flowPhyto 1.19.0
Chris Berthiaume
| Snapshot Date: 2014-11-16 17:20:26 -0800 (Sun, 16 Nov 2014) | | URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/flowPhyto | | Last Changed Rev: 95443 / Revision: 96805 | | Last Changed Date: 2014-10-13 14:47:41 -0700 (Mon, 13 Oct 2014) |
| zin2 | Linux (Ubuntu 14.04.1 LTS) / x86_64 | NotNeeded | OK | OK | |
| 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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### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch flowPhyto_1.19.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.1-bioc/meat/flowPhyto.Rcheck’
* using R Under development (unstable) (2014-10-07 r66723)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘flowPhyto/DESCRIPTION’ ... OK
* this is package ‘flowPhyto’ version ‘1.19.0’
* 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 ‘flowPhyto’ can be installed ... [8s/8s] 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
Warning in rgl.init(initValue, onlyNULL) :
RGL: GLX extension missing on server
Warning in fun(libname, pkgname) : error in rgl_init
.DBcon: no visible global function definition for ‘dbConnect’
.DBcon: no visible global function definition for ‘dbDriver’
.DBcon: no visible binding for global variable ‘.db.driver’
.DBcon: no visible binding for global variable ‘.db.user’
.DBcon: no visible binding for global variable ‘.db.pass’
.DBcon: no visible binding for global variable ‘.db.name’
.DBcon: no visible binding for global variable ‘.db.host’
.interpolateSDSLatLon: no visible global function definition for
‘na.approx’
.loadSDS: no visible global function definition for ‘dbReadTable’
.loadSDS: no visible binding for global variable ‘.db.cruise.tab.nm’
.loadSDS: no visible global function definition for ‘dbGetQuery’
.loadSDS: no visible binding for global variable ‘.db.sds.tab.nm’
.loadSDS: no visible binding for global variable ‘.db.cruise.fkey.nm’
.loadSDS: no visible global function definition for ‘dbListFields’
.loadSDS: no visible global function definition for ‘dbWriteTable’
.loadStats: no visible global function definition for ‘dbReadTable’
.loadStats: no visible binding for global variable ‘.db.cruise.tab.nm’
.loadStats: no visible global function definition for ‘dbGetQuery’
.loadStats: no visible binding for global variable ‘.db.stats.tab.nm’
.loadStats: no visible binding for global variable ‘.db.cruise.fkey.nm’
.loadStats: no visible global function definition for ‘dbListFields’
.loadStats: no visible global function definition for ‘dbWriteTable’
.prePlotLevel2: no visible binding for global variable ‘.SOURCE.DIR’
.queryStats: no visible binding for global variable ‘.db.stats.tab.nm’
.queryStats: no visible binding for global variable
‘.db.cruise.fkey.nm’
.queryStats: no visible binding for global variable ‘.db.cruise.tab.nm’
classify: no visible binding for global variable ‘pe’
classify: no visible binding for global variable ‘chl_small’
classify: no visible binding for global variable ‘fsc_perp’
classify: no visible binding for global variable ‘fsc_small’
classify: no visible binding for global variable ‘chl_big’
classify: no visible binding for global variable ‘pop’
filter: no visible binding for global variable ‘D1’
filter: no visible binding for global variable ‘D2’
filter: no visible binding for global variable ‘fsc_small’
plotCruiseStats: no visible binding for global variable ‘resamp’
plotCytogram: no visible binding for global variable ‘pop’
plotLatLongMap: no visible global function definition for
‘color.legend’
summarize: no visible binding for global variable ‘pop’
summarizeFile: no visible binding for global variable ‘pop’
* 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 ... [478s/473s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
plotCytogram 59.633 89.548 136.007
classify 56.416 85.942 129.450
census 55.626 85.114 128.056
pipeline 21.613 1.774 25.730
writeSeaflow 0.243 0.205 30.084
* 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
NOTE: There was 1 note.
See
‘/Users/biocbuild/bbs-3.1-bioc/meat/flowPhyto.Rcheck/00check.log’
for details.
* installing *source* package ‘flowPhyto’ ...
** R
** inst
** preparing package for lazy loading
Warning in rgl.init(initValue, onlyNULL) :
RGL: GLX extension missing on server
Warning in fun(libname, pkgname) : error in rgl_init
** 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 in fun(libname, pkgname) : error in rgl_init
* DONE (flowPhyto)