geneRxCluster 1.8.0
Charles Berry
| Snapshot Date: 2016-10-12 17:20:15 -0700 (Wed, 12 Oct 2016) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_3/madman/Rpacks/geneRxCluster | | Last Changed Rev: 117079 / Revision: 122332 | | Last Changed Date: 2016-05-03 14:20:18 -0700 (Tue, 03 May 2016) |
| zin2 | Linux (Ubuntu 14.04.2 LTS) / x86_64 | NotNeeded | OK | OK | |  |
| moscato2 | Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 | NotNeeded | OK | OK | OK | |
| oaxaca | 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 geneRxCluster_1.8.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.3-bioc/meat/geneRxCluster.Rcheck’
* using R version 3.3.1 (2016-06-21)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘geneRxCluster/DESCRIPTION’ ... OK
* this is package ‘geneRxCluster’ version ‘1.8.0’
* 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 ‘geneRxCluster’ 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
* 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
.gRxCluster: no visible global function definition for ‘tail’
.gRxCluster: no visible global function definition for ‘head’
.gRxCluster: no visible global function definition for ‘metadata’
.gRxCluster: no visible global function definition for ‘metadata<-’
critVal.alpha : <anonymous>: no visible global function definition for
‘pbinom’
critVal.alpha : <anonymous>: no visible global function definition for
‘tail’
critVal.alpha : <anonymous>: no visible global function definition for
‘head’
critVal.power: no visible global function definition for ‘plogis’
critVal.power: no visible global function definition for ‘qlogis’
critVal.power : <anonymous>: no visible global function definition for
‘qbinom’
critVal.power : <anonymous>: no visible global function definition for
‘dbinom’
critVal.power : <anonymous>: no visible global function definition for
‘pbinom’
critVal.target : <anonymous>: no visible global function definition for
‘pbinom’
critVal.target : <anonymous>: no visible global function definition for
‘tail’
critVal.target : <anonymous>: no visible global function definition for
‘head’
gRxCluster: no visible global function definition for ‘runValue’
gRxCluster: no visible global function definition for ‘metadata’
gRxCluster: no visible global function definition for ‘metadata<-’
gRxPlot: no visible global function definition for ‘qlogis’
gRxPlot: no visible global function definition for ‘hist’
gRxPlot: no visible global function definition for ‘plot’
gRxPlot: no visible global function definition for ‘metadata’
gRxPlotClumps: no visible global function definition for ‘metadata’
gRxPlotClumps: no visible global function definition for ‘seqlengths’
gRxPlotClumps: no visible global function definition for ‘runValue’
gRxPlotClumps: no visible global function definition for ‘seqlengths<-’
gRxPlotClumps: no visible global function definition for ‘queryHits’
gRxPlotClumps: no visible global function definition for ‘subjectHits’
gRxPlotClumps: no visible global function definition for ‘par’
gRxPlotClumps: no visible global function definition for ‘plot’
gRxPlotClumps: no visible global function definition for ‘box’
gRxPlotClumps: no visible global function definition for ‘segments’
gRxPlotClumps: no visible global function definition for ‘text’
gRxSummary: no visible global function definition for ‘metadata’
plot.cutpoints: no visible global function definition for ‘barplot’
plot.cutpoints: no visible global function definition for ‘points’
prune.loglik : x.max: no visible global function definition for
‘subjectHits’
Undefined global functions or variables:
barplot box dbinom head hist metadata metadata<- par pbinom plogis
plot points qbinom qlogis queryHits runValue segments seqlengths
seqlengths<- subjectHits tail text
Consider adding
importFrom("graphics", "barplot", "box", "hist", "par", "plot",
"points", "segments", "text")
importFrom("stats", "dbinom", "pbinom", "plogis", "qbinom", "qlogis")
importFrom("utils", "head", "tail")
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 line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking for GNU extensions in Makefiles ... OK
* checking compiled code ... OK
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘doRunit.R’
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 NOTE
See
‘/Users/biocbuild/bbs-3.3-bioc/meat/geneRxCluster.Rcheck/00check.log’
for details.
* installing *source* package ‘geneRxCluster’ ...
** libs
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -fPIC -Wall -mtune=core2 -g -O2 -c cluster.c -o cluster.o
cluster.c:83:5: warning: add explicit braces to avoid dangling else [-Wdangling-else]
else if (*pvj==HITAIL)
^
1 warning generated.
clang -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o geneRxCluster.so cluster.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.3-bioc/meat/geneRxCluster.Rcheck/geneRxCluster/libs
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (geneRxCluster)