Package: geneRxCluster

Version: 1.14.0

Command: rm -rf geneRxCluster.buildbin-libdir geneRxCluster.Rcheck && mkdir geneRxCluster.buildbin-libdir geneRxCluster.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=geneRxCluster.buildbin-libdir geneRxCluster_1.14.0.tar.gz >geneRxCluster.Rcheck\00install.out 2>&1 && cp geneRxCluster.Rcheck\00install.out geneRxCluster-install.out && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=geneRxCluster.buildbin-libdir --install="check:geneRxCluster-install.out" --force-multiarch --no-vignettes --timings geneRxCluster_1.14.0.tar.gz

StartedAt: 2018-04-12 00:14:44 -0400 (Thu, 12 Apr 2018)

EndedAt: 2018-04-12 00:16:46 -0400 (Thu, 12 Apr 2018)

EllapsedTime: 121.7 seconds

RetCode: 0

Status:  OK

CheckDir: geneRxCluster.Rcheck

Warnings: 0

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf geneRxCluster.buildbin-libdir geneRxCluster.Rcheck && mkdir geneRxCluster.buildbin-libdir geneRxCluster.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=geneRxCluster.buildbin-libdir geneRxCluster_1.14.0.tar.gz >geneRxCluster.Rcheck\00install.out 2>&1 && cp geneRxCluster.Rcheck\00install.out geneRxCluster-install.out  &&  C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=geneRxCluster.buildbin-libdir --install="check:geneRxCluster-install.out" --force-multiarch --no-vignettes --timings geneRxCluster_1.14.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.6-bioc/meat/geneRxCluster.Rcheck'
* using R version 3.4.4 (2018-03-15)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'geneRxCluster/DESCRIPTION' ... OK
* this is package 'geneRxCluster' version '1.14.0'
* 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 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 ... NOTE
Note: information on .o files for i386 is not available
Note: information on .o files for x64 is not available
File 'C:/Users/biocbuild/bbs-3.6-bioc/meat/geneRxCluster.buildbin-libdir/geneRxCluster/libs/i386/geneRxCluster.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs. The detected symbols are linked into the code but
might come from libraries and not actually be called.

See 'Writing portable packages' in the 'Writing R Extensions' manual.
* checking installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
** running examples for arch 'x64' ... OK
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'doRunit.R'
 OK
** running tests for arch 'x64' ...
  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
  'C:/Users/biocbuild/bbs-3.6-bioc/meat/geneRxCluster.Rcheck/00check.log'
for details.

install for i386

* installing *source* package 'geneRxCluster' ...
** libs
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG     -I"C:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=generic -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);
  ^
C:/Rtools/mingw_32/bin/g++ -shared -s -static-libgcc -o geneRxCluster.dll tmp.def cluster.o -LC:/local323/lib/i386 -LC:/local323/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.6-bioc/meat/geneRxCluster.buildbin-libdir/geneRxCluster/libs/i386
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
  converting help for package 'geneRxCluster'
    finding HTML links ... done
    critVal.alpha                           html  
    critVal.power                           html  
    critVal.target                          html  
    gRxCluster-object                       html  
    finding level-2 HTML links ... done

    gRxCluster                              html  
    gRxPlot                                 html  
    gRxPlotClumps                           html  
    gRxSummary                              html  
    geneRxCluster                           html  
    noprune                                 html  
    plot.cutpoints                          html  
    prune.loglik                            html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL

install for x64

* installing *source* package 'geneRxCluster' ...
** libs
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG     -I"C:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=generic -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);
  ^
C:/Rtools/mingw_64/bin/g++ -shared -s -static-libgcc -o geneRxCluster.dll tmp.def cluster.o -LC:/local323/lib/x64 -LC:/local323/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.6-bioc/meat/geneRxCluster.buildbin-libdir/geneRxCluster/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'geneRxCluster' as geneRxCluster_1.14.0.zip
* DONE (geneRxCluster)
In R CMD INSTALL
In R CMD INSTALL

R version 3.4.4 (2018-03-15) -- "Someone to Lean On"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-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] "C:/Users/biocbuild/bbs-3.6-bioc/meat/geneRxCluster.Rcheck/tests_i386"

$pathToUnitTests
[1] "C:/Users/biocbuild/bbs-3.6-bioc/meat/geneRxCluster.buildbin-libdir/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, cbind, colMeans, colSums, colnames, 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 -- Thu Apr 12 00:16:34 2018 
*********************************************** 
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 
   5.43    0.15    5.57 

R version 3.4.4 (2018-03-15) -- "Someone to Lean On"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (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] "C:/Users/biocbuild/bbs-3.6-bioc/meat/geneRxCluster.Rcheck/tests_x64"

$pathToUnitTests
[1] "C:/Users/biocbuild/bbs-3.6-bioc/meat/geneRxCluster.buildbin-libdir/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, cbind, colMeans, colSums, colnames, 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 -- Thu Apr 12 00:16:41 2018 
*********************************************** 
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 
   6.62    0.17    6.79