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### Running command:
###
###   D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:GSReg.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings GSReg_1.29.0.tar.gz
###
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* using log directory 'D:/biocbuild/bbs-3.15-bioc/meat/GSReg.Rcheck'
* using R Under development (unstable) (2021-11-21 r81221)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'GSReg/DESCRIPTION' ... OK
* this is package 'GSReg' version '1.29.0'
* 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
* 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
* 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 ... OK
* 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 documentation object 'GSReg.GeneSets.DIRAC':
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 documentation object 'GSReg.GeneSets.EVA':
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 documentation object 'GSReg.kendall.tau.distance':
  'GSReg.kendall.tau.distance.template'

Bad \usage lines found in documentation object 'GSReg.overlapJunction':
   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 documentation object 'GSReg.SEVA':
   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 'D:/biocbuild/bbs-3.15-bioc/R/library/GSReg/libs/x64/GSReg.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 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 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: 3 WARNINGs, 4 NOTEs
See
  'D:/biocbuild/bbs-3.15-bioc/meat/GSReg.Rcheck/00check.log'
for details.

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###
### Running command:
###
###   D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL GSReg
###
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* installing to library 'D:/biocbuild/bbs-3.15-bioc/R/library'
* installing *source* package 'GSReg' ...
** using staged installation
** libs
"C:/rtools40/mingw64/bin/"gcc  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c init.c -o init.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c kendallTauDistance.cc -o kendallTauDistance.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c kendallTauDistanceFromTemp.cc -o kendallTauDistanceFromTemp.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c kendallTauDistanceRestricted.cc -o kendallTauDistanceRestricted.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c nij.cc -o nij.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c vect2compC.cc -o vect2compC.o
C:/rtools40/mingw64/bin/g++ -std=gnu++11 -shared -s -static-libgcc -o GSReg.dll tmp.def init.o kendallTauDistance.o kendallTauDistanceFromTemp.o kendallTauDistanceRestricted.o nij.o vect2compC.o -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LD:/biocbuild/bbs-3.15-bioc/R/bin/x64 -lR
installing to D:/biocbuild/bbs-3.15-bioc/R/library/00LOCK-GSReg/00new/GSReg/libs/x64
** R
** data
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'GSReg'
    finding HTML links ... done
    GSReg-package                           html  
    GSReg_GeneSets_DIRAC                    html  
    GSReg_GeneSets_VReg.                    html  
    GSReg_Kendall                           html  
    GSReg_OverlapJunction                   html  
    GSReg_SEVA                              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
* DONE (GSReg)
Making 'packages.html' ... done