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### Running command:
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###   C:\Users\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:biomvRCNS.install-out.txt --library=C:\Users\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings biomvRCNS_1.45.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.20-bioc/meat/biomvRCNS.Rcheck'
* using R version 4.4.1 (2024-06-14 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 'biomvRCNS/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'biomvRCNS' version '1.45.0'
* 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 'biomvRCNS' can be installed ... OK
* used C compiler: 'gcc.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
'library' or 'require' calls in package code:
  'GenomicFeatures' 'cluster' 'dynamicTreeCut' 'parallel'
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
biomvRGviz: no visible global function definition for 'rainbow'
biomvRGviz: no visible global function definition for 'hasArg'
biomvRGviz: no visible global function definition for 'graphics.off'
biomvRGviz: no visible global function definition for 'setEPS'
biomvRGviz: no visible global function definition for 'postscript'
biomvRGviz: no visible global function definition for 'pdf'
biomvRGviz: no visible global function definition for 'dev.off'
biomvRhsmm: no visible global function definition for 'is'
biomvRhsmm: no visible binding for global variable 'mclapply'
biomvRhsmm : <anonymous> : <anonymous>: no visible global function
  definition for 'DataFrame'
biomvRhsmm : <anonymous> : <anonymous>: no visible global function
  definition for 'Rle'
biomvRhsmm: no visible global function definition for 'DataFrame'
biomvRhsmm: no visible binding for global variable 'DataFrame'
biomvRhsmm: no visible global function definition for 'new'
biomvRmgmr: no visible global function definition for 'seqlevels<-'
biomvRmgmr: no visible global function definition for 'DataFrame'
biomvRmgmr: no visible global function definition for 'new'
biomvRseg: no visible global function definition for 'seqlevels<-'
biomvRseg: no visible global function definition for 'DataFrame'
biomvRseg: no visible global function definition for 'new'
estEmis: no visible global function definition for 'clara'
gammaFit: no visible global function definition for 'cov.wt'
hsmmRun: no visible global function definition for 'Rle'
hsmmRun : <anonymous>: no visible global function definition for 'Rle'
hsmmRun: no visible global function definition for 'seqlevels<-'
initEmis : <anonymous>: no visible global function definition for
  'dpois'
initEmis : <anonymous>: no visible global function definition for
  'dnorm'
initEmis : <anonymous>: no visible global function definition for
  'dnbinom'
initEmis : <anonymous>: no visible global function definition for
  'cov2cor'
initEmis : <anonymous>: no visible global function definition for 'dt'
initEmis : <anonymous>: no visible global function definition for
  'cov.wt'
initEmis : <anonymous>: no visible global function definition for
  'weighted.mean'
initSojDd : <anonymous>: no visible global function definition for
  'dgamma'
initSojDd : <anonymous>: no visible global function definition for
  'dpois'
initSojDd : <anonymous>: no visible global function definition for
  'dnbinom'
maxGapminRun: no visible global function definition for 'Rle'
maxGapminRun: no visible global function definition for 'runValue'
nbinomCLLDD: no visible global function definition for 'cov.wt'
nbinomCLLDD: no visible global function definition for 'dnbinom'
poisFit : <anonymous>: no visible global function definition for
  'dpois'
preClustGrp: no visible global function definition for 'dist'
preClustGrp: no visible global function definition for 'hclust'
preClustGrp: no visible global function definition for 'cutreeDynamic'
regionSegAlphaNB: no visible global function definition for 'mclapply'
regionSegCost: no visible global function definition for 'mclapply'
simSegData: no visible global function definition for 'runValue'
simSegData: no visible global function definition for 'Rle'
simSegData: no visible global function definition for 'pdf'
simSegData: no visible global function definition for 'ts.plot'
simSegData: no visible global function definition for 'dev.off'
simUvSegData: no visible global function definition for 'rnorm'
simUvSegData: no visible global function definition for 'rt'
simUvSegData: no visible global function definition for 'rgamma'
simUvSegData: no visible global function definition for 'rpois'
simUvSegData: no visible global function definition for 'rnbinom'
sojournAnno: no visible global function definition for 'is'
sojournAnno: no visible global function definition for 'transcripts'
sojournAnno: no visible global function definition for 'seqlengths'
sojournAnno: no visible global function definition for 'exons'
sojournAnno: no visible global function definition for
  'intronsByTranscript'
splitFarNeighbouryhat: no visible global function definition for
  'runValue'
tmvtfFit: no visible global function definition for 'cov.wt'
unifMJ : <anonymous>: no visible global function definition for 'dunif'
unifMJ : <anonymous> : <anonymous>: no visible global function
  definition for 'dunif'
plot,biomvRCNS-ANY: no visible binding for global variable 'ssetst'
Undefined global functions or variables:
  DataFrame Rle clara cov.wt cov2cor cutreeDynamic dev.off dgamma dist
  dnbinom dnorm dpois dt dunif exons graphics.off hasArg hclust
  intronsByTranscript is mclapply new pdf postscript rainbow rgamma
  rnbinom rnorm rpois rt runValue seqlengths seqlevels<- setEPS ssetst
  transcripts ts.plot weighted.mean
Consider adding
  importFrom("grDevices", "dev.off", "graphics.off", "pdf", "postscript",
             "rainbow", "setEPS")
  importFrom("methods", "hasArg", "is", "new")
  importFrom("stats", "cov.wt", "cov2cor", "dgamma", "dist", "dnbinom",
             "dnorm", "dpois", "dt", "dunif", "hclust", "rgamma",
             "rnbinom", "rnorm", "rpois", "rt", "ts.plot",
             "weighted.mean")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* checking Rd files ... NOTE
checkRd: (-1) sojournAnno.Rd:32: Lost braces
    32 | \item{\\code{...}}{distribution parameters, 'lambda' and 'shift' for 'pois'; 'size', 'mu' and 'shift' for 'nbinom'; 'scale' and 'shape' for 'gamma'}
       |             ^
* 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 compiled code ... NOTE
Note: information on .o files for x64 is not available
File 'C:/Users/biocbuild/bbs-3.20-bioc/R/library/biomvRCNS/libs/x64/biomvRCNS.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' ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
           user system elapsed
biomvRGviz 7.17   0.11    7.42
biomvRhsmm 5.32   0.08    5.40
* 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: 4 NOTEs
See
  'C:/Users/biocbuild/bbs-3.20-bioc/meat/biomvRCNS.Rcheck/00check.log'
for details.

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD INSTALL biomvRCNS
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* installing to library 'C:/Users/biocbuild/bbs-3.20-bioc/R/library'
* installing *source* package 'biomvRCNS' ...
** using staged installation
** libs
using C compiler: 'gcc.exe (GCC) 13.2.0'
gcc  -I"C:/Users/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 biomvRCNS.c -o biomvRCNS.o
gcc -shared -s -static-libgcc -o biomvRCNS.dll tmp.def biomvRCNS.o -LC:/rtools44/x86_64-w64-mingw32.static.posix/lib/x64 -LC:/rtools44/x86_64-w64-mingw32.static.posix/lib -LC:/Users/biocbuild/bbs-3.20-bioc/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.20-bioc/R/library/00LOCK-biomvRCNS/00new/biomvRCNS/libs/x64
** R
** data
** inst
** 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 (biomvRCNS)