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BioC 3.5: CHECK report for geneRxCluster on malbec2

This page was generated on 2017-08-16 13:15:27 -0400 (Wed, 16 Aug 2017).

Package 522/1382HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
geneRxCluster 1.12.0
Charles Berry
Snapshot Date: 2017-08-15 17:17:57 -0400 (Tue, 15 Aug 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_5/madman/Rpacks/geneRxCluster
Last Changed Rev: 129126 / Revision: 131943
Last Changed Date: 2017-04-24 15:25:24 -0400 (Mon, 24 Apr 2017)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  NotNeeded  OK [ OK ]UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository
veracruz2 OS X 10.11.6 El Capitan / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: geneRxCluster
Version: 1.12.0
Command: /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD check --no-vignettes --timings geneRxCluster_1.12.0.tar.gz
StartedAt: 2017-08-15 23:18:35 -0400 (Tue, 15 Aug 2017)
EndedAt: 2017-08-15 23:19:45 -0400 (Tue, 15 Aug 2017)
EllapsedTime: 69.9 seconds
RetCode: 0
Status:  OK 
CheckDir: geneRxCluster.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD check --no-vignettes --timings geneRxCluster_1.12.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.5-bioc/meat/geneRxCluster.Rcheck’
* using R version 3.4.1 (2017-06-30)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘geneRxCluster/DESCRIPTION’ ... OK
* this is package ‘geneRxCluster’ version ‘1.12.0’
* 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 ‘as’
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:
  as 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("methods", "as")
  importFrom("stats", "dbinom", "pbinom", "plogis", "qbinom", "qlogis")
  importFrom("utils", "head", "tail")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* 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 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
  ‘/home/biocbuild/bbs-3.5-bioc/meat/geneRxCluster.Rcheck/00check.log’
for details.


geneRxCluster.Rcheck/00install.out:

* installing *source* package ‘geneRxCluster’ ...
** libs
gcc -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c cluster.c -o cluster.o
cluster.c: In function ‘cutptClean_new_elt’:
cluster.c:80:6: warning: suggest explicit braces to avoid ambiguous ‘else’ [-Wparentheses]
   if (*pvj!=NOTAIL)
      ^
cluster.c: In function ‘gRxC_cluster’:
cluster.c:682:2: warning: ‘cutptFunRes’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  SET_VECTOR_ELT(final,2,cutptFunRes);
  ^
gcc -shared -L/home/biocbuild/bbs-3.5-bioc/R/lib -L/usr/local/lib -o geneRxCluster.so cluster.o -L/home/biocbuild/bbs-3.5-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.5-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)

geneRxCluster.Rcheck/geneRxCluster-Ex.timings:

nameusersystemelapsed
critVal.alpha0.2480.0000.249
critVal.power0.0480.0080.056
critVal.target0.0640.0000.065
gRxPlot1.1960.0081.203
gRxPlotClumps0.8080.0000.810
gRxSummary0.3720.0000.376