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This page was generated on 2024-02-18 02:28:58 -0500 (Sun, 18 Feb 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_64R Under development (unstable) (2024-01-16 r85808) -- "Unsuffered Consequences" 4657
palomino3Windows Server 2022 Datacenterx64R Under development (unstable) (2024-01-14 r85805 ucrt) -- "Unsuffered Consequences" 4397
merida1macOS 12.7.1 Montereyx86_64R Under development (unstable) (2024-01-16 r85808) -- "Unsuffered Consequences" 4424
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch64R Under development (unstable) (2024-01-16 r85812) -- "Unsuffered Consequences" 4400
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

Package 1491/2244HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
pathview 1.43.0  (landing page)
Weijun Luo
Snapshot Date: 2024-02-16 14:10:20 -0500 (Fri, 16 Feb 2024)
git_url: https://git.bioconductor.org/packages/pathview
git_branch: devel
git_last_commit: c1d40b2
git_last_commit_date: 2023-10-24 09:53:13 -0500 (Tue, 24 Oct 2023)
nebbiolo1Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    ERROR  
palomino3Windows Server 2022 Datacenter / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
merida1macOS 12.7.1 Monterey / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
kunpeng2Linux (openEuler 22.03 LTS-SP1) / aarch64  OK    OK    WARNINGS  

CHECK results for pathview on merida1


To the developers/maintainers of the pathview package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/pathview.git to reflect on this report. See Troubleshooting Build Report for more information.
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results


Summary

Package: pathview
Version: 1.43.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:pathview.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings pathview_1.43.0.tar.gz
StartedAt: 2024-02-17 08:10:48 -0500 (Sat, 17 Feb 2024)
EndedAt: 2024-02-17 08:16:11 -0500 (Sat, 17 Feb 2024)
EllapsedTime: 323.1 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: pathview.Rcheck
Warnings: 1

Command output

##############################################################################
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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:pathview.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings pathview_1.43.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.19-bioc/meat/pathview.Rcheck’
* using R Under development (unstable) (2024-01-16 r85808)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘pathview/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘pathview’ version ‘1.43.0’
* 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 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: \#
* 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
               user system elapsed
pathview     15.144  1.980  22.587
sim.mol.data  0.668  0.066   9.165
* 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
  ‘/Users/biocbuild/bbs-3.19-bioc/meat/pathview.Rcheck/00check.log’
for details.



Installation output

pathview.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL pathview
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/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)

Tests output

pathview.Rcheck/tests/runTests.Rout


R Under development (unstable) (2024-01-16 r85808) -- "Unsuffered Consequences"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20

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 -- Sat Feb 17 08:15:56 2024 
*********************************************** 
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 
 12.663   0.858  15.613 

Example timings

pathview.Rcheck/pathview-Ex.timings

nameusersystemelapsed
cpd.accs0.1100.0190.147
cpdidmap0.2420.0340.304
download.kegg0.1100.0243.908
eg2id2.0920.0982.513
kegg.species.code0.0810.0040.335
korg0.0340.0050.039
mol.sum1.4120.0382.018
node.color0.3850.0120.479
node.info0.7740.1061.049
node.map0.4390.0590.591
pathview15.144 1.98022.587
sim.mol.data0.6680.0669.165
wordwrap0.0010.0010.002