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### Running command:
###
###   F:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:R3CPET.install-out.txt --library=F:\biocbuild\bbs-3.19-bioc\R\library --no-vignettes --timings R3CPET_1.35.1.tar.gz
###
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* using log directory 'F:/biocbuild/bbs-3.19-bioc/meat/R3CPET.Rcheck'
* using R Under development (unstable) (2024-03-16 r86144 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 13.2.0
    GNU Fortran (GCC) 13.2.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'R3CPET/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'R3CPET' version '1.35.1'
* 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 ... NOTE
Found the following hidden files and directories:
  .BBSoptions
These were most likely included in error. See section 'Package
structure' in the 'Writing R Extensions' manual.
* checking for portable file names ... OK
* checking whether package 'R3CPET' can be installed ... OK
* used C compiler: 'gcc.exe (GCC) 13.2.0'
* used C++ compiler: 'G__~1.EXE (GCC) 13.2.0'
* checking installed package size ... NOTE
  installed size is  6.9Mb
  sub-directories of 1Mb or more:
    data      3.0Mb
    example   1.0Mb
* 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 code 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 ... 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 ... WARNING
checkRd: (5) ChiapetExperimentData-class.Rd:109-124: \item in \describe must have non-empty label
checkRd: (5) ChiapetExperimentData-class.Rd:125-128: \item in \describe must have non-empty label
checkRd: (5) ChiapetExperimentData-class.Rd:129-132: \item in \describe must have non-empty label
* 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 x64 is not available
File 'F:/biocbuild/bbs-3.19-bioc/R/library/R3CPET/libs/x64/R3CPET.dll':
  Found '_exit', possibly from '_exit' (C)
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
  Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
  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 nor [v]sprintf. 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 sizes of PDF files under 'inst/doc' ... 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 'tests.R'
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 1 WARNING, 6 NOTEs
See
  'F:/biocbuild/bbs-3.19-bioc/meat/R3CPET.Rcheck/00check.log'
for details.

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###
### Running command:
###
###   F:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD INSTALL R3CPET
###
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* installing to library 'F:/biocbuild/bbs-3.19-bioc/R/library'
* installing *source* package 'R3CPET' ...
** using staged installation
** libs
using C compiler: 'gcc.exe (GCC) 13.2.0'
using C++ compiler: 'G__~1.EXE (GCC) 13.2.0'
gcc  -I"F:/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.19-bioc/R/library/Rcpp/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c R3CPET_init.c -o R3CPET_init.o
g++ -std=gnu++17  -I"F:/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.19-bioc/R/library/Rcpp/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++17  -I"F:/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.19-bioc/R/library/Rcpp/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c corpus.cpp -o corpus.o
g++ -std=gnu++17  -I"F:/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.19-bioc/R/library/Rcpp/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c main.cpp -o main.o
g++ -std=gnu++17  -I"F:/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.19-bioc/R/library/Rcpp/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/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 [-Wmaybe-uninitialized]
  253 |   return int(old_k != k);
      |          ^~~~~~~~~~~~~~~
state.cpp:193:19: note: 'k' was declared here
  193 |   int old_k = -1, k;
      |                   ^
g++ -std=gnu++17  -I"F:/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.19-bioc/R/library/Rcpp/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c stirln.cpp -o stirln.o
g++ -std=gnu++17  -I"F:/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.19-bioc/R/library/Rcpp/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c utils.cpp -o utils.o
g++ -std=gnu++17 -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:/rtools44/x86_64-w64-mingw32.static.posix/lib/x64 -LC:/rtools44/x86_64-w64-mingw32.static.posix/lib -LF:/biocbuild/bbs-3.19-bioc/R/bin/x64 -lR
installing to F:/biocbuild/bbs-3.19-bioc/R/library/00LOCK-R3CPET/00new/R3CPET/libs/x64
** 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
** 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
* DONE (R3CPET)

R Under development (unstable) (2024-03-16 r86144 ucrt) -- "Unsuffered Consequences"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64

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 
   0.15    0.10    0.25