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### Running command:
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###   /home/biocbuild/R/R-beta-2024-04-15_r86425/bin/R CMD check --install=check:pathview.install-out.txt --library=/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library --no-vignettes --timings pathview_1.44.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/pathview.Rcheck’
* using R version 4.4.0 beta (2024-04-15 r86425)
* using platform: aarch64-unknown-linux-gnu
* 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 ‘pathview/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘pathview’ version ‘1.44.0’
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘pathview’ 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 ... WARNING
'::' or ':::' import not declared from: ‘BiocManager’
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
File ‘pathview/R/zzz.R’:
  .onLoad calls:
    installed.packages()
    packageStartupMessage(wordwrap(disclaimer, 80))

Package startup functions should not call ‘installed.packages’.
See section ‘Good practice’ in '?.onAttach'.

Warning in formals(fun) : argument is not a function
Warning in body(fun) : argument is not a function
col.key: no visible binding for global variable ‘node.sizes’
cpd2kegg: no visible binding for global variable ‘rn.list’
cpdidmap: no visible binding for global variable ‘cpd.accs’
cpdkegg2name: no visible binding for global variable ‘kegg.met’
cpdname2kegg: no visible binding for global variable ‘cpd.names’
download.kegg: no visible global function definition for
  ‘download.file’
eg2id: no visible binding for global variable ‘gene.idtype.list’
geneannot.map: no visible binding for global variable ‘bods’
id2eg: no visible binding for global variable ‘gene.idtype.list’
kegg.species.code: no visible binding for global variable ‘korg.1’
pathview: no visible binding for global variable ‘bods’
pathview: no visible binding for global variable ‘gene.idtype.bods’
pathview: no visible binding for global variable ‘rn.list’
sim.mol.data: no visible binding for global variable ‘bods’
sim.mol.data: no visible binding for global variable ‘gene.idtype.bods’
sim.mol.data: no visible binding for global variable ‘cpd.accs’
sim.mol.data: no visible binding for global variable ‘cpd.simtypes’
sim.mol.data: no visible binding for global variable ‘rn.list’
sim.mol.data: no visible binding for global variable ‘ko.ids’
Undefined global functions or variables:
  bods cpd.accs cpd.names cpd.simtypes download.file gene.idtype.bods
  gene.idtype.list kegg.met ko.ids korg.1 node.sizes rn.list
Consider adding
  importFrom("utils", "download.file")
to your NAMESPACE file.
* checking Rd files ... NOTE
checkRd: (-1) node.color.Rd:71: Escaped LaTeX specials: \#
checkRd: (-1) pathview.Rd:204: Escaped LaTeX specials: \#
checkRd: (-1) pathview.Rd:396: Lost braces
   396 |   code{keggview.graph} are both a list of graph plotting
       |       ^
* 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 ... NOTE
Auto-generated content requiring editing in Rd file 'pathview-package.Rd':
  \details: ‘...the package, including the most important ~~ ~~ functions ~~’
* checking for unstated dependencies in examples ... OK
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking LazyData ... OK
* 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
pathview 18.133  0.627  20.028
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.R’
 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: 1 WARNING, 3 NOTEs
See
  ‘/home/biocbuild/bbs-3.19-bioc/meat/pathview.Rcheck/00check.log’
for details.