BioC 3.5: CHECK report for explorase on malbec2

Package: explorase

Version: 1.40.0

Command: /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD check --no-vignettes --timings explorase_1.40.0.tar.gz

StartedAt: 2017-08-15 22:55:53 -0400 (Tue, 15 Aug 2017)

EndedAt: 2017-08-15 22:56:23 -0400 (Tue, 15 Aug 2017)

EllapsedTime: 30.5 seconds

RetCode: 0

Status:  OK

CheckDir: explorase.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD check --no-vignettes --timings explorase_1.40.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.5-bioc/meat/explorase.Rcheck’
* using R version 3.4.1 (2017-06-30)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘explorase/DESCRIPTION’ ... OK
* this is package ‘explorase’ version ‘1.40.0’
* 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 for sufficient/correct file permissions ... 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 loading without being on the library search path ... 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 installed files from ‘inst/doc’ ... 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
  ‘/home/biocbuild/bbs-3.5-bioc/meat/explorase.Rcheck/00check.log’
for details.

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