 'require' call to 'cairoDevice' in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
aggregateReps: warning in exp_designFrame(treatment = TRUE): partial
  argument match of 'treatment' to 'treatments_only'
exp_showPatterns: warning in addInfoColumns(cbind(patterns,
  pattern_frm)[sync, , drop = F], type, update = F): partial argument
  match of 'update' to 'update_view'
findPatternWindow: warning in gtkButton(stock = "gtk-find"): partial
  argument match of 'stock' to 'stock.id'
findPatternWindow: warning in gtkButton(stock = "gtk-refresh"): partial
  argument match of 'stock' to 'stock.id'
MnuCompareCorr_cb: no visible binding for global variable 'cor'
MnuCompareCov_cb: no visible binding for global variable 'cov'
MnuHClust : <anonymous>: no visible global function definition for
  'hclust'
MnuHClust: no visible global function definition for 'as.dist'
MnuHClust_canberra_cb : <anonymous>: no visible global function
  definition for 'dist'
MnuHClust_euclidean_cb: no visible binding for global variable 'dist'
MnuHClust_euclidean_std_cb : <anonymous>: no visible global function
  definition for 'dist'
MnuHClust_spearman_cb : <anonymous>: no visible global function
  definition for 'dist'
MnuSaveEntityInfo_cb: no visible global function definition for
  'write.table'
MnuSaveEntityLists_cb : <anonymous>: no visible global function
  definition for 'write.csv'
MnuSaveProject_cb : <anonymous>: no visible global function definition
  for 'write.csv'
applyLimma_cb: no visible global function definition for 'model.matrix'
applyLimma_cb : fitContrast: no visible global function definition for
  'p.adjust'
applyLimma_cb : fitContrast: no visible global function definition for
  'fitted'
applyTemporal_cb: no visible global function definition for 'terms'
applyTemporal_cb: no visible global function definition for
  'as.formula'
applyTemporal_cb : <anonymous>: no visible global function definition
  for 'lm'
applyTemporal_cb : <anonymous>: no visible global function definition
  for 'coef'
applyTemporal_cb : <anonymous>: no visible global function definition
  for 'pf'
browseBtn_cb: no visible global function definition for 'browseURL'
calcMinRepVar: no visible binding for global variable 'var'
color.click.dn: no visible global function definition for 'identify'
exp_calcMahalanobisDist: no visible global function definition for
  'var'
exp_calcResiduals: no visible global function definition for 'lm'
exp_calcResiduals: no visible global function definition for 'var'
exp_expressionSet: no visible global function definition for 'new'
exp_featureData: no visible global function definition for 'as'
exp_loadDesign: no visible global function definition for 'is'
exp_loadDesign: no visible global function definition for 'pData'
exp_loadExpressionSet: no visible global function definition for
  'phenoData'
exp_loadExpressionSet: no visible global function definition for
  'featureData'
exp_loadExpressionSet: no visible global function definition for
  'exprs'
exp_loadFiles: no visible binding for global variable 'read.csv'
exp_loadFiles : <anonymous>: no visible global function definition for
  'read.csv'
exp_loadInfo: no visible global function definition for 'is'
exp_loadInfo: no visible global function definition for 'pData'
exp_phenoData: no visible global function definition for 'as'
exp_showClustering: no visible global function definition for 'Cairo'
explorase: no visible global function definition for 'is'
explorase: no visible global function definition for 'exp_loadNetwork'
findExtensions: no visible global function definition for 'tail'
getExploraseVersion: no visible global function definition for
  'installed.packages'
ggobiTreeWindow : <anonymous>: no visible global function definition
  for 'dev.off'
gobi.plot.tree: no visible global function definition for 'dev.cur'
gobitreeco: no visible global function definition for 'dev.cur'
gobitreepl: no visible global function definition for 'lines'
gobitreepl: no visible global function definition for 'par'
gobitreepl: no visible global function definition for 'plot'
gobitreepl: no visible global function definition for 'text'
hopach_discor: no visible global function definition for 'cor'
limmaWindow : genInteractions: no visible global function definition
  for 'combn'
limmaWindow: no visible binding for global variable 'p.adjust.methods'
makeContrastTrt: no visible global function definition for 'head'
median_cb: no visible binding for global variable 'median'
setup.gobidend: no visible global function definition for 'plot'
setup.gobidend: no visible global function definition for 'points'
setup.gobidend: no visible global function definition for 'lines'
stddev_cb: no visible binding for global variable 'sd'
toGdkColors: no visible global function definition for 'read.table'
Undefined global functions or variables:
  Cairo as as.dist as.formula browseURL coef combn cor cov dev.cur
  dev.off dist exp_loadNetwork exprs featureData fitted hclust head
  identify installed.packages is lines lm median model.matrix new
  p.adjust p.adjust.methods pData par pf phenoData plot points read.csv
  read.table sd tail terms text var write.csv write.table
Consider adding
  importFrom("grDevices", "dev.cur", "dev.off")
  importFrom("graphics", "identify", "lines", "par", "plot", "points",
             "text")
  importFrom("methods", "as", "is", "new")
  importFrom("stats", "as.dist", "as.formula", "coef", "cor", "cov",
             "dist", "fitted", "hclust", "lm", "median", "model.matrix",
             "p.adjust", "p.adjust.methods", "pf", "sd", "terms", "var")
  importFrom("utils", "browseURL", "combn", "head", "installed.packages",
             "read.csv", "read.table", "tail", "write.csv",
             "write.table")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* checking Rd files ... NOTE
prepare_Rd: exp-addEntityType-vx.Rd:19: Dropping empty section \examples
prepare_Rd: exp-addFilterRule-rn.Rd:19: Dropping empty section \details
prepare_Rd: exp-addFilterRule-rn.Rd:21: Dropping empty section \examples
prepare_Rd: exp-calcAngleDist-31.Rd:15: Dropping empty section \details
prepare_Rd: exp-calcAngleDist-31.Rd:17: Dropping empty section \examples
prepare_Rd: exp-calcCanberraDist.Rd:16: Dropping empty section \details
prepare_Rd: exp-calcCanberraDist.Rd:18: Dropping empty section \examples
prepare_Rd: exp-calcCorrelationDist-45.Rd:16: Dropping empty section \details
prepare_Rd: exp-calcCorrelationDist-45.Rd:18: Dropping empty section \examples
prepare_Rd: exp-calcDiff-y4.Rd:15: Dropping empty section \details
prepare_Rd: exp-calcDiff-y4.Rd:17: Dropping empty section \examples
prepare_Rd: exp-calcEuclideanDist-dn.Rd:16: Dropping empty section \details
prepare_Rd: exp-calcEuclideanDist-dn.Rd:18: Dropping empty section \examples
prepare_Rd: exp-calcMahalanobisDist-r1.Rd:14: Dropping empty section \details
prepare_Rd: exp-calcMahalanobisDist-r1.Rd:16: Dropping empty section \examples
prepare_Rd: exp-calcResiduals-ps.Rd:15: Dropping empty section \details
prepare_Rd: exp-calcResiduals-ps.Rd:17: Dropping empty section \examples
prepare_Rd: exp-calcZeroCorDist-by.Rd:16: Dropping empty section \details
prepare_Rd: exp-calcZeroCorDist-by.Rd:18: Dropping empty section \examples
prepare_Rd: exp-colorEntities-1h.Rd:15: Dropping empty section \details
prepare_Rd: exp-colorEntities-1h.Rd:17: Dropping empty section \examples
prepare_Rd: exp-dataset-6l.Rd:26: Dropping empty section \examples
prepare_Rd: exp-designFactors-72.Rd:16: Dropping empty section \details
prepare_Rd: exp-designFactors-72.Rd:18: Dropping empty section \examples
prepare_Rd: exp-designFrame-d0.Rd:16: Dropping empty section \details
prepare_Rd: exp-designFrame-d0.Rd:18: Dropping empty section \examples
prepare_Rd: exp-designSelection-5s.Rd:10-12: Dropping empty section \arguments
prepare_Rd: exp-designSelection-5s.Rd:14: Dropping empty section \details
prepare_Rd: exp-designSelection-5s.Rd:16: Dropping empty section \examples
prepare_Rd: exp-entitiesInList-df.Rd:15: Dropping empty section \details
prepare_Rd: exp-entitiesInList-df.Rd:17: Dropping empty section \examples
prepare_Rd: exp-entityFrame-4j.Rd:14: Dropping empty section \details
prepare_Rd: exp-entityFrame-4j.Rd:16: Dropping empty section \examples
prepare_Rd: exp-entitySelection-11.Rd:14: Dropping empty section \details
prepare_Rd: exp-entitySelection-11.Rd:16: Dropping empty section \examples
prepare_Rd: exp-entityType-69.Rd:10-12: Dropping empty section \arguments
prepare_Rd: exp-entityType-69.Rd:14: Dropping empty section \details
prepare_Rd: exp-entityType-69.Rd:16: Dropping empty section \examples
prepare_Rd: exp-entityTypes-9e.Rd:10-12: Dropping empty section \arguments
prepare_Rd: exp-entityTypes-9e.Rd:14: Dropping empty section \details
prepare_Rd: exp-entityTypes-9e.Rd:16: Dropping empty section \examples
prepare_Rd: exp-filterRules-vt.Rd:14: Dropping empty section \details
prepare_Rd: exp-filterRules-vt.Rd:16: Dropping empty section \examples
prepare_Rd: exp-findPatterns-yw.Rd:20: Dropping empty section \details
prepare_Rd: exp-findPatterns-yw.Rd:22: Dropping empty section \examples
prepare_Rd: exp-ggobi-69.Rd:10-12: Dropping empty section \arguments
prepare_Rd: exp-ggobi-69.Rd:14: Dropping empty section \details
prepare_Rd: exp-ggobi-69.Rd:16: Dropping empty section \examples
prepare_Rd: exp-isRunning-fo.Rd:10-12: Dropping empty section \arguments
prepare_Rd: exp-isRunning-fo.Rd:14: Dropping empty section \details
prepare_Rd: exp-isRunning-fo.Rd:16: Dropping empty section \examples
prepare_Rd: exp-listFrame-gp.Rd:10-12: Dropping empty section \arguments
prepare_Rd: exp-listFrame-gp.Rd:14: Dropping empty section \details
prepare_Rd: exp-listFrame-gp.Rd:16: Dropping empty section \examples
prepare_Rd: exp-listSelection.Rd:11: Dropping empty section \details
prepare_Rd: exp-listSelection.Rd:13: Dropping empty section \examples
prepare_Rd: exp-loadData-bo.Rd:28: Dropping empty section \examples
prepare_Rd: exp-loadDesign-35.Rd:16: Dropping empty section \details
prepare_Rd: exp-loadDesign-35.Rd:18: Dropping empty section \examples
prepare_Rd: exp-loadFiles-1w.Rd:24: Dropping empty section \examples
prepare_Rd: exp-loadInfo-gk.Rd:28: Dropping empty section \examples
prepare_Rd: exp-loadLists-pr.Rd:19: Dropping empty section \examples
prepare_Rd: exp-loadProject-1g.Rd:17: Dropping empty section \examples
prepare_Rd: exp-newList-bs.Rd:16: Dropping empty section \details
prepare_Rd: exp-newList-bs.Rd:18: Dropping empty section \examples
prepare_Rd: exp-removeFilterRules-1i.Rd:15: Dropping empty section \details
prepare_Rd: exp-removeFilterRules-1i.Rd:17: Dropping empty section \examples
prepare_Rd: exp-showClustering-b7.Rd:16: Dropping empty section \details
prepare_Rd: exp-showClustering-b7.Rd:18: Dropping empty section \examples
prepare_Rd: exp-showPatterns-bh.Rd:18: Dropping empty section \details
prepare_Rd: exp-showPatterns-bh.Rd:20: Dropping empty section \examples
prepare_Rd: exp-showResults-sk.Rd:22: Dropping empty section \details
prepare_Rd: exp-showResults-sk.Rd:24: Dropping empty section \examples
prepare_Rd: exp-toggleFilterRules-ts.Rd:16: Dropping empty section \details
prepare_Rd: exp-toggleFilterRules-ts.Rd:18: Dropping empty section \examples
prepare_Rd: exp_bioc.Rd:44-45: Dropping empty section \examples
* 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 files in 'vignettes' ... OK
* checking examples ... NONE
* 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: 5 NOTEs
See
  'C:/Users/biocbuild/bbs-3.9-bioc/meat/explorase.Rcheck/00check.log'
for details.

Installation output

explorase.Rcheck/00install.out

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe --arch i386 CMD INSTALL --no-multiarch explorase
###
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* installing to library 'C:/Users/biocbuild/bbs-3.9-bioc/R/library'
* installing *source* package 'explorase' ...
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'explorase'
    finding HTML links ... done
    exp-addEntityType-vx                    html  
    exp-addFilterRule-rn                    html  
    exp-calcAngleDist-31                    html  
    exp-calcCanberraDist                    html  
    exp-calcCorrelationDist-45              html  
    exp-calcDiff-y4                         html  
    exp-calcEuclideanDist-dn                html  
    exp-calcMahalanobisDist-r1              html  
    exp-calcResiduals-ps                    html  
    exp-calcZeroCorDist-by                  html  
    exp-close                               html  
    exp-colorEntities-1h                    html  
    exp-dataset-6l                          html  
    exp-designFactors-72                    html  
    exp-designFrame-d0                      html  
    exp-designSelection-5s                  html  
    exp-entitiesInList-df                   html  
    exp-entityFrame-4j                      html  
    exp-entitySelection-11                  html  
    exp-entityType-69                       html  
    exp-entityTypes-9e                      html  
    exp-filterRules-vt                      html  
    exp-findPatterns-yw                     html  
    exp-ggobi-69                            html  
    exp-isRunning-fo                        html  
    exp-listFrame-gp                        html  
    exp-listSelection                       html  
    exp-loadData-bo                         html  
    exp-loadDesign-35                       html  
    exp-loadFiles-1w                        html  
    exp-loadInfo-gk                         html  
    exp-loadLists-pr                        html  
    exp-loadProject-1g                      html  
    exp-newList-bs                          html  
    exp-removeFilterRules-1i                html  
    exp-showClustering-b7                   html  
    exp-showPatterns-bh                     html  
    exp-showResults-sk                      html  
    exp-toggleFilterRules-ts                html  
    exp_bioc                                html  
    explorase                               html  
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (explorase)
Making 'packages.html' ... done

Tests output

Example timings