Package: R3CPET

Version: 1.12.0

Command: C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:R3CPET.install-out.txt --library=C:\Users\biocbuild\bbs-3.7-bioc\R\library --no-vignettes --timings R3CPET_1.12.0.tar.gz

StartedAt: 2018-10-17 04:12:44 -0400 (Wed, 17 Oct 2018)

EndedAt: 2018-10-17 04:19:20 -0400 (Wed, 17 Oct 2018)

EllapsedTime: 395.9 seconds

RetCode: 0

Status:  OK

CheckDir: R3CPET.Rcheck

Warnings: 0

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### Running command:
###
###   C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:R3CPET.install-out.txt --library=C:\Users\biocbuild\bbs-3.7-bioc\R\library --no-vignettes --timings R3CPET_1.12.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.7-bioc/meat/R3CPET.Rcheck'
* using R version 3.5.1 Patched (2018-07-24 r75005)
* 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 '1.12.0'
* 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 whether package 'R3CPET' can be installed ... OK
* checking installed package size ... NOTE
  installed size is  7.5Mb
  sub-directories of 1Mb or more:
    data      3.0Mb
    example   1.0Mb
    libs      1.6Mb
* 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'
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'
createServer,ChiapetExperimentData-NetworkCollection-ChromMaintainers:
  no visible global function definition for 'runApp'
Undefined global functions or variables:
  TxDb.Hsapiens.UCSC.hg19.knownGene annotatePeakInBatch
  formatAnnotationReport formatGene2Gene formatGeneReport
  formatGeneReportFull formatList getBM org.Hs.eg.db org.Hs.egUCSCKG
  runApp select toTable useDataset useMart
* 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 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-3.7-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)

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-3.7-bioc/meat/R3CPET.Rcheck/00check.log'
for details.

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.7/bioc/src/contrib/R3CPET_1.12.0.tar.gz && rm -rf R3CPET.buildbin-libdir && mkdir R3CPET.buildbin-libdir && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=R3CPET.buildbin-libdir R3CPET_1.12.0.tar.gz && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL R3CPET_1.12.0.zip && rm R3CPET_1.12.0.tar.gz R3CPET_1.12.0.zip
###
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100 5377k  100 5377k    0     0  39.4M      0 --:--:-- --:--:-- --:--:-- 41.6M

install for i386

* installing *source* package 'R3CPET' ...
** libs
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include"   -I"C:/extsoft/include"     -O3 -Wall  -std=gnu99 -mtune=generic -c R3CPET_init.c -o R3CPET_init.o
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c RcppExports.cpp -o RcppExports.o
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c corpus.cpp -o corpus.o
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c main.cpp -o main.o
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c state.cpp -o state.o
state.cpp: In member function 'int HDP::sample_word_assignment(DocState*, int, bool, vct*)':
state.cpp:253:20: warning: 'k' may be used uninitialized in this function [-Wmaybe-uninitialized]
   return int(old_k != k);
                    ^
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c stirln.cpp -o stirln.o
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c utils.cpp -o utils.o
C:/Rtools/mingw_32/bin/g++ -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˜1.7-B/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.7-bioc/meat/R3CPET.buildbin-libdir/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  
    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
In R CMD INSTALL

install for x64

* installing *source* package 'R3CPET' ...
** libs
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include"   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c R3CPET_init.c -o R3CPET_init.o
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c RcppExports.cpp -o RcppExports.o
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c corpus.cpp -o corpus.o
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c main.cpp -o main.o
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c state.cpp -o state.o
state.cpp: In member function 'int HDP::sample_word_assignment(DocState*, int, bool, vct*)':
state.cpp:253:20: warning: 'k' may be used uninitialized in this function [-Wmaybe-uninitialized]
   return int(old_k != k);
                    ^
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c stirln.cpp -o stirln.o
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c utils.cpp -o utils.o
C:/Rtools/mingw_64/bin/g++ -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˜1.7-B/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.7-bioc/meat/R3CPET.buildbin-libdir/R3CPET/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'R3CPET' as R3CPET_1.12.0.zip
* DONE (R3CPET)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.7-bioc/R/library'
package 'R3CPET' successfully unpacked and MD5 sums checked
In R CMD INSTALL

R version 3.5.1 Patched (2018-07-24 r75005) -- "Feather Spray"
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.

> 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    0.04    0.28 

R version 3.5.1 Patched (2018-07-24 r75005) -- "Feather Spray"
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.

> 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 
   0.18    0.06    0.21