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###
### Running command:
###
###   /home/biocbuild/R/R-4.3.1/bin/R CMD check --install=check:compartmap.install-out.txt --library=/home/biocbuild/R/R-4.3.1/site-library --no-vignettes --timings compartmap_1.20.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.18-bioc/meat/compartmap.Rcheck’
* using R version 4.3.1 (2023-06-16)
* using platform: aarch64-unknown-linux-gnu (64-bit)
* R was compiled by
    gcc (GCC) 10.3.1
    GNU Fortran (GCC) 10.3.1
* running under: openEuler 22.03 (LTS-SP1)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘compartmap/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘compartmap’ version ‘1.20.0’
* 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 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 loading without being on the library search path ... 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 ... ERROR
Running examples in ‘compartmap-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: scCompartments
> ### Title: Estimate A/B compartments from single-cell sequencing data
> ### Aliases: scCompartments
> 
> ### ** Examples
> 
> data("k562_scrna_chr14", package = "compartmap")
> sc_compartments <- scCompartments(k562_scrna_chr14, parallel=FALSE, chr="chr14", bootstrap=FALSE, genome="hg19")
Working on A10_hg19Aligned.sortedByCoord.out.bw
Computing compartments for chr14
Calculating correlations...
Done...
Calculating eigenvectors.
Smoothing eigenvector.
Done smoothing.
Working on A2_hg19Aligned.sortedByCoord.out.bw
Computing compartments for chr14
Calculating correlations...
Done...
Calculating eigenvectors.
Smoothing eigenvector.
Done smoothing.
Working on A3_hg19Aligned.sortedByCoord.out.bw
Computing compartments for chr14
Calculating correlations...
Done...
Calculating eigenvectors.
Smoothing eigenvector.
Done smoothing.
Working on A4_hg19Aligned.sortedByCoord.out.bw
Computing compartments for chr14
Calculating correlations...
Done...
Calculating eigenvectors.
Smoothing eigenvector.
Done smoothing.
Working on A5_hg19Aligned.sortedByCoord.out.bw
Computing compartments for chr14
Calculating correlations...
Done...
Calculating eigenvectors.
Smoothing eigenvector.
Done smoothing.
Working on A6_hg19Aligned.sortedByCoord.out.bw
Computing compartments for chr14
Calculating correlations...
Done...
Calculating eigenvectors.
Smoothing eigenvector.
Done smoothing.
Working on A7_hg19Aligned.sortedByCoord.out.bw
Computing compartments for chr14
Calculating correlations...
Done...
Calculating eigenvectors.
Smoothing eigenvector.
Done smoothing.
Working on A8_hg19Aligned.sortedByCoord.out.bw
Computing compartments for chr14
Calculating correlations...
Done...
Calculating eigenvectors.
Smoothing eigenvector.
Done smoothing.
Working on A9_hg19Aligned.sortedByCoord.out.bw
Computing compartments for chr14
Calculating correlations...
Done...
Calculating eigenvectors.
Smoothing eigenvector.
Done smoothing.
Working on B1_hg19Aligned.sortedByCoord.out.bw
Computing compartments for chr14
Calculating correlations...
Done...
Calculating eigenvectors.
Smoothing eigenvector.
Done smoothing.
Working on B2_hg19Aligned.sortedByCoord.out.bw
Computing compartments for chr14
Calculating correlations...
Done...
Calculating eigenvectors.
Smoothing eigenvector.
Done smoothing.
Working on B3_hg19Aligned.sortedByCoord.out.bw
Computing compartments for chr14
Calculating correlations...
Done...
Calculating eigenvectors.
Smoothing eigenvector.
Done smoothing.
Working on B4_hg19Aligned.sortedByCoord.out.bw
Computing compartments for chr14
Calculating correlations...
Done...
Calculating eigenvectors.
Smoothing eigenvector.
Done smoothing.
Working on B5_hg19Aligned.sortedByCoord.out.bw
Computing compartments for chr14
Calculating correlations...
Done...
Calculating eigenvectors.
Smoothing eigenvector.
Done smoothing.
Working on B6_hg19Aligned.sortedByCoord.out.bw
Computing compartments for chr14
Calculating correlations...
Done...
Calculating eigenvectors.
Smoothing eigenvector.
Done smoothing.
Working on B7_hg19Aligned.sortedByCoord.out.bw
Computing compartments for chr14
Calculating correlations...
Done...
Calculating eigenvectors.
Smoothing eigenvector.
Done smoothing.
Working on B8_hg19Aligned.sortedByCoord.out.bw
Computing compartments for chr14
Calculating correlations...
Done...
Calculating eigenvectors.
Smoothing eigenvector.
Done smoothing.
Working on B9_hg19Aligned.sortedByCoord.out.bw
Computing compartments for chr14
Calculating correlations...
Done...
Calculating eigenvectors.
Smoothing eigenvector.
Done smoothing.
Working on C1_hg19Aligned.sortedByCoord.out.bw
Computing compartments for chr14
Calculating correlations...
Done...
Calculating eigenvectors.
Smoothing eigenvector.
Done smoothing.
Working on C2_hg19Aligned.sortedByCoord.out.bw
Computing compartments for chr14
Calculating correlations...
Done...
Calculating eigenvectors.
Smoothing eigenvector.
Done smoothing.
Working on C3_hg19Aligned.sortedByCoord.out.bw
Computing compartments for chr14
Calculating correlations...
Done...
Calculating eigenvectors.
Smoothing eigenvector.
Done smoothing.
Working on C4_hg19Aligned.sortedByCoord.out.bw
Computing compartments for chr14
Calculating correlations...
Done...
Calculating eigenvectors.
Smoothing eigenvector.
Done smoothing.
Working on C5_hg19Aligned.sortedByCoord.out.bw
Computing compartments for chr14
Calculating correlations...
Done...
Calculating eigenvectors.
Smoothing eigenvector.
Done smoothing.
Working on C6_hg19Aligned.sortedByCoord.out.bw
Computing compartments for chr14
Calculating correlations...
Done...
Calculating eigenvectors.
Smoothing eigenvector.
Done smoothing.
Working on C7_hg19Aligned.sortedByCoord.out.bw
Computing compartments for chr14
Calculating correlations...
Done...
Calculating eigenvectors.
Smoothing eigenvector.
Done smoothing.
Working on C8_hg19Aligned.sortedByCoord.out.bw
Computing compartments for chr14
Calculating correlations...
Done...
Calculating eigenvectors.
Smoothing eigenvector.
Done smoothing.
Working on C9_hg19Aligned.sortedByCoord.out.bw
Computing compartments for chr14
Calculating correlations...
Done...
Calculating eigenvectors.
Smoothing eigenvector.
Done smoothing.
Working on D1_hg19Aligned.sortedByCoord.out.bw
Computing compartments for chr14
Calculating correlations...
Done...
Calculating eigenvectors.
Smoothing eigenvector.
Done smoothing.
Working on D2_hg19Aligned.sortedByCoord.out.bw
Computing compartments for chr14
Calculating correlations...
Done...
Calculating eigenvectors.
Smoothing eigenvector.
Done smoothing.
Working on D3_hg19Aligned.sortedByCoord.out.bw
Computing compartments for chr14
Calculating correlations...
Done...
Calculating eigenvectors.
Smoothing eigenvector.
Done smoothing.
Working on D4_hg19Aligned.sortedByCoord.out.bw
Computing compartments for chr14
* 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: 1 ERROR, 1 WARNING, 3 NOTEs
See
  ‘/home/biocbuild/bbs-3.18-bioc/meat/compartmap.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /home/biocbuild/R/R-4.3.1/bin/R CMD INSTALL compartmap
###
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* installing to library ‘/home/biocbuild/R/R-4.3.1/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
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (compartmap)