Back to Multiple platform build/check report for BioC 3.16
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This page was generated on 2022-06-01 11:06:43 -0400 (Wed, 01 Jun 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.2.0 RC (2022-04-21 r82226) -- "Vigorous Calisthenics" 4364
palomino4Windows Server 2022 Datacenterx644.2.0 Patched (2022-04-24 r82246 ucrt) -- "Vigorous Calisthenics" 4168
lconwaymacOS 12.2.1 Montereyx86_644.2.0 Patched (2022-04-24 r82246) -- "Vigorous Calisthenics" 4180
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

CHECK results for pathview on palomino4


To the developers/maintainers of the pathview package:
- Please 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 How and When does the builder pull? When will my changes propagate? for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 1405/2116HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
pathview 1.37.0  (landing page)
Weijun Luo
Snapshot Date: 2022-05-31 14:00:04 -0400 (Tue, 31 May 2022)
git_url: https://git.bioconductor.org/packages/pathview
git_branch: master
git_last_commit: 272618d
git_last_commit_date: 2022-04-26 11:13:56 -0400 (Tue, 26 Apr 2022)
nebbiolo2Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
palomino4Windows Server 2022 Datacenter / x64  OK    OK    ERROR    OK  
lconwaymacOS 12.2.1 Monterey / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published

Summary

Package: pathview
Version: 1.37.0
Command: F:\biocbuild\bbs-3.16-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:pathview.install-out.txt --library=F:\biocbuild\bbs-3.16-bioc\R\library --no-vignettes --timings pathview_1.37.0.tar.gz
StartedAt: 2022-06-01 03:46:49 -0400 (Wed, 01 Jun 2022)
EndedAt: 2022-06-01 03:49:10 -0400 (Wed, 01 Jun 2022)
EllapsedTime: 140.3 seconds
RetCode: 1
Status:   ERROR  
CheckDir: pathview.Rcheck
Warnings: NA

Command output

##############################################################################
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###
### Running command:
###
###   F:\biocbuild\bbs-3.16-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:pathview.install-out.txt --library=F:\biocbuild\bbs-3.16-bioc\R\library --no-vignettes --timings pathview_1.37.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'F:/biocbuild/bbs-3.16-bioc/meat/pathview.Rcheck'
* using R version 4.2.0 Patched (2022-04-24 r82246 ucrt)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'pathview/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'pathview' version '1.37.0'
* 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 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 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 ... OK
* 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 sizes of PDF files under 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ... ERROR
Running examples in 'pathview-Ex.R' failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: pathview
> ### Title: Pathway based data integration and visualization
> ### Aliases: pathview keggview.native keggview.graph
> 
> ### ** Examples
> 
> #load data
> data(gse16873.d)
> data(demo.paths)
> 
> #KEGG view: gene data only
> i <- 1
> pv.out <- pathview(gene.data = gse16873.d[, 1], pathway.id =
+ demo.paths$sel.paths[i], species = "hsa", out.suffix = "gse16873",
+ kegg.native = TRUE)
Info: Downloading xml files for hsa04110, 1/1 pathways..
Warning in download.file(xml.url, xml.target, quiet = T) :
  URL 'https://rest.kegg.jp/get/hsa04110/kgml': status was 'Failure when receiving data from the peer'
Warning: Download of hsa04110 xml file failed!
This pathway may not exist!
Info: Downloading png files for hsa04110, 1/1 pathways..
Warning: Download of hsa04110 png file failed!
This pathway may not exist!
Warning: Failed to download KEGG xml/png files, hsa04110 skipped!
> str(pv.out)
 num 0
> head(pv.out$plot.data.gene)
Error in pv.out$plot.data.gene : $ operator is invalid for atomic vectors
Calls: head
Execution halted
* 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 ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 1 ERROR, 1 WARNING, 1 NOTE
See
  'F:/biocbuild/bbs-3.16-bioc/meat/pathview.Rcheck/00check.log'
for details.


Installation output

pathview.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.16/bioc/src/contrib/pathview_1.37.0.tar.gz && rm -rf pathview.buildbin-libdir && mkdir pathview.buildbin-libdir && F:\biocbuild\bbs-3.16-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=pathview.buildbin-libdir pathview_1.37.0.tar.gz && F:\biocbuild\bbs-3.16-bioc\R\bin\R.exe CMD INSTALL pathview_1.37.0.zip && rm pathview_1.37.0.tar.gz pathview_1.37.0.zip
###
##############################################################################
##############################################################################


  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100 2182k  100 2182k    0     0  16.9M      0 --:--:-- --:--:-- --:--:-- 17.0M
only one architecture so ignoring '--merge-multiarch'
* 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
* MD5 sums
packaged installation of 'pathview' as pathview_1.37.0.zip
* DONE (pathview)
* installing to library 'F:/biocbuild/bbs-3.16-bioc/R/library'
package 'pathview' successfully unpacked and MD5 sums checked

Tests output

pathview.Rcheck/tests/runTests.Rout


R version 4.2.0 Patched (2022-04-24 r82246 ucrt) -- "Vigorous Calisthenics"
Copyright (C) 2022 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (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 -- Wed Jun  1 03:49:00 2022 
*********************************************** 
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 
   5.57    0.39    5.93 

Example timings

pathview.Rcheck/pathview-Ex.timings

nameusersystemelapsed
cpd.accs0.060.040.09
cpdidmap0.560.030.60
download.kegg0.070.045.81
eg2id0.860.040.91
kegg.species.code0.030.060.40
korg0.030.000.03
mol.sum0.510.030.55
node.color0.190.000.19
node.info0.310.010.33
node.map0.240.000.23