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BioC 3.4: CHECK report for flowMerge on moscato1

This page was generated on 2016-09-21 03:42:48 -0700 (Wed, 21 Sep 2016).

Package 424/1257HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
flowMerge 2.21.0
Greg Finak
Snapshot Date: 2016-09-19 19:15:14 -0700 (Mon, 19 Sep 2016)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/flowMerge
Last Changed Rev: 117081 / Revision: 121152
Last Changed Date: 2016-05-03 14:30:44 -0700 (Tue, 03 May 2016)
zin1 Linux (Ubuntu 16.04 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
moscato1 Windows Server 2008 R2 Standard (64-bit) / x64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository
morelia Mac OS X Mavericks (10.9.5) / x86_64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository

Summary

Package: flowMerge
Version: 2.21.0
Command: rm -rf flowMerge.buildbin-libdir flowMerge.Rcheck && mkdir flowMerge.buildbin-libdir flowMerge.Rcheck && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=flowMerge.buildbin-libdir flowMerge_2.21.0.tar.gz >flowMerge.Rcheck\00install.out 2>&1 && cp flowMerge.Rcheck\00install.out flowMerge-install.out && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD check --library=flowMerge.buildbin-libdir --install="check:flowMerge-install.out" --force-multiarch --no-vignettes --timings flowMerge_2.21.0.tar.gz
StartedAt: 2016-09-20 08:21:09 -0700 (Tue, 20 Sep 2016)
EndedAt: 2016-09-20 08:23:37 -0700 (Tue, 20 Sep 2016)
EllapsedTime: 148.9 seconds
RetCode: 0
Status:  OK  
CheckDir: flowMerge.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf flowMerge.buildbin-libdir flowMerge.Rcheck && mkdir flowMerge.buildbin-libdir flowMerge.Rcheck && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=flowMerge.buildbin-libdir flowMerge_2.21.0.tar.gz >flowMerge.Rcheck\00install.out 2>&1 && cp flowMerge.Rcheck\00install.out flowMerge-install.out  && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD check --library=flowMerge.buildbin-libdir --install="check:flowMerge-install.out" --force-multiarch --no-vignettes --timings flowMerge_2.21.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'D:/biocbld/bbs-3.4-bioc/meat/flowMerge.Rcheck'
* using R version 3.3.1 (2016-06-21)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'flowMerge/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'flowMerge' version '2.21.0'
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Packages which this enhances but not available for checking:
  'doMC' 'multicore'

Depends: includes the non-default packages:
  'graph' 'feature' 'flowClust' 'Rgraphviz' 'foreach' 'snow'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
* 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 'flowMerge' 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
* 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 dependencies in R code ... NOTE
Packages in Depends field not imported from:
  'foreach' 'snow'
  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
.compMD: no visible global function definition for 'mahalanobis'
initPFlowMerge: no visible global function definition for
  'clusterEvalQ'
mergeClusters: no visible global function definition for '%dopar%'
mergeClusters: no visible global function definition for 'foreach'
mergeClusters: no visible global function definition for '%do%'
pFlowClust : <anonymous>: no visible global function definition for
  'clusterMap'
pFlowClust: no visible global function definition for 'clusterMap'
ptree : <anonymous>: no visible global function definition for 'rgb'
ptree: no visible global function definition for 'subGraph'
ptree : <anonymous>: no visible global function definition for
  'nodeDataDefaults<-'
ptree : <anonymous>: no visible global function definition for
  'nodeData<-'
ptree : <anonymous>: no visible global function definition for
  'subGraph'
ptree : <anonymous>: no visible global function definition for
  'nodeRenderInfo<-'
flagOutliers,flowMerge: no visible global function definition for 'qf'
Undefined global functions or variables:
  %do% %dopar% clusterEvalQ clusterMap foreach mahalanobis nodeData<-
  nodeDataDefaults<- nodeRenderInfo<- qf rgb subGraph
Consider adding
  importFrom("grDevices", "rgb")
  importFrom("stats", "mahalanobis", "qf")
to your NAMESPACE file.
* 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 contents of 'data' directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
** running examples for arch 'x64' ... OK
* 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: 3 NOTEs
See
  'D:/biocbld/bbs-3.4-bioc/meat/flowMerge.Rcheck/00check.log'
for details.


flowMerge.Rcheck/00install.out:


install for i386

* installing *source* package 'flowMerge' ...
** R
** data
** inst
** preparing package for lazy loading
Creating a generic function for 'merge' from package 'base' in package 'flowMerge'
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded

install for x64

* installing *source* package 'flowMerge' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'flowMerge' as flowMerge_2.21.0.zip
* DONE (flowMerge)

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

nameusersystemelapsed
NENT000
fitPiecewiseLinreg000
flowClust.res000
flowMerge-package000
flowObj000
map000
merge-methods000
merge000
pFlowMerge0.000.010.34
plot-methods0.020.000.02
updateU000

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

nameusersystemelapsed
NENT000
fitPiecewiseLinreg000
flowClust.res000
flowMerge-package000
flowObj000
map000
merge-methods000
merge000
pFlowMerge0.020.000.01
plot-methods000
updateU000