##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:pathview.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/library --timings pathview_1.39.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/pathview.Rcheck’
* using R Under development (unstable) (2023-01-14 r83615)
* using platform: aarch64-unknown-linux-gnu (64-bit)
* R was compiled by
    gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
    GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
* running under: Ubuntu 22.04.1 LTS
* using session charset: UTF-8
* checking for file ‘pathview/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘pathview’ version ‘1.39.0’
* 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 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 ... WARNING
Invalid citation information in ‘inst/CITATION’:
  Warning message:
  In utils::packageDescription(basename(dir), dirname(dir)) :
    no package 'pathview' was found
* 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 ... WARNING
Error in library(pathview, lib.loc = "/home/biocbuild/bbs-3.17-bioc/R/library") : 
  there is no package called ‘pathview’
Execution halted

It looks like this package has a loading problem when not on .libPaths:
see the messages for details.
* 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: \#
* 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 LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... SKIPPED
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ...
  ‘pathview.Rnw’... failed
 ERROR
Errors in running code in vignettes:
when running code in ‘pathview.Rnw’
  ...
Warning: Failed to download KEGG xml/png files, hsa00640 skipped!

> str(pv.out)
 num 0

> head(pv.out$plot.data.cpd)

  When sourcing ‘pathview.R’:
Error: $ operator is invalid for atomic vectors
Execution halted

* checking re-building of vignette outputs ... NOTE
Error(s) in re-building vignettes:
--- re-building ‘pathview.Rnw’ using Sweave

##############################################################################
Pathview is an open source software package distributed under GNU General
Public License version 3 (GPLv3). Details of GPLv3 is available at
http://www.gnu.org/licenses/gpl-3.0.html. Particullary, users are required to
formally cite the original Pathview paper (not just mention it) in publications
or products. For details, do citation("pathview") within R.

The pathview downloads and uses KEGG data. Non-academic uses may require a KEGG
license agreement (details at http://www.kegg.jp/kegg/legal.html).
##############################################################################
Info: Downloading xml files for hsa04110, 1/1 pathways..
Info: Downloading png files for hsa04110, 1/1 pathways..
'select()' returned 1:1 mapping between keys and columns
Info: Working in directory /home/biocbuild/bbs-3.17-bioc/meat/pathview.Rcheck/vign_test/pathview/vignettes
Info: Writing image file hsa04110.gse16873.png
'select()' returned 1:1 mapping between keys and columns
Info: Working in directory /home/biocbuild/bbs-3.17-bioc/meat/pathview.Rcheck/vign_test/pathview/vignettes
Info: Writing image file hsa04110.gse16873.2layer.png
'select()' returned 1:1 mapping between keys and columns
Info: Working in directory /home/biocbuild/bbs-3.17-bioc/meat/pathview.Rcheck/vign_test/pathview/vignettes
Info: Writing image file hsa04110.gse16873.pdf
'select()' returned 1:1 mapping between keys and columns
Info: Working in directory /home/biocbuild/bbs-3.17-bioc/meat/pathview.Rcheck/vign_test/pathview/vignettes
Info: Writing image file hsa04110.gse16873.2layer.pdf
'select()' returned 1:1 mapping between keys and columns
Info: Working in directory /home/biocbuild/bbs-3.17-bioc/meat/pathview.Rcheck/vign_test/pathview/vignettes
Info: Writing image file hsa04110.gse16873.split.pdf
'select()' returned 1:1 mapping between keys and columns
Info: Working in directory /home/biocbuild/bbs-3.17-bioc/meat/pathview.Rcheck/vign_test/pathview/vignettes
Info: Writing image file hsa04110.gse16873.split.expanded.pdf
Info: Downloading xml files for hsa00640, 1/1 pathways..
Info: Downloading png files for hsa00640, 1/1 pathways..
Killed

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

Status: 1 ERROR, 3 WARNINGs, 3 NOTEs
See
  ‘/home/biocbuild/bbs-3.17-bioc/meat/pathview.Rcheck/00check.log’
for details.

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL pathview
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.17-bioc/R/site-library’
* installing *source* package ‘pathview’ ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** 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 (pathview)

R Under development (unstable) (2023-01-14 r83615) -- "Unsuffered Consequences"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: aarch64-unknown-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> BiocGenerics:::testPackage("pathview")

##############################################################################
Pathview is an open source software package distributed under GNU General
Public License version 3 (GPLv3). Details of GPLv3 is available at
http://www.gnu.org/licenses/gpl-3.0.html. Particullary, users are required to
formally cite the original Pathview paper (not just mention it) in publications
or products. For details, do citation("pathview") within R.

The pathview downloads and uses KEGG data. Non-academic uses may require a KEGG
license agreement (details at http://www.kegg.jp/kegg/legal.html).
##############################################################################
Note: multiple compounds may map to a input ID, only the first one kept!
Note: None of the compound ids mapped to the specified type!
Note: A native KEGG compound ID type, no need to map!
'select()' returned 1:1 mapping between keys and columns
'select()' returned 1:1 mapping between keys and columns
[1] "Note: 3 of 6 unique input IDs unmapped."
'select()' returned 1:1 mapping between keys and columns
'select()' returned 1:1 mapping between keys and columns
[1] "Note: 3 of 6 unique input IDs unmapped."


RUNIT TEST PROTOCOL -- Sun Jan 29 05:51:22 2023 
*********************************************** 
Number of test functions: 3 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
pathview RUnit Tests - 3 test functions, 0 errors, 0 failures
Number of test functions: 3 
Number of errors: 0 
Number of failures: 0 
> 
> proc.time()
   user  system elapsed 
  7.101   0.217   7.313