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### Running command:
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###   /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:compartmap.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings compartmap_1.21.1.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/compartmap.Rcheck’
* using R Under development (unstable) (2024-03-18 r86148)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
    GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
* running under: Ubuntu 22.04.4 LTS
* using session charset: UTF-8
* checking for file ‘compartmap/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘compartmap’ version ‘1.21.1’
* package encoding: UTF-8
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘compartmap’ 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 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 loading without being on the library search path ... OK
* checking whether startup messages can be suppressed ... OK
* checking dependencies in R code ... NOTE
package 'methods' is used but not declared
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
.ebayes: no visible global function definition for ‘sd’
.jse: no visible global function definition for ‘sd’
.unitarize: no visible global function definition for ‘median’
.window.mean: no visible global function definition for ‘weighted.mean’
.window.mean.rcpp: no visible global function definition for
  ‘weighted.mean’
.window.mean.rcpp: no visible binding for global variable ‘x’
checkAssayType: no visible global function definition for ‘is’
condenseRE: no visible global function definition for ‘is’
condenseSE: no visible global function definition for ‘is’
estRMT: no visible global function definition for ‘cov’
estRMT : <anonymous>: no visible global function definition for ‘optim’
extractOpenClosed: no visible global function definition for ‘is’
filterCompartments: no visible global function definition for ‘is’
fixCompartments: no visible global function definition for ‘is’
getATACABsignal : atacCompartments: no visible global function
  definition for ‘keepSeqlevels’
getATACABsignal : atacCompartments: no visible global function
  definition for ‘as’
getATACABsignal : <anonymous>: no visible global function definition
  for ‘as’
getATACABsignal: no visible global function definition for ‘as’
getBinMatrix: no visible global function definition for ‘IRanges’
getCorMatrix: no visible global function definition for ‘cor’
getDenoisedCorMatrix: no visible global function definition for
  ‘keepSeqlevels’
getDomainInflections: no visible global function definition for ‘is’
getDomainInflections: no visible global function definition for ‘data’
getDomainInflections: no visible global function definition for
  ‘seqlengths’
getDomainInflections: no visible global function definition for
  ‘queryHits’
getDomainInflections: no visible global function definition for
  ‘subjectHits’
getDomainInflections : .getInflections: no visible global function
  definition for ‘IRanges’
getDomainInflections: no visible global function definition for ‘as’
getRNAABsignal : atacCompartments: no visible global function
  definition for ‘keepSeqlevels’
getRNAABsignal : atacCompartments: no visible global function
  definition for ‘as’
getRNAABsignal : <anonymous>: no visible global function definition for
  ‘as’
getRNAABsignal: no visible global function definition for ‘as’
getSVD: no visible global function definition for ‘cor’
getSeqLengths: no visible global function definition for ‘data’
getSeqLengths: no visible global function definition for ‘seqlevels’
getSeqLengths: no visible global function definition for ‘seqlengths’
hdf5TFIDF: no visible global function definition for ‘is’
hdf5TFIDF: no visible global function definition for ‘as’
importBigWig: no visible global function definition for
  ‘seqlevelsStyle<-’
importBigWig: no visible global function definition for ‘seqlengths’
importBigWig: no visible global function definition for
  ‘keepStandardChromosomes’
importBigWig: no visible global function definition for ‘keepSeqlevels’
importBigWig: no visible global function definition for ‘seqlevels’
importBigWig: no visible global function definition for ‘SimpleList’
meanSmoother: no visible global function definition for ‘median’
plotAB: no visible global function definition for ‘is’
plotAB: no visible global function definition for ‘keepSeqlevels’
plotAB: no visible global function definition for ‘as’
plotAB: no visible global function definition for ‘par’
plotAB: no visible global function definition for ‘barplot’
plotAB: no visible global function definition for ‘abline’
plotAB: no visible global function definition for ‘median’
plotCorMatrix: no visible binding for global variable ‘Var2’
plotCorMatrix: no visible binding for global variable ‘Var1’
plotCorMatrix: no visible binding for global variable ‘value’
precomputeBootstrapMeans : <anonymous>: no visible global function
  definition for ‘SimpleList’
sparseToDenseMatrix: no visible global function definition for ‘as’
sparseToDenseMatrix : <anonymous>: no visible global function
  definition for ‘as’
summarizeBootstraps : <anonymous>: no visible global function
  definition for ‘subjectHits’
summarizeBootstraps : <anonymous>: no visible global function
  definition for ‘queryHits’
transformTFIDF: no visible global function definition for ‘is’
as.matrix,GRanges: no visible global function definition for ‘as’
coerce,GRanges-matrix: no visible global function definition for ‘as’
coerce,matrix-GRanges: no visible global function definition for ‘as’
granges,matrix: no visible global function definition for ‘as’
Undefined global functions or variables:
  IRanges SimpleList Var1 Var2 abline as barplot cor cov data is
  keepSeqlevels keepStandardChromosomes median optim par queryHits sd
  seqlengths seqlevels seqlevelsStyle<- subjectHits value weighted.mean
  x
Consider adding
  importFrom("graphics", "abline", "barplot", "par")
  importFrom("methods", "as", "is")
  importFrom("stats", "cor", "cov", "median", "optim", "sd",
             "weighted.mean")
  importFrom("utils", "data")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* checking Rd files ... NOTE
prepare_Rd: filterCompartments.Rd:22-24: Dropping empty section \examples
prepare_Rd: fixCompartments.Rd:24-26: Dropping empty section \examples
prepare_Rd: summarizeBootstraps.Rd:24-26: Dropping empty section \examples
* 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 ... WARNING
  Error loading dataset 'k562_scatac_chr14':
   Error in .requirePackage(package) : 
    unable to find required package 'csaw'
  
  Error loading dataset 'ss3_umi_sce':
   Error in .requirePackage(package) : 
    unable to find required package 'SingleCellExperiment'
  
  The dataset(s) may use package(s) not declared in Depends/Imports.
* checking data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                    user system elapsed
scCompartments    76.795  1.531   78.33
getDenoisedMatrix  7.048  0.192    7.24
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... ERROR
Error(s) in re-building vignettes:
  ...
--- re-building ‘compartmap_vignette.Rmd’ using rmarkdown

Quitting from lines 2-16 (compartmap_vignette.Rmd)
Error: processing vignette 'compartmap_vignette.Rmd' failed with diagnostics:
there is no package called 'BiocStyle'
--- failed re-building ‘compartmap_vignette.Rmd’

SUMMARY: processing the following file failed:
  ‘compartmap_vignette.Rmd’

Error: Vignette re-building failed.
Execution halted

* checking PDF version of manual ... OK
* DONE

Status: 1 ERROR, 1 WARNING, 3 NOTEs
See
  ‘/home/biocbuild/bbs-3.19-bioc/meat/compartmap.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD INSTALL compartmap
###
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* installing to library ‘/home/biocbuild/bbs-3.19-bioc/R/site-library’
* installing *source* package ‘compartmap’ ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
*** copying figures
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
Warning in fun(libname, pkgname) :
  Package 'compartmap' is deprecated and will be removed from
  Bioconductor version 3.20
** testing if installed package can be loaded from final location
Warning in fun(libname, pkgname) :
  Package 'compartmap' is deprecated and will be removed from
  Bioconductor version 3.20
** testing if installed package keeps a record of temporary installation path
* DONE (compartmap)