explorase 1.32.0
Michael Lawrence
| Snapshot Date: 2015-10-08 17:20:21 -0700 (Thu, 08 Oct 2015) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_1/madman/Rpacks/explorase | | Last Changed Rev: 102591 / Revision: 109384 | | Last Changed Date: 2015-04-16 12:42:01 -0700 (Thu, 16 Apr 2015) |
| zin2 | Linux (Ubuntu 14.04.2 LTS) / x86_64 | NotNeeded | OK | [ OK ] | |  |
| moscato2 | Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 | NotNeeded | OK | OK | OK | |
| petty | Mac OS X Snow Leopard (10.6.8) / x86_64 | ...NOT SUPPORTED...NOT SUPPORTED...NOT SUPPORTED... |
| morelia | Mac OS X Mavericks (10.9.5) / x86_64 | ...NOT SUPPORTED...NOT SUPPORTED...NOT SUPPORTED... |
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### Running command:
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### /home/biocbuild/bbs-3.1-bioc/R/bin/R CMD check --no-vignettes --timings explorase_1.32.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.1-bioc/meat/explorase.Rcheck’
* using R version 3.2.2 (2015-08-14)
* 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 ‘1.32.0’
* 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 ... [2s/2s] 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'
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_loadInfo: no visible global function definition for ‘pData’
exp_showClustering: no visible global function definition for ‘Cairo’
explorase: no visible global function definition for ‘exp_loadNetwork’
* 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 sizes of PDF files under ‘inst/doc’ ... 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-3.1-bioc/meat/explorase.Rcheck/00check.log’
for details.
* installing *source* package ‘explorase’ ...
** R
** inst
** preparing package for lazy loading
Xlib: extension "RANDR" missing on display ":1.0".
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Xlib: extension "RANDR" missing on display ":1.0".
* DONE (explorase)