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### Running command:
###
###   F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:GSReg.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings GSReg_1.39.0.tar.gz
###
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* using log directory 'F:/biocbuild/bbs-3.20-bioc/meat/GSReg.Rcheck'
* using R version 4.4.0 RC (2024-04-16 r86468 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 'GSReg/DESCRIPTION' ... OK
* this is package 'GSReg' version '1.39.0'
* 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 'GSReg' 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 ... 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 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
Packages in Depends field not imported from:
  'AnnotationDbi' 'GenomicFeatures' 'Homo.sapiens' 'org.Hs.eg.db'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
GSReg.DIRAC.Pathways: no visible global function definition for 'pnorm'
GSReg.DIRAC.mu: no visible global function definition for 'var'
GSReg.Variance: no visible global function definition for 'var'
GSReg.Variance: no visible global function definition for 'pnorm'
GSReg.kendall.tau.distance.Restricted.Sparse.internal: no visible
  global function definition for 'as'
GSReg.overlapJunction: no visible binding for global variable
  'TxDb.Hsapiens.UCSC.hg19.knownGene'
GSReg.overlapJunction: no visible binding for global variable
  'org.Hs.eg.db'
GSReg.overlapJunction: no visible global function definition for
  'genes'
GSReg.overlapJunction: no visible global function definition for
  'mapIds'
GSReg.overlapJunction: no visible global function definition for
  'GRanges'
GSReg.overlapJunction: no visible global function definition for 'Rle'
GSReg.overlapJunction: no visible global function definition for
  'IRanges'
GSReg.overlapJunction: no visible global function definition for
  'findOverlaps'
GSReg.overlapJunction: no visible global function definition for
  'queryHits'
GSReg.overlapJunction: no visible global function definition for
  'subjectHits'
GSReg.overlapJunction : <anonymous>: no visible global function
  definition for 'findOverlaps'
GSReg.overlapJunction : <anonymous>: no visible global function
  definition for 'Matrix'
GSReg.overlapJunction : <anonymous>: no visible global function
  definition for 'queryHits'
GSReg.overlapJunction : <anonymous>: no visible global function
  definition for 'subjectHits'
Undefined global functions or variables:
  GRanges IRanges Matrix Rle TxDb.Hsapiens.UCSC.hg19.knownGene as
  findOverlaps genes mapIds org.Hs.eg.db pnorm queryHits subjectHits
  var
Consider adding
  importFrom("methods", "as")
  importFrom("stats", "pnorm", "var")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* checking Rd files ... NOTE
checkRd: (-1) GSReg-package.Rd:20: Lost braces; missing escapes or markup?
    20 |   {B)  Calculate the DIRAC measure and p-value for it based on permutation test;}
       |   ^
checkRd: (-1) GSReg-package.Rd:22: Lost braces; missing escapes or markup?
    22 |   {C)  Calculate for a modified DIRAC method and a fast-efficient p-valuebased on U-Statistic theory;}
       |   ^
checkRd: (-1) GSReg-package.Rd:24: Lost braces; missing escapes or markup?
    24 |   {D)  Alternative Splicing Events in genes from a phenotype to other phenotype using their junction expression;}
       |   ^
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... WARNING
Undocumented code objects:
  'GSReg.kendall.tau.distance.template'
Undocumented data sets:
  'geneExrsGSReg' 'junc.RPM.Simulated' 'phenotypes'
All user-level objects in a package should have documentation entries.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
* checking for code/documentation mismatches ... WARNING
Codoc mismatches from Rd file 'GSReg_GeneSets_DIRAC.Rd':
GSReg.GeneSets.DIRAC
  Code: function(geneexpres, pathways, phenotypes, Nperm = 0, alpha =
                 0, minGeneNum = 5)
  Docs: function(geneexpres, pathways, phenotypes, Nperm = 0, alpha =
                 0.05, minGeneNum = 5)
  Mismatches in argument default values:
    Name: 'alpha' Code: 0 Docs: 0.05

Codoc mismatches from Rd file 'GSReg_GeneSets_VReg..Rd':
GSReg.GeneSets.EVA
  Code: function(geneexpres, pathways, phenotypes, verbose = T,
                 minGeneNum = 5, distFunc = GSReg.kendall.tau.distance,
                 distparamPathways, ...)
  Docs: function(geneexpres, pathways, phenotypes, minGeneNum = 5)
  Argument names in code not in docs:
    verbose distFunc distparamPathways ...
  Mismatches in argument names:
    Position: 4 Code: verbose Docs: minGeneNum

* checking Rd \usage sections ... WARNING
Objects in \usage without \alias in Rd file 'GSReg_Kendall.Rd':
  'GSReg.kendall.tau.distance.template'

Bad \usage lines found in Rd file 'GSReg_OverlapJunction.Rd':
   GSReg.overlapJunction <- function(juncExprs,
                                    GenestoStudy=NULL,
                                    geneexpr=NULL,
                                    minmeanloggeneexp= 3,
                                    alpha =0,
                                    sparse = F,
                                    genesCoordinatesTxDB = TxDb.Hsapiens.UCSC.hg19.knownGene, 
                                    geneIDInTxDB = 'ENTREZID', 
                                    geneIDOut = 'SYMBOL',
                                    org=org.Hs.eg.db, ...) 
Bad \usage lines found in Rd file 'GSReg_SEVA.Rd':
   function(juncExprs,
  		  phenoVect, 
            verbose=T,
            sparse =F, ...)

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
* 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 compiled code ... NOTE
Note: information on .o files for x64 is not available
File 'F:/biocbuild/bbs-3.20-bioc/R/library/GSReg/libs/x64/GSReg.dll':
  Found '_exit', possibly from '_exit' (C)
  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 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 files in 'vignettes' ... NOTE
The following files look like leftovers/mistakes:
  'Rplots.pdf'
Please remove them from your package.
* checking examples ... 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: 3 WARNINGs, 5 NOTEs
See
  'F:/biocbuild/bbs-3.20-bioc/meat/GSReg.Rcheck/00check.log'
for details.

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###
### Running command:
###
###   F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD INSTALL GSReg
###
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* installing to library 'F:/biocbuild/bbs-3.20-bioc/R/library'
* installing *source* package 'GSReg' ...
** 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-3.20-bioc/R/include" -DNDEBUG     -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c init.c -o init.o
g++ -std=gnu++17  -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG     -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c kendallTauDistance.cc -o kendallTauDistance.o
g++ -std=gnu++17  -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG     -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c kendallTauDistanceFromTemp.cc -o kendallTauDistanceFromTemp.o
g++ -std=gnu++17  -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG     -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c kendallTauDistanceRestricted.cc -o kendallTauDistanceRestricted.o
g++ -std=gnu++17  -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG     -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c nij.cc -o nij.o
g++ -std=gnu++17  -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG     -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c vect2compC.cc -o vect2compC.o
g++ -std=gnu++17 -shared -s -static-libgcc -o GSReg.dll tmp.def init.o kendallTauDistance.o kendallTauDistanceFromTemp.o kendallTauDistanceRestricted.o nij.o vect2compC.o -LC:/rtools44/x86_64-w64-mingw32.static.posix/lib/x64 -LC:/rtools44/x86_64-w64-mingw32.static.posix/lib -LF:/biocbuild/bbs-3.20-bioc/R/bin/x64 -lR
installing to F:/biocbuild/bbs-3.20-bioc/R/library/00LOCK-GSReg/00new/GSReg/libs/x64
** R
** data
** byte-compile and prepare package for lazy loading
** 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 (GSReg)