Back to the "Multiple platform build/check report" A  B  C  D  E  F  G  H  I  J  K  L  M  N  O [P] Q  R  S  T  U  V  W  X  Y  Z 

BioC 3.2: CHECK report for phenoDist on moscato1

This page was generated on 2015-07-30 12:40:23 -0700 (Thu, 30 Jul 2015).

Package 734/1055HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
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 UNNEEDED, same version exists in internal repository
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 UNNEEDED, same version exists in internal repository
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: phenoDist
Version: 1.17.0
Command: rm -rf phenoDist.buildbin-libdir phenoDist.Rcheck && mkdir phenoDist.buildbin-libdir phenoDist.Rcheck && D:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=phenoDist.buildbin-libdir phenoDist_1.17.0.tar.gz >phenoDist.Rcheck\00install.out 2>&1 && cp phenoDist.Rcheck\00install.out phenoDist-install.out && D:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD check --library=phenoDist.buildbin-libdir --install="check:phenoDist-install.out" --force-multiarch --no-vignettes --timings phenoDist_1.17.0.tar.gz
StartedAt: 2015-07-30 07:06:55 -0700 (Thu, 30 Jul 2015)
EndedAt: 2015-07-30 07:11:08 -0700 (Thu, 30 Jul 2015)
EllapsedTime: 252.8 seconds
RetCode: 1
Status:  ERROR  
CheckDir: phenoDist.Rcheck
Warnings: NA

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf phenoDist.buildbin-libdir phenoDist.Rcheck && mkdir phenoDist.buildbin-libdir phenoDist.Rcheck && D:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=phenoDist.buildbin-libdir phenoDist_1.17.0.tar.gz >phenoDist.Rcheck\00install.out 2>&1 && cp phenoDist.Rcheck\00install.out phenoDist-install.out  && D:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD check --library=phenoDist.buildbin-libdir --install="check:phenoDist-install.out" --force-multiarch --no-vignettes --timings phenoDist_1.17.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'D:/biocbld/bbs-3.2-bioc/meat/phenoDist.Rcheck'
* using R version 3.2.1 Patched (2015-07-19 r68700)
* 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 '1.17.0'
* 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 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' ... ERROR
Running examples in 'phenoDist-Ex.R' failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: PDMByFactorAnalysis
> ### Title: Calculate phenotypic distance matrix by factor analysis
> ### Aliases: PDMByFactorAnalysis
> 
> ### ** Examples
> 
>   library('phenoDist')
> 
>   ## load the imageHTS object
>   load(system.file('kimorph', 'kimorph.rda', package='phenoDist'))
>   x@localPath <- file.path(tempdir(), 'kimorph')
>   
>   ## segmentation and feature extraction
>   unames <- setdiff(getUnames(x), getUnames(x, content='empty'))
> 
>   ## calculate pair-wise svm distance matrix
>   load(system.file('kimorph', 'selectedFtrs.rda', package='phenoDist'))
>   pdm <- PDMByFactorAnalysis(x, unames=getUnames(x, plate=1, row=2:3, col=3), selectedCellFtrs, distMethod='euclidean', nFactors=10, scores='regression')
001-01-B03: trying URL 'http://www.ebi.ac.uk/˜gpau/imageHTS/screens/kimorph/data/001-01/001-01-B03_ftrs.tab'
Warning in fileHTS(x, type = type, ..., access = access) :
  cannot download the file pointed by "http://www.ebi.ac.uk/˜gpau/imageHTS/screens/kimorph/data/001-01/001-01-B03_ftrs.tab" to the location "D:\biocbld\bbs-3.2-bioc\tmpdir\RtmpScuY5M/kimorph/data/001-01/001-01-B03_ftrs.tab"
Error in readHTS(x, "ftrs", uname = u, access = access) : 
  cannot find filename=D:\biocbld\bbs-3.2-bioc\tmpdir\RtmpScuY5M/kimorph/data/001-01/001-01-B03_ftrs.tab
NA
001-01-C03: trying URL 'http://www.ebi.ac.uk/˜gpau/imageHTS/screens/kimorph/data/001-01/001-01-C03_ftrs.tab'
Warning in fileHTS(x, type = type, ..., access = access) :
  cannot download the file pointed by "http://www.ebi.ac.uk/˜gpau/imageHTS/screens/kimorph/data/001-01/001-01-C03_ftrs.tab" to the location "D:\biocbld\bbs-3.2-bioc\tmpdir\RtmpScuY5M/kimorph/data/001-01/001-01-C03_ftrs.tab"
Error in readHTS(x, "ftrs", uname = u, access = access) : 
  cannot find filename=D:\biocbld\bbs-3.2-bioc\tmpdir\RtmpScuY5M/kimorph/data/001-01/001-01-C03_ftrs.tab
NA
001-02-B03: trying URL 'http://www.ebi.ac.uk/˜gpau/imageHTS/screens/kimorph/data/001-02/001-02-B03_ftrs.tab'
Warning in fileHTS(x, type = type, ..., access = access) :
  cannot download the file pointed by "http://www.ebi.ac.uk/˜gpau/imageHTS/screens/kimorph/data/001-02/001-02-B03_ftrs.tab" to the location "D:\biocbld\bbs-3.2-bioc\tmpdir\RtmpScuY5M/kimorph/data/001-02/001-02-B03_ftrs.tab"
Error in readHTS(x, "ftrs", uname = u, access = access) : 
  cannot find filename=D:\biocbld\bbs-3.2-bioc\tmpdir\RtmpScuY5M/kimorph/data/001-02/001-02-B03_ftrs.tab
NA
001-02-C03: trying URL 'http://www.ebi.ac.uk/˜gpau/imageHTS/screens/kimorph/data/001-02/001-02-C03_ftrs.tab'
Warning in fileHTS(x, type = type, ..., access = access) :
  cannot download the file pointed by "http://www.ebi.ac.uk/˜gpau/imageHTS/screens/kimorph/data/001-02/001-02-C03_ftrs.tab" to the location "D:\biocbld\bbs-3.2-bioc\tmpdir\RtmpScuY5M/kimorph/data/001-02/001-02-C03_ftrs.tab"
Error in readHTS(x, "ftrs", uname = u, access = access) : 
  cannot find filename=D:\biocbld\bbs-3.2-bioc\tmpdir\RtmpScuY5M/kimorph/data/001-02/001-02-C03_ftrs.tab
NA
Error in cellFtrs[, selectedCellFtrs] : incorrect number of dimensions
Calls: PDMByFactorAnalysis
Execution halted
** running examples for arch 'x64' ... ERROR
Running examples in 'phenoDist-Ex.R' failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: PDMByFactorAnalysis
> ### Title: Calculate phenotypic distance matrix by factor analysis
> ### Aliases: PDMByFactorAnalysis
> 
> ### ** Examples
> 
>   library('phenoDist')
> 
>   ## load the imageHTS object
>   load(system.file('kimorph', 'kimorph.rda', package='phenoDist'))
>   x@localPath <- file.path(tempdir(), 'kimorph')
>   
>   ## segmentation and feature extraction
>   unames <- setdiff(getUnames(x), getUnames(x, content='empty'))
> 
>   ## calculate pair-wise svm distance matrix
>   load(system.file('kimorph', 'selectedFtrs.rda', package='phenoDist'))
>   pdm <- PDMByFactorAnalysis(x, unames=getUnames(x, plate=1, row=2:3, col=3), selectedCellFtrs, distMethod='euclidean', nFactors=10, scores='regression')
001-01-B03: trying URL 'http://www.ebi.ac.uk/˜gpau/imageHTS/screens/kimorph/data/001-01/001-01-B03_ftrs.tab'
Warning in fileHTS(x, type = type, ..., access = access) :
  cannot download the file pointed by "http://www.ebi.ac.uk/˜gpau/imageHTS/screens/kimorph/data/001-01/001-01-B03_ftrs.tab" to the location "D:\biocbld\bbs-3.2-bioc\tmpdir\RtmpuqKYW2/kimorph/data/001-01/001-01-B03_ftrs.tab"
Error in readHTS(x, "ftrs", uname = u, access = access) : 
  cannot find filename=D:\biocbld\bbs-3.2-bioc\tmpdir\RtmpuqKYW2/kimorph/data/001-01/001-01-B03_ftrs.tab
NA
001-01-C03: trying URL 'http://www.ebi.ac.uk/˜gpau/imageHTS/screens/kimorph/data/001-01/001-01-C03_ftrs.tab'
Warning in fileHTS(x, type = type, ..., access = access) :
  cannot download the file pointed by "http://www.ebi.ac.uk/˜gpau/imageHTS/screens/kimorph/data/001-01/001-01-C03_ftrs.tab" to the location "D:\biocbld\bbs-3.2-bioc\tmpdir\RtmpuqKYW2/kimorph/data/001-01/001-01-C03_ftrs.tab"
Error in readHTS(x, "ftrs", uname = u, access = access) : 
  cannot find filename=D:\biocbld\bbs-3.2-bioc\tmpdir\RtmpuqKYW2/kimorph/data/001-01/001-01-C03_ftrs.tab
NA
001-02-B03: trying URL 'http://www.ebi.ac.uk/˜gpau/imageHTS/screens/kimorph/data/001-02/001-02-B03_ftrs.tab'
Warning in fileHTS(x, type = type, ..., access = access) :
  cannot download the file pointed by "http://www.ebi.ac.uk/˜gpau/imageHTS/screens/kimorph/data/001-02/001-02-B03_ftrs.tab" to the location "D:\biocbld\bbs-3.2-bioc\tmpdir\RtmpuqKYW2/kimorph/data/001-02/001-02-B03_ftrs.tab"
Error in readHTS(x, "ftrs", uname = u, access = access) : 
  cannot find filename=D:\biocbld\bbs-3.2-bioc\tmpdir\RtmpuqKYW2/kimorph/data/001-02/001-02-B03_ftrs.tab
NA
001-02-C03: trying URL 'http://www.ebi.ac.uk/˜gpau/imageHTS/screens/kimorph/data/001-02/001-02-C03_ftrs.tab'
Warning in fileHTS(x, type = type, ..., access = access) :
  cannot download the file pointed by "http://www.ebi.ac.uk/˜gpau/imageHTS/screens/kimorph/data/001-02/001-02-C03_ftrs.tab" to the location "D:\biocbld\bbs-3.2-bioc\tmpdir\RtmpuqKYW2/kimorph/data/001-02/001-02-C03_ftrs.tab"
Error in readHTS(x, "ftrs", uname = u, access = access) : 
  cannot find filename=D:\biocbld\bbs-3.2-bioc\tmpdir\RtmpuqKYW2/kimorph/data/001-02/001-02-C03_ftrs.tab
NA
Error in cellFtrs[, selectedCellFtrs] : incorrect number of dimensions
Calls: PDMByFactorAnalysis
Execution halted
* 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 ERRORs, 2 NOTEs
See
  'D:/biocbld/bbs-3.2-bioc/meat/phenoDist.Rcheck/00check.log'
for details.

phenoDist.Rcheck/00install.out:


install for i386

* 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'

install for x64

* installing *source* package 'phenoDist' ...
** testing if installed package can be loaded
Warning: replacing previous import by 'BiocGenerics::mad' when loading 'IRanges'
* MD5 sums
packaged installation of 'phenoDist' as phenoDist_1.17.0.zip
* DONE (phenoDist)

phenoDist.Rcheck/examples_i386/phenoDist-Ex.timings:

nameusersystemelapsed

phenoDist.Rcheck/examples_x64/phenoDist-Ex.timings:

nameusersystemelapsed