Back to Multiple platform build/check report for BioC 3.14
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This page was generated on 2021-11-24 15:05:42 -0500 (Wed, 24 Nov 2021).

CHECK results for R3CPET on tokay2

To the developers/maintainers of the R3CPET package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/R3CPET.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 1515/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
R3CPET 1.26.0  (landing page)
Mohamed Nadhir Djekidel
Snapshot Date: 2021-11-23 04:15:06 -0500 (Tue, 23 Nov 2021)
git_url: https://git.bioconductor.org/packages/R3CPET
git_branch: RELEASE_3_14
git_last_commit: bbe68cd
git_last_commit_date: 2021-10-26 12:20:21 -0500 (Tue, 26 Oct 2021)
nebbiolo2Linux (Ubuntu 20.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: R3CPET
Version: 1.26.0
Command: C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:R3CPET.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings R3CPET_1.26.0.tar.gz
StartedAt: 2021-11-24 03:07:14 -0500 (Wed, 24 Nov 2021)
EndedAt: 2021-11-24 03:14:44 -0500 (Wed, 24 Nov 2021)
EllapsedTime: 450.2 seconds
RetCode: 0
Status:   OK  
CheckDir: R3CPET.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:R3CPET.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings R3CPET_1.26.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.14-bioc/meat/R3CPET.Rcheck'
* using R version 4.1.2 (2021-11-01)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'R3CPET/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'R3CPET' version '1.26.0'
* 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 'R3CPET' can be installed ... OK
* checking installed package size ... NOTE
  installed size is  8.4Mb
  sub-directories of 1Mb or more:
    data      3.0Mb
    example   1.0Mb
    libs      2.1Mb
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Package listed in more than one of Depends, Imports, Suggests, Enhances:
  'methods'
A package should be listed in only one of these fields.
* 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
* 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 dependencies in R code ... NOTE
Namespace in Imports field not imported from: 'BiocGenerics'
  All declared Imports should be used.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
.GetClusterInfo: no visible binding for global variable
  'TxDb.Hsapiens.UCSC.hg19.knownGene'
.GetClusterInfo: no visible global function definition for 'toTable'
.GetClusterInfo: no visible binding for global variable
  'org.Hs.egUCSCKG'
.GetClusterInfo: no visible global function definition for 'select'
.GetClusterInfo: no visible binding for global variable 'org.Hs.eg.db'
.formatDAVIDResult: no visible global function definition for
  'formatGeneReportFull'
.formatDAVIDResult: no visible global function definition for
  'formatGeneReport'
.formatDAVIDResult: no visible global function definition for
  'formatList'
.formatDAVIDResult: no visible global function definition for
  'formatGene2Gene'
.formatDAVIDResult: no visible global function definition for
  'formatAnnotationReport'
.get.NetworksGenes: no visible global function definition for
  'annotatePeakInBatch'
.plot.sota: no visible global function definition for 'legend'
.plot.sota: no visible global function definition for 'lines'
EnsemblToHGNC: no visible global function definition for 'useMart'
EnsemblToHGNC: no visible global function definition for 'useDataset'
EnsemblToHGNC: no visible global function definition for 'getBM'
EntrezToHGNC: no visible global function definition for 'useMart'
EntrezToHGNC: no visible global function definition for 'useDataset'
EntrezToHGNC: no visible global function definition for 'getBM'
RunHLDA: no visible binding for global variable '_R3CPET_RunHLDA'
createServer,ChiapetExperimentData-NetworkCollection-ChromMaintainers:
  no visible global function definition for 'runApp'
plot3CPETRes,ChromMaintainers: no visible global function definition
  for 'plotCurves'
plot3CPETRes,ChromMaintainers: no visible global function definition
  for 'plotAvgCurves'
Undefined global functions or variables:
  TxDb.Hsapiens.UCSC.hg19.knownGene _R3CPET_RunHLDA annotatePeakInBatch
  formatAnnotationReport formatGene2Gene formatGeneReport
  formatGeneReportFull formatList getBM legend lines org.Hs.eg.db
  org.Hs.egUCSCKG plotAvgCurves plotCurves runApp select toTable
  useDataset useMart
Consider adding
  importFrom("graphics", "legend", "lines")
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 contents of 'data' directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking use of PKG_*FLAGS 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-3.14-bioc/R/library/R3CPET/libs/i386/R3CPET.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
  Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
  Found 'printf', possibly from 'printf' (C)
  Found 'rand', possibly from 'rand' (C)
File 'C:/Users/biocbuild/bbs-3.14-bioc/R/library/R3CPET/libs/x64/R3CPET.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
  Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
  Found 'printf', possibly from 'printf' (C)
  Found 'rand', possibly from 'rand' (C)

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 'tests.R'
 OK
** running tests for arch 'x64' ...
  Running 'tests.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: 5 NOTEs
See
  'C:/Users/biocbuild/bbs-3.14-bioc/meat/R3CPET.Rcheck/00check.log'
for details.



Installation output

R3CPET.Rcheck/00install.out

##############################################################################
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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.14/bioc/src/contrib/R3CPET_1.26.0.tar.gz && rm -rf R3CPET.buildbin-libdir && mkdir R3CPET.buildbin-libdir && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=R3CPET.buildbin-libdir R3CPET_1.26.0.tar.gz && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL R3CPET_1.26.0.zip && rm R3CPET_1.26.0.tar.gz R3CPET_1.26.0.zip
###
##############################################################################
##############################################################################


  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
 11 5374k   11  643k    0     0  1162k      0  0:00:04 --:--:--  0:00:04 1163k
 51 5374k   51 2744k    0     0  1760k      0  0:00:03  0:00:01  0:00:02 1759k
100 5374k  100 5374k    0     0  2206k      0  0:00:02  0:00:02 --:--:-- 2207k

install for i386

* installing *source* package 'R3CPET' ...
** using staged installation
** libs
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c R3CPET_init.c -o R3CPET_init.o
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c RcppExports.cpp -o RcppExports.o
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c corpus.cpp -o corpus.o
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c main.cpp -o main.o
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c state.cpp -o state.o
state.cpp: In member function 'int HDP::sample_word_assignment(DocState*, int, bool, vct*)':
state.cpp:253:10: warning: 'k' may be used uninitialized in this function [-Wmaybe-uninitialized]
   return int(old_k != k);
          ^~~~~~~~~~~~~~~
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c stirln.cpp -o stirln.o
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c utils.cpp -o utils.o
C:/rtools40/mingw32/bin/g++ -std=gnu++11 -shared -s -static-libgcc -o R3CPET.dll tmp.def R3CPET_init.o RcppExports.o corpus.o main.o state.o stirln.o utils.o -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.14-/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.14-bioc/meat/R3CPET.buildbin-libdir/00LOCK-R3CPET/00new/R3CPET/libs/i386
** R
** data
** inst
** byte-compile and prepare package for lazy loading
NOTE: arguments in definition for validity method for class 'ChromMaintainers' changed from (x) to (object)
NOTE: arguments in definition for validity method for class 'HLDAResult' changed from (x) to (object)
NOTE: arguments in definition for validity method for class 'NetworkCollection' changed from (x) to (object)
** help
*** installing help indices
  converting help for package 'R3CPET'
    finding HTML links ... done
    Biogrid                                 html  
    finding level-2 HTML links ... done

    ChiapetExperimentData-class             html  
    ChromMaintainers-class                  html  
    CreateCenteredBED-methods               html  
    EnsemblToHGNC                           html  
    EntrezToHGNC                            html  
    GOEnrich-methods                        html  
    GenerateNetworks-methods                html  
    HLDAResult-class                        html  
    HPRD                                    html  
    InferNetworks-methods                   html  
    NetworkCollection-class                 html  
    PrepareData-methods                     html  
    R3CPET-package                          html  
    RPKMS                                   html  
    annotateExpression-methods              html  
    buildNetworks-methods                   html  
    chromosoms                              html  
REDIRECT:topic	 Previous alias or file overwritten by alias: C:/Users/biocbuild/bbs-3.14-bioc/meat/R3CPET.buildbin-libdir/00LOCK-R3CPET/00new/R3CPET/help/Chromosoms.html
    cluesOrSota-class                       html  
    clusterInteractions-methods             html  
    createIndexes-methods                   html  
    createServer-methods                    html  
    geneLocations                           html  
    getRegionsInNetwork-methods             html  
    getRegionsIncluster-methods             html  
    loadPETs-methods                        html  
    loadPPI-methods                         html  
    loadTFBS-methods                        html  
    outputGenesPerClusterToDir-methods      html  
    outputGenesPerNetworkToDir-methods      html  
    plotRes-methods                         html  
    plotTrack                               html  
    updateResults-methods                   html  
    visualizeCircos-methods                 html  
    visualizeInteractions-methods           html  
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path

install for x64

* installing *source* package 'R3CPET' ...
** libs
"C:/rtools40/mingw64/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c R3CPET_init.c -o R3CPET_init.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c RcppExports.cpp -o RcppExports.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c corpus.cpp -o corpus.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c main.cpp -o main.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c state.cpp -o state.o
state.cpp: In member function 'int HDP::sample_word_assignment(DocState*, int, bool, vct*)':
state.cpp:253:10: warning: 'k' may be used uninitialized in this function [-Wmaybe-uninitialized]
   return int(old_k != k);
          ^~~~~~~~~~~~~~~
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c stirln.cpp -o stirln.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c utils.cpp -o utils.o
C:/rtools40/mingw64/bin/g++ -std=gnu++11 -shared -s -static-libgcc -o R3CPET.dll tmp.def R3CPET_init.o RcppExports.o corpus.o main.o state.o stirln.o utils.o -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.14-/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.14-bioc/meat/R3CPET.buildbin-libdir/R3CPET/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'R3CPET' as R3CPET_1.26.0.zip
* DONE (R3CPET)
* installing to library 'C:/Users/biocbuild/bbs-3.14-bioc/R/library'
package 'R3CPET' successfully unpacked and MD5 sums checked

Tests output

R3CPET.Rcheck/tests_i386/tests.Rout


R version 4.1.2 (2021-11-01) -- "Bird Hippie"
Copyright (C) 2021 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.

> test_create_ChiapetExperimentData <- function(){
+     x <- ChiapetExperimentData()
+     checkTrue(class(x) == "ChiapetExperimentData", 
+                 "No problem creating ChiapetExperimentData ")
+ }
> 
> test_interactions_file <- function(){
+     petFile <- file.path(system.file("example",package="R3CPET"),
+                          "HepG2_interactions.txt")
+     
+     chechTrue(file.exists(petFile))
+ }
> 
> test_TFBS_file <- function(){
+     tfFile <- file.path(system.file("example",package="R3CPET"),
+                         "HepG2_TF.txt.gz")
+     chechTrue(file.exists(tfFile))
+ }
> 
> test_loadPETS <- function(){
+     x <- ChiapetExperimentData()
+     checkEquals(class(x),"ChiapetExperimentData")
+     petFile <- file.path(system.file("example",package="R3CPET"),
+                          "HepG2_interactions.txt")
+     
+     test_interactions_file()
+     
+     x <- loadPETs(x,petFile=petFile, IsBed=FALSE)
+     
+     checkTrue(length(pet(x)) >0, "PETs can be loadded")
+ }
> 
> test_loadPETS <- function(){
+     x <- ChiapetExperimentData()
+     checkEquals(class(x),"ChiapetExperimentData")
+     tfFile <- file.path(system.file("example",package="R3CPET"),
+                         "HepG2_TF.txt.gz")
+     
+     test_TFBS_file()
+     
+     x <- loadTFBS(x,tfbsFile= tfFile)
+     
+     checkTrue(length(tfbs(x)) >0, "TFBS can be loadded")
+ }
> 
> 
> test_createIndex <- function(){
+     x <- ChiapetExperimentData()
+     
+     
+     tfFile <- file.path(system.file("example",package="R3CPET"),
+                         "HepG2_TF.txt.gz")
+     x <- loadTFBS(x,tfbsFile= tfFile)
+     
+     petFile <- file.path(system.file("example",package="R3CPET"),
+                          "HepG2_interactions.txt")
+     x <- loadPETs(x,petFile=petFile, IsBed=FALSE)
+     
+     x<- createIndexes(x)
+     
+     checkEquals(length(x@.dt),3)
+     checkIdentical(names(x@.dt), c("PET","motifs", "hasMotif"))
+     
+     for(i in 1:3) checkTrue("data.table" %in% class(x@.dt[[i]]) )
+ }
> 
> proc.time()
   user  system elapsed 
   0.26    0.06    0.31 

R3CPET.Rcheck/tests_x64/tests.Rout


R version 4.1.2 (2021-11-01) -- "Bird Hippie"
Copyright (C) 2021 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.

> test_create_ChiapetExperimentData <- function(){
+     x <- ChiapetExperimentData()
+     checkTrue(class(x) == "ChiapetExperimentData", 
+                 "No problem creating ChiapetExperimentData ")
+ }
> 
> test_interactions_file <- function(){
+     petFile <- file.path(system.file("example",package="R3CPET"),
+                          "HepG2_interactions.txt")
+     
+     chechTrue(file.exists(petFile))
+ }
> 
> test_TFBS_file <- function(){
+     tfFile <- file.path(system.file("example",package="R3CPET"),
+                         "HepG2_TF.txt.gz")
+     chechTrue(file.exists(tfFile))
+ }
> 
> test_loadPETS <- function(){
+     x <- ChiapetExperimentData()
+     checkEquals(class(x),"ChiapetExperimentData")
+     petFile <- file.path(system.file("example",package="R3CPET"),
+                          "HepG2_interactions.txt")
+     
+     test_interactions_file()
+     
+     x <- loadPETs(x,petFile=petFile, IsBed=FALSE)
+     
+     checkTrue(length(pet(x)) >0, "PETs can be loadded")
+ }
> 
> test_loadPETS <- function(){
+     x <- ChiapetExperimentData()
+     checkEquals(class(x),"ChiapetExperimentData")
+     tfFile <- file.path(system.file("example",package="R3CPET"),
+                         "HepG2_TF.txt.gz")
+     
+     test_TFBS_file()
+     
+     x <- loadTFBS(x,tfbsFile= tfFile)
+     
+     checkTrue(length(tfbs(x)) >0, "TFBS can be loadded")
+ }
> 
> 
> test_createIndex <- function(){
+     x <- ChiapetExperimentData()
+     
+     
+     tfFile <- file.path(system.file("example",package="R3CPET"),
+                         "HepG2_TF.txt.gz")
+     x <- loadTFBS(x,tfbsFile= tfFile)
+     
+     petFile <- file.path(system.file("example",package="R3CPET"),
+                          "HepG2_interactions.txt")
+     x <- loadPETs(x,petFile=petFile, IsBed=FALSE)
+     
+     x<- createIndexes(x)
+     
+     checkEquals(length(x@.dt),3)
+     checkIdentical(names(x@.dt), c("PET","motifs", "hasMotif"))
+     
+     for(i in 1:3) checkTrue("data.table" %in% class(x@.dt[[i]]) )
+ }
> 
> proc.time()
   user  system elapsed 
   0.26    0.06    0.31 

Example timings

R3CPET.Rcheck/examples_i386/R3CPET-Ex.timings

nameusersystemelapsed
Biogrid1.080.031.11
ChiapetExperimentData-class000
ChromMaintainers-class0.020.000.02
CreateCenteredBED-methods0.010.001.09
EnsemblToHGNC000
EntrezToHGNC000
GOEnrich-methods0.020.000.02
GenerateNetworks-methods000
HLDAResult-class000
HPRD0.140.000.14
InferNetworks-methods000
NetworkCollection-class000
PrepareData-methods000
RPKMS0.130.000.13
annotateExpression-methods000
buildNetworks-methods000
chromosoms0.010.000.01
cluesOrSota-class000
clusterInteractions-methods0.110.010.13
createIndexes-methods000
createServer-methods000
geneLocations0.190.020.21
getRegionsInNetwork-methods000
getRegionsIncluster-methods0.000.020.01
loadPETs-methods0.280.090.39
loadPPI-methods0.670.060.74
loadTFBS-methods0.610.080.72
outputGenesPerClusterToDir-methods000
outputGenesPerNetworkToDir-methods0.010.000.01
plotRes-methods000
plotTrack000
updateResults-methods000
visualizeCircos-methods0.000.020.02
visualizeInteractions-methods000

R3CPET.Rcheck/examples_x64/R3CPET-Ex.timings

nameusersystemelapsed
Biogrid0.500.030.53
ChiapetExperimentData-class000
ChromMaintainers-class000
CreateCenteredBED-methods000
EnsemblToHGNC0.000.020.01
EntrezToHGNC000
GOEnrich-methods000
GenerateNetworks-methods000
HLDAResult-class000
HPRD1.140.001.14
InferNetworks-methods000
NetworkCollection-class000
PrepareData-methods000
RPKMS0.060.000.06
annotateExpression-methods000
buildNetworks-methods000
chromosoms000
cluesOrSota-class0.010.000.02
clusterInteractions-methods0.050.000.05
createIndexes-methods000
createServer-methods000
geneLocations0.080.010.09
getRegionsInNetwork-methods000
getRegionsIncluster-methods000
loadPETs-methods0.220.000.22
loadPPI-methods0.340.020.36
loadTFBS-methods0.390.000.40
outputGenesPerClusterToDir-methods000
outputGenesPerNetworkToDir-methods000
plotRes-methods000
plotTrack000
updateResults-methods000
visualizeCircos-methods000
visualizeInteractions-methods000