phenoDist 1.17.0
Xian Zhang
| Snapshot Date: 2015-07-29 16:24:10 -0700 (Wed, 29 Jul 2015) | | URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/phenoDist | | Last Changed Rev: 102594 / Revision: 106906 | | Last Changed Date: 2015-04-16 13:02:44 -0700 (Thu, 16 Apr 2015) |
| zin1 | Linux (Ubuntu 14.04.2 LTS) / x86_64 | NotNeeded | OK | OK | |  |
| moscato1 | Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 | NotNeeded | OK | ERROR | 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 | |
##############################################################################
##############################################################################
###
### Running command:
###
### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings phenoDist_1.17.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.2-bioc/meat/phenoDist.Rcheck’
* using R version 3.2.1 Patched (2015-07-20 r68706)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘phenoDist/DESCRIPTION’ ... OK
* this is package ‘phenoDist’ version ‘1.17.0’
* 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 ‘phenoDist’ can be installed ... [19s/20s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* 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 ‘MASS’ in package code.
Please use :: or requireNamespace() instead.
See section 'Suggested packages' in the 'Writing R Extensions' manual.
Package in Depends field not imported from: ‘e1071’
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
cleanDistMatrix: no visible global function definition for
‘getWellFeatures’
clusterDist: no visible global function definition for
‘getWellFeatures’
ctlSeparatn: no visible global function definition for
‘getWellFeatures’
ctlSeparatn: no visible global function definition for ‘zprime’
distToNeg : <anonymous>: no visible global function definition for
‘uname2prw’
distToNeg : <anonymous>: no visible global function definition for
‘getUnames’
enrichAnalysis : <anonymous>: no visible global function definition for
‘hyperGTest’
getBadWells: no visible global function definition for ‘prw2uname’
getReplicate: no visible global function definition for ‘uname2prw’
getReplicate: no visible global function definition for ‘getUnames’
PDMByFactorAnalysis: no visible global function definition for
‘collectCellFeatures’
PDMByKS: no visible global function definition for
‘collectCellFeatures’
PDMByKS: no visible global function definition for ‘uname2prw’
PDMByKS : <anonymous>: no visible global function definition for
‘getUnames’
PDMByKS : <anonymous> : <anonymous>: no visible global function
definition for ‘collectCellFeatures’
PDMByKS : <anonymous>: no visible global function definition for
‘collectCellFeatures’
PDMByKS : <anonymous>: no visible global function definition for
‘uname2prw’
PDMBySvmAccuracy: no visible global function definition for
‘collectCellFeatures’
PDMBySvmAccuracy : <anonymous>: no visible global function definition
for ‘collectCellFeatures’
PDMBySvmAccuracy : <anonymous> : <anonymous>: no visible global
function definition for ‘svm’
PDMBySvmWeightVector: no visible global function definition for
‘collectCellFeatures’
PDMBySvmWeightVector: no visible global function definition for
‘uname2prw’
PDMBySvmWeightVector : <anonymous>: no visible global function
definition for ‘getUnames’
PDMBySvmWeightVector : <anonymous> : <anonymous>: no visible global
function definition for ‘collectCellFeatures’
PDMBySvmWeightVector : <anonymous>: no visible global function
definition for ‘collectCellFeatures’
PDMBySvmWeightVector : <anonymous>: no visible global function
definition for ‘uname2prw’
PDMBySvmWeightVector : <anonymous> : <anonymous>: no visible global
function definition for ‘svm’
repCorr: no visible global function definition for ‘getUnames’
* 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [194s/223s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
distToNeg 140.608 0.848 141.516
PDMBySvmWeightVector 17.465 0.176 17.643
PDMBySvmAccuracy 9.974 0.099 10.075
PDMByKS 8.237 0.314 27.195
PDMByFactorAnalysis 3.654 0.156 12.880
* 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: 2 NOTEs
See
‘/Users/biocbuild/bbs-3.2-bioc/meat/phenoDist.Rcheck/00check.log’
for details.
* installing *source* package ‘phenoDist’ ...
** R
** inst
** preparing package for lazy loading
Warning: replacing previous import by ‘BiocGenerics::mad’ when loading ‘IRanges’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Warning: replacing previous import by ‘BiocGenerics::mad’ when loading ‘IRanges’
* DONE (phenoDist)