flowMerge 2.19.0
Greg Finak
| Snapshot Date: 2016-04-20 17:20:35 -0700 (Wed, 20 Apr 2016) | | URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/flowMerge | | Last Changed Rev: 109592 / Revision: 116626 | | Last Changed Date: 2015-10-13 12:59:53 -0700 (Tue, 13 Oct 2015) |
| zin2 | Linux (Ubuntu 14.04.2 LTS) / x86_64 | OK | OK | OK | |  |
| moscato2 | Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 | OK | OK | OK | OK | |
| morelia | Mac OS X Mavericks (10.9.5) / x86_64 | OK | OK | [ WARNINGS ] | OK | |
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### Running command:
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### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings flowMerge_2.19.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.3-bioc/meat/flowMerge.Rcheck’
* using R version 3.3.0 beta (2016-04-06 r70435)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘flowMerge/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘flowMerge’ version ‘2.19.0’
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘flowMerge’ can be installed ... [14s/15s] WARNING
Found the following significant warnings:
Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Users/biocbuild/bbs-3.3-bioc/meat/flowMerge.Rcheck/00install.out’ for details.
* 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 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [7s/7s] 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: 1 WARNING, 3 NOTEs
See
‘/Users/biocbuild/bbs-3.3-bioc/meat/flowMerge.Rcheck/00check.log’
for details.
* installing *source* package ‘flowMerge’ ...
** R
** data
** inst
** preparing package for lazy loading
Warning in rgl.init(initValue, onlyNULL) :
RGL: GLX extension missing on server
Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
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
Warning in rgl.init(initValue, onlyNULL) :
RGL: GLX extension missing on server
Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
* DONE (flowMerge)