phenoDist 1.16.0
Xian Zhang
| Snapshot Date: 2015-07-27 17:20:08 -0700 (Mon, 27 Jul 2015) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_1/madman/Rpacks/phenoDist | | Last Changed Rev: 102591 / Revision: 106815 | | Last Changed Date: 2015-04-16 12:42:01 -0700 (Thu, 16 Apr 2015) |
| 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 | NotNeeded | OK | OK | OK | |
| morelia | Mac OS X Mavericks (10.9.5) / x86_64 | NotNeeded | OK | OK | OK | |
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### Running command:
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### rm -rf phenoDist.buildbin-libdir phenoDist.Rcheck && mkdir phenoDist.buildbin-libdir phenoDist.Rcheck && E:\biocbld\bbs-3.1-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=phenoDist.buildbin-libdir phenoDist_1.16.0.tar.gz >phenoDist.Rcheck\00install.out 2>&1 && cp phenoDist.Rcheck\00install.out phenoDist-install.out && E:\biocbld\bbs-3.1-bioc\R\bin\R.exe CMD check --library=phenoDist.buildbin-libdir --install="check:phenoDist-install.out" --force-multiarch --no-vignettes --timings phenoDist_1.16.0.tar.gz
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* using log directory 'E:/biocbld/bbs-3.1-bioc/meat/phenoDist.Rcheck'
* using R version 3.2.1 (2015-06-18)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'phenoDist/DESCRIPTION' ... OK
* this is package 'phenoDist' version '1.16.0'
* 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 'phenoDist' can be installed ... 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
* 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
'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
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'
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'
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 installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... [188s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
distToNeg 104.66 0.02 104.68
PDMBySvmWeightVector 18.52 0.10 18.61
PDMBySvmAccuracy 12.59 0.01 12.65
PDMByKS 7.14 0.10 27.52
PDMByFactorAnalysis 3.38 0.03 13.99
** running examples for arch 'x64' ... [200s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
distToNeg 120.07 0.03 120.11
PDMBySvmWeightVector 15.63 0.08 15.74
PDMBySvmAccuracy 12.57 0.06 12.63
PDMByKS 7.11 0.15 26.41
PDMByFactorAnalysis 2.56 0.06 12.75
* 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
'E:/biocbld/bbs-3.1-bioc/meat/phenoDist.Rcheck/00check.log'
for details.
install for i386
* installing *source* package 'phenoDist' ...
** R
** inst
** preparing package for lazy loading
Creating a generic function for 'nchar' from package 'base' in package 'S4Vectors'
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Creating a generic function for 'nchar' from package 'base' in package 'S4Vectors'
install for x64
* installing *source* package 'phenoDist' ...
** testing if installed package can be loaded
Creating a generic function for 'nchar' from package 'base' in package 'S4Vectors'
* MD5 sums
packaged installation of 'phenoDist' as phenoDist_1.16.0.zip
* DONE (phenoDist)