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This page was generated on 2025-03-26 11:44 -0400 (Wed, 26 Mar 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.1 LTS)x86_64R Under development (unstable) (2025-03-13 r87965) -- "Unsuffered Consequences" 4783
palomino7Windows Server 2022 Datacenterx64R Under development (unstable) (2025-03-01 r87860 ucrt) -- "Unsuffered Consequences" 4552
lconwaymacOS 12.7.1 Montereyx86_64R Under development (unstable) (2025-03-02 r87868) -- "Unsuffered Consequences" 4581
kjohnson3macOS 13.7.1 Venturaarm64R Under development (unstable) (2025-03-02 r87868) -- "Unsuffered Consequences" 4533
kunpeng2Linux (openEuler 24.03 LTS)aarch64R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" 4463
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 1527/2315HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
pathview 1.47.0  (landing page)
Weijun Luo
Snapshot Date: 2025-03-25 13:40 -0400 (Tue, 25 Mar 2025)
git_url: https://git.bioconductor.org/packages/pathview
git_branch: devel
git_last_commit: 87ffb7b
git_last_commit_date: 2024-10-29 09:45:02 -0400 (Tue, 29 Oct 2024)
nebbiolo1Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    ERROR  skipped
palomino7Windows Server 2022 Datacenter / x64  OK    ERROR  skippedskipped
lconwaymacOS 12.7.1 Monterey / x86_64  OK    ERROR  skippedskipped
kjohnson3macOS 13.7.1 Ventura / arm64  OK    ERROR  skippedskipped
kunpeng2Linux (openEuler 24.03 LTS) / aarch64  OK    ERROR  skipped

BUILD results for pathview on palomino7

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: 1.47.0
Command: chmod a+r pathview -R && E:\biocbuild\bbs-3.21-bioc\R\bin\R.exe CMD build --keep-empty-dirs --no-resave-data pathview
StartedAt: 2025-03-25 20:59:17 -0400 (Tue, 25 Mar 2025)
EndedAt: 2025-03-25 21:00:58 -0400 (Tue, 25 Mar 2025)
EllapsedTime: 100.5 seconds
RetCode: 1
Status:   ERROR  
PackageFile: None
PackageFileSize: NA

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   chmod a+r pathview -R && E:\biocbuild\bbs-3.21-bioc\R\bin\R.exe CMD build --keep-empty-dirs --no-resave-data pathview
###
##############################################################################
##############################################################################


* checking for file 'pathview/DESCRIPTION' ... OK
* preparing 'pathview':
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- 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 E:/biocbuild/bbs-3.21-bioc/tmpdir/Rtmpwr1kCv/Rbuild2351861b22fbb/pathview/vignettes
Info: Writing image file hsa04110.gse16873.png
'select()' returned 1:1 mapping between keys and columns
Info: Working in directory E:/biocbuild/bbs-3.21-bioc/tmpdir/Rtmpwr1kCv/Rbuild2351861b22fbb/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 E:/biocbuild/bbs-3.21-bioc/tmpdir/Rtmpwr1kCv/Rbuild2351861b22fbb/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 E:/biocbuild/bbs-3.21-bioc/tmpdir/Rtmpwr1kCv/Rbuild2351861b22fbb/pathview/vignettes
Info: Writing image file hsa04110.gse16873.2layer.pdf
'select()' returned 1:1 mapping between keys and columns
Info: Working in directory E:/biocbuild/bbs-3.21-bioc/tmpdir/Rtmpwr1kCv/Rbuild2351861b22fbb/pathview/vignettes
Info: Writing image file hsa04110.gse16873.split.pdf
'select()' returned 1:1 mapping between keys and columns
Info: Working in directory E:/biocbuild/bbs-3.21-bioc/tmpdir/Rtmpwr1kCv/Rbuild2351861b22fbb/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 E:/biocbuild/bbs-3.21-bioc/tmpdir/Rtmpwr1kCv/Rbuild2351861b22fbb/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 E:/biocbuild/bbs-3.21-bioc/tmpdir/Rtmpwr1kCv/Rbuild2351861b22fbb/pathview/vignettes
Info: Writing image file hsa00640.gse16873.cpd.pdf
'select()' returned 1:1 mapping between keys and columns
Info: Working in directory E:/biocbuild/bbs-3.21-bioc/tmpdir/Rtmpwr1kCv/Rbuild2351861b22fbb/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 E:/biocbuild/bbs-3.21-bioc/tmpdir/Rtmpwr1kCv/Rbuild2351861b22fbb/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 E:/biocbuild/bbs-3.21-bioc/tmpdir/Rtmpwr1kCv/Rbuild2351861b22fbb/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
Loading required package: generics

Attaching package: 'generics'

The following objects are masked from 'package:base':

    as.difftime, as.factor, as.ordered, intersect, is.element, setdiff,
    setequal, union


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, is.unsorted, lapply,
    mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int,
    rank, rbind, rownames, sapply, saveRDS, table, tapply, 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


Attaching package: 'IRanges'

The following object is masked from 'package:grDevices':

    windows

'select()' returned 1:1 mapping between keys and columns
Info: Working in directory E:/biocbuild/bbs-3.21-bioc/tmpdir/Rtmpwr1kCv/Rbuild2351861b22fbb/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 E:/biocbuild/bbs-3.21-bioc/tmpdir/Rtmpwr1kCv/Rbuild2351861b22fbb/pathview/vignettes
Info: Writing image file hsa00640.sel.genes.cpd.png
Note: "CAS Registry Number" has only 4643 unique IDs!
Note: "ENSEMBLPROT" has only 22648 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 E:/biocbuild/bbs-3.21-bioc/tmpdir/Rtmpwr1kCv/Rbuild2351861b22fbb/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 E:/biocbuild/bbs-3.21-bioc/tmpdir/Rtmpwr1kCv/Rbuild2351861b22fbb/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 E:/biocbuild/bbs-3.21-bioc/tmpdir/Rtmpwr1kCv/Rbuild2351861b22fbb/pathview/vignettes
Info: Writing image file eco00640.eco.kegg.png
Loading required namespace: org.EcK12.eg.db


Error: processing vignette 'pathview.Rnw' failed with diagnostics:
 chunk 34 (label = eco.dat.kegg) 
Error : incomplete input

--- failed re-building 'pathview.Rnw'

SUMMARY: processing the following file failed:
  'pathview.Rnw'

Error: Vignette re-building failed.
Execution halted