##############################################################################
##############################################################################
###
### 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/site-library --timings pathview_1.40.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/pathview.Rcheck’
* using R version 4.3.1 (2023-06-16)
* using platform: x86_64-pc-linux-gnu (64-bit)
* R was compiled by
    gcc (Ubuntu 11.3.0-1ubuntu1~22.04.1) 11.3.0
    GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04.1) 11.3.0
* running under: Ubuntu 22.04.3 LTS
* using session charset: UTF-8
* checking for file ‘pathview/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘pathview’ version ‘1.40.0’
* 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 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 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: \#
* 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 ... OK
Examples with CPU (user + system) or elapsed time > 5s
                user system elapsed
pathview      16.441  1.027  29.483
sim.mol.data   0.914  0.017  11.008
download.kegg  0.549  0.011   6.992
* 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
 WARNING
Errors in running code in vignettes:
when running code in ‘pathview.Rnw’
  ...
Info: Writing image file eco00640.eco.kegg.png

> eco.dat.entrez <- sim.mol.data(mol.type = "gene", 
+     id.type = "entrez", species = "eco", nmol = 3000)
Loading required namespace: org.EcK12.eg.db
Failed with error:  ‘there is no package called ‘org.EcK12.eg.db’’

  When sourcing ‘pathview.R’:
Error: there is no package called ‘BiocManager’
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
Warning: reconcile groups sharing member nodes!
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
Warning: reconcile groups sharing member nodes!
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..
'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 hsa00640.gse16873.cpd.png
Warning in .local(from, to, graph) :
  edges replaced: ‘180|60’, ‘122|119’, ‘122|120’, ‘84|77’, ‘84|199’
'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 hsa00640.gse16873.cpd.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 hsa00640.gse16873.cpd.3-2s.multi.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 hsa00640.gse16873.cpd.3-2s.match.multi.png
Warning in .local(from, to, graph) :
  edges replaced: ‘180|60’, ‘122|119’, ‘122|120’, ‘84|77’, ‘84|199’
'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 hsa00640.gse16873.cpd.3-2s.multi.pdf
Loading required package: org.Hs.eg.db
Loading required package: AnnotationDbi
Loading required package: stats4
Loading required package: BiocGenerics

Attaching package: ‘BiocGenerics’

The following objects are masked from ‘package:stats’:

    IQR, mad, sd, var, xtabs

The following objects are masked from ‘package:base’:

    Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append,
    as.data.frame, basename, cbind, colnames, dirname, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
    pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
    tapply, union, unique, unsplit, which.max, which.min

Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

Loading required package: IRanges
Loading required package: S4Vectors

Attaching package: ‘S4Vectors’

The following object is masked from ‘package:utils’:

    findMatches

The following objects are masked from ‘package:base’:

    I, expand.grid, unname

'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 hsa00640.sel.genes.sel.cpd.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 hsa00640.sel.genes.cpd.png
Note: "CAS Registry Number" has only 4643 unique IDs!
Note: "ENSEMBLPROT" has only 21439 unique IDs!
'select()' returned 1:many mapping between keys and columns
Note: multiple compounds may map to a input ID, only the first one kept!
'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 hsa00640.gene.ensprot.cpd.cas.png
Note: multiple compounds may map to a input ID, only the first one kept!
'select()' returned 1:many mapping between keys and columns
'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 hsa00640.gene.entrez.cpd.kc.png
Info: Downloading xml files for eco00640, 1/1 pathways..
Info: Downloading png files for eco00640, 1/1 pathways..
Info: Working in directory /home/biocbuild/bbs-3.17-bioc/meat/pathview.Rcheck/vign_test/pathview/vignettes
Info: Writing image file eco00640.eco.kegg.png
Loading required namespace: org.EcK12.eg.db
Failed with error:  ‘there is no package called ‘org.EcK12.eg.db’’

Error: processing vignette 'pathview.Rnw' failed with diagnostics:
 chunk 34 (label = eco.dat.kegg) 
Error in loadNamespace(x) : there is no package called ‘BiocManager’

--- failed re-building ‘pathview.Rnw’

SUMMARY: processing the following file failed:
  ‘pathview.Rnw’

Error: Vignette re-building failed.
Execution halted

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

Status: 2 WARNINGs, 3 NOTEs
See
  ‘/home/biocbuild/bbs-3.17-bioc/meat/pathview.Rcheck/00check.log’
for details.

##############################################################################
##############################################################################
###
### 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 version 4.3.1 (2023-06-16) -- "Beagle Scouts"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: x86_64-pc-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 Oct 15 23:49:10 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 
  9.034   0.396  13.050