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CHECK report for geneRxCluster on malbec1

This page was generated on 2019-04-16 11:50:21 -0400 (Tue, 16 Apr 2019).

Package 606/1649HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
geneRxCluster 1.18.0
Charles Berry
Snapshot Date: 2019-04-15 17:01:12 -0400 (Mon, 15 Apr 2019)
URL: https://git.bioconductor.org/packages/geneRxCluster
Branch: RELEASE_3_8
Last Commit: 8c75128
Last Changed Date: 2018-10-30 11:41:52 -0400 (Tue, 30 Oct 2018)
malbec1 Linux (Ubuntu 16.04.6 LTS) / x86_64  OK  OK [ OK ]UNNEEDED, same version exists in internal repository
merida1 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: geneRxCluster
Version: 1.18.0
Command: /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD check --install=check:geneRxCluster.install-out.txt --library=/home/biocbuild/bbs-3.8-bioc/R/library --no-vignettes --timings geneRxCluster_1.18.0.tar.gz
StartedAt: 2019-04-16 00:09:23 -0400 (Tue, 16 Apr 2019)
EndedAt: 2019-04-16 00:10:35 -0400 (Tue, 16 Apr 2019)
EllapsedTime: 72.1 seconds
RetCode: 0
Status:  OK 
CheckDir: geneRxCluster.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD check --install=check:geneRxCluster.install-out.txt --library=/home/biocbuild/bbs-3.8-bioc/R/library --no-vignettes --timings geneRxCluster_1.18.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.8-bioc/meat/geneRxCluster.Rcheck’
* using R version 3.5.3 (2019-03-11)
* 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 ‘1.18.0’
* 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 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 include directives in Makefiles ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
* 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: 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.8-bioc/meat/geneRxCluster.Rcheck/00check.log’
for details.



Installation output

geneRxCluster.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD INSTALL geneRxCluster
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.8-bioc/R/library’
* installing *source* package ‘geneRxCluster’ ...
** libs
gcc -I"/home/biocbuild/bbs-3.8-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-3.8-bioc/R/lib -L/usr/local/lib -o geneRxCluster.so cluster.o -L/home/biocbuild/bbs-3.8-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.8-bioc/R/library/geneRxCluster/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (geneRxCluster)

Tests output

geneRxCluster.Rcheck/tests/doRunit.Rout


R version 3.5.3 (2019-03-11) -- "Great Truth"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> ## unit tests will not be done if RUnit is not available
> if(require("RUnit", quietly=TRUE)) {
+  
+   ## --- Setup ---
+  
+   pkg <- "geneRxCluster" # <-- Change to package name!
+   if(Sys.getenv("RCMDCHECK") == "FALSE") {
+     ## Path to unit tests for standalone running under Makefile (not R CMD check)
+     ## PKG/tests/../inst/unitTests
+     path <- file.path(getwd(), "..", "inst", "unitTests")
+   } else {
+     ## Path to unit tests for R CMD check
+     ## PKG.Rcheck/tests/../PKG/unitTests
+     path <- system.file(package=pkg, "unitTests")
+   }
+   cat("\nRunning unit tests\n")
+   print(list(pkg=pkg, getwd=getwd(), pathToUnitTests=path))
+  
+   library(package=pkg, character.only=TRUE)
+  
+   ## If desired, load the name space to allow testing of private functions
+   ## if (is.element(pkg, loadedNamespaces()))
+   ##     attach(loadNamespace(pkg), name=paste("namespace", pkg, sep=":"), pos=3)
+   ##
+   ## or simply call PKG:::myPrivateFunction() in tests
+  
+   ## --- Testing ---
+  
+   ## Define tests
+   testSuite <- defineTestSuite(name=paste(pkg, "unit testing"),
+                                           dirs=path)
+   ## Run
+   tests <- runTestSuite(testSuite)
+  
+   ## Default report name
+   pathReport <- file.path(path, "report")
+  
+   ## Report to stdout and text files
+   cat("------------------- UNIT TEST SUMMARY ---------------------\n\n")
+   printTextProtocol(tests, showDetails=FALSE)
+   printTextProtocol(tests, showDetails=FALSE,
+                     fileName=paste(pathReport, "Summary.txt", sep=""))
+   printTextProtocol(tests, showDetails=TRUE,
+                     fileName=paste(pathReport, ".txt", sep=""))
+  
+   ## Report to HTML file
+   printHTMLProtocol(tests, fileName=paste(pathReport, ".html", sep=""))
+  
+   ## Return stop() to cause R CMD check stop in case of
+   ##  - failures i.e. FALSE to unit tests or
+   ##  - errors i.e. R errors
+   tmp <- getErrors(tests)
+   if(tmp$nFail > 0 | tmp$nErr > 0) {
+     stop(paste("\n\nunit testing failed (#test failures: ", tmp$nFail,
+                ", #R errors: ",  tmp$nErr, ")\n\n", sep=""))
+   }
+ } else {
+   warning("cannot run unit tests -- package RUnit is not available")
+ }

Running unit tests
$pkg
[1] "geneRxCluster"

$getwd
[1] "/home/biocbuild/bbs-3.8-bioc/meat/geneRxCluster.Rcheck/tests"

$pathToUnitTests
[1] "/home/biocbuild/bbs-3.8-bioc/R/library/geneRxCluster/unitTests"

Loading required package: GenomicRanges
Loading required package: stats4
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, basename, cbind, colMeans, colSums, colnames,
    dirname, do.call, duplicated, eval, evalq, get, grep, grepl,
    intersect, is.unsorted, lapply, lengths, mapply, match, mget,
    order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind,
    rowMeans, rowSums, rownames, sapply, setdiff, sort, table, tapply,
    union, unique, unsplit, which, which.max, which.min

Loading required package: S4Vectors

Attaching package: 'S4Vectors'

The following object is masked from 'package:base':

    expand.grid

Loading required package: IRanges
Loading required package: GenomeInfoDb


Executing test function test_bad_args_gRxCluster  ... Error in gRxCluster(rep("a", 100), 0:100L, c(rep(TRUE, 5), rep(c(FALSE,  : 
  object, starts, and group must have same lengths
 done successfully.



Executing test function test_crossover_gRxCluster  ...  done successfully.



Executing test function test_permutation_both_ways_gRxCluster  ...  done successfully.



Executing test function test_prune_gRxCluster  ...  done successfully.



Executing test function test_simply_grx_clust_Call  ...  done successfully.

------------------- UNIT TEST SUMMARY ---------------------

RUNIT TEST PROTOCOL -- Tue Apr 16 00:10:32 2019 
*********************************************** 
Number of test functions: 5 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
geneRxCluster unit testing - 5 test functions, 0 errors, 0 failures
> 
> proc.time()
   user  system elapsed 
  4.156   0.148   4.328 

Example timings

geneRxCluster.Rcheck/geneRxCluster-Ex.timings

nameusersystemelapsed
critVal.alpha0.3240.0000.323
critVal.power0.0400.0000.043
critVal.target0.0480.0040.053
gRxPlot1.0600.0401.101
gRxPlotClumps0.4440.0000.444
gRxSummary0.7520.0000.754