Back to Multiple platform build/check report for BioC 3.21:   simplified   long
ABCDEFGHIJKLMNO[P]QRSTUVWXYZ

This page was generated on 2024-12-23 11:47 -0500 (Mon, 23 Dec 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.1 LTS)x86_64R Under development (unstable) (2024-10-21 r87258) -- "Unsuffered Consequences" 4754
palomino7Windows Server 2022 Datacenterx64R Under development (unstable) (2024-10-26 r87273 ucrt) -- "Unsuffered Consequences" 4472
lconwaymacOS 12.7.1 Montereyx86_64R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" 4426
kjohnson3macOS 13.7.1 Venturaarm64R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" 4381
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch64R Under development (unstable) (2024-11-24 r87369) -- "Unsuffered Consequences" 4372
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 1503/2274HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
pathRender 1.75.0  (landing page)
Vince Carey
Snapshot Date: 2024-12-22 13:40 -0500 (Sun, 22 Dec 2024)
git_url: https://git.bioconductor.org/packages/pathRender
git_branch: devel
git_last_commit: 3e88ace
git_last_commit_date: 2024-10-29 09:25:34 -0500 (Tue, 29 Oct 2024)
nebbiolo1Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino7Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson3macOS 13.7.1 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published
kunpeng2Linux (openEuler 22.03 LTS-SP1) / aarch64  OK    OK    OK  


CHECK results for pathRender on kunpeng2

To the developers/maintainers of the pathRender package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/pathRender.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.
- See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host.

raw results


Summary

Package: pathRender
Version: 1.75.0
Command: /home/biocbuild/R/R/bin/R CMD check --install=check:pathRender.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings pathRender_1.75.0.tar.gz
StartedAt: 2024-12-23 10:34:37 -0000 (Mon, 23 Dec 2024)
EndedAt: 2024-12-23 10:36:37 -0000 (Mon, 23 Dec 2024)
EllapsedTime: 120.1 seconds
RetCode: 0
Status:   OK  
CheckDir: pathRender.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD check --install=check:pathRender.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings pathRender_1.75.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/pathRender.Rcheck’
* using R Under development (unstable) (2024-11-24 r87369)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
    aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0
    GNU Fortran (GCC) 14.2.0
* running under: openEuler 24.03 (LTS)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘pathRender/DESCRIPTION’ ... OK
* this is package ‘pathRender’ version ‘1.75.0’
* checking package namespace information ... OK
* checking package dependencies ... INFO
Depends: includes the non-default packages:
  'graph', 'Rgraphviz', 'RColorBrewer', 'cMAP', 'AnnotationDbi',
  'stats4'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
* 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 ‘pathRender’ 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 code 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 dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
graphcMAP: no visible binding for global variable ‘cMAPKEGGPATHWAY’
graphcMAP: no visible binding for global variable ‘cMAPCARTAPATHWAY’
graphcMAP: no visible binding for global variable ‘cMAPKEGGINTERACTION’
graphcMAP: no visible binding for global variable ‘cMAPKEGGMOLECULE’
graphcMAP: no visible binding for global variable
  ‘cMAPCARTAINTERACTION’
graphcMAP: no visible binding for global variable ‘cMAPCARTAMOLECULE’
plotExGraph: no visible global function definition for
  ‘colorRampPalette’
plotExGraph: no visible global function definition for ‘exprs’
quantizeByRow : <anonymous>: no visible global function definition for
  ‘quantile’
quantizeByRow: no visible global function definition for ‘featureNames’
quantizeByRow: no visible global function definition for ‘exprs<-’
quantizeByRow: no visible global function definition for ‘exprs’
quantizeByRow: no visible global function definition for
  ‘featureNames<-’
reduceES: no visible global function definition for ‘na.omit’
reduceES: no visible global function definition for ‘featureData<-’
reduceES: no visible global function definition for ‘exprs’
reduceES: no visible global function definition for ‘phenoData’
rendercMAPPathway: no visible binding for global variable
  ‘cMAPKEGGPATHWAY’
rendercMAPPathway: no visible binding for global variable
  ‘cMAPCARTAPATHWAY’
rendercMAPPathway: no visible binding for global variable
  ‘cMAPKEGGINTERACTION’
rendercMAPPathway: no visible binding for global variable
  ‘cMAPKEGGMOLECULE’
rendercMAPPathway: no visible binding for global variable
  ‘cMAPCARTAINTERACTION’
rendercMAPPathway: no visible binding for global variable
  ‘cMAPCARTAMOLECULE’
plot,coloredGraph-ANY: no visible global function definition for
  ‘palette’
Undefined global functions or variables:
  cMAPCARTAINTERACTION cMAPCARTAMOLECULE cMAPCARTAPATHWAY
  cMAPKEGGINTERACTION cMAPKEGGMOLECULE cMAPKEGGPATHWAY colorRampPalette
  exprs exprs<- featureData<- featureNames featureNames<- na.omit
  palette phenoData quantile
Consider adding
  importFrom("grDevices", "colorRampPalette", "palette")
  importFrom("stats", "na.omit", "quantile")
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 files in ‘vignettes’ ... OK
* checking examples ... 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 NOTE
See
  ‘/home/biocbuild/bbs-3.21-bioc/meat/pathRender.Rcheck/00check.log’
for details.


Installation output

pathRender.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD INSTALL pathRender
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library’
* installing *source* package ‘pathRender’ ...
** using staged installation
** R
** 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 (pathRender)

Tests output


Example timings

pathRender.Rcheck/pathRender-Ex.timings

nameusersystemelapsed
colorNodes0.1960.0080.220
coloredGraph-class0.140.000.14
graphcMAP0.3400.0120.357
plotExGraph2.3970.1162.537
pwayGraph-class0.0680.0080.077
reduceES1.6440.0281.675
rendercMAP0.3810.0000.382