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This page was generated on 2024-12-24 11:47 -0500 (Tue, 24 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" 4373
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 2026/2274HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
SplineDV 0.99.11  (landing page)
Shreyan Gupta
Snapshot Date: 2024-12-23 13:40 -0500 (Mon, 23 Dec 2024)
git_url: https://git.bioconductor.org/packages/SplineDV
git_branch: devel
git_last_commit: ef9afbe
git_last_commit_date: 2024-11-19 14:12:35 -0500 (Tue, 19 Nov 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 SplineDV on kunpeng2

To the developers/maintainers of the SplineDV package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/SplineDV.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: SplineDV
Version: 0.99.11
Command: /home/biocbuild/R/R/bin/R CMD check --install=check:SplineDV.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings SplineDV_0.99.11.tar.gz
StartedAt: 2024-12-24 11:35:06 -0000 (Tue, 24 Dec 2024)
EndedAt: 2024-12-24 11:39:36 -0000 (Tue, 24 Dec 2024)
EllapsedTime: 270.3 seconds
RetCode: 0
Status:   OK  
CheckDir: SplineDV.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD check --install=check:SplineDV.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings SplineDV_0.99.11.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/SplineDV.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 ‘SplineDV/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘SplineDV’ version ‘0.99.11’
* package encoding: UTF-8
* 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 ‘SplineDV’ 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 ... NOTE
File
  LICENSE
is not mentioned in the DESCRIPTION file.
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ...Warning: program compiled against libxml 212 using older 211
 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
DVPlot: no visible binding for global variable ‘mu1’
DVPlot: no visible binding for global variable ‘mu2’
HVGPlot: no visible binding for global variable ‘logMean’
splineDV: no visible binding for global variable ‘X_dvecx’
splineDV: no visible binding for global variable ‘X_dvecy’
splineDV: no visible binding for global variable ‘X_dvecz’
splineDV: no visible binding for global variable ‘Y_dvecx’
splineDV: no visible binding for global variable ‘Y_dvecy’
splineDV: no visible binding for global variable ‘Y_dvecz’
splineDV: no visible binding for global variable ‘dist1’
splineDV: no visible binding for global variable ‘dist2’
splineDV: no visible binding for global variable ‘vectorDist’
splineDV: no visible binding for global variable ‘Z’
splineDV: no visible binding for global variable ‘Pval’
splineDV: no visible binding for global variable ‘FDR’
splineDV: no visible binding for global variable ‘genes’
splineDV: no visible binding for global variable ‘mu1’
splineDV: no visible binding for global variable ‘mu2’
splineDV: no visible binding for global variable ‘CV1’
splineDV: no visible binding for global variable ‘CV2’
splineDV: no visible binding for global variable ‘drop1’
splineDV: no visible binding for global variable ‘drop2’
splineDV: no visible binding for global variable ‘X_splinex’
splineDV: no visible binding for global variable ‘X_spliney’
splineDV: no visible binding for global variable ‘X_splinez’
splineDV: no visible binding for global variable ‘Y_splinex’
splineDV: no visible binding for global variable ‘Y_spliney’
splineDV: no visible binding for global variable ‘Y_splinez’
splineDV: no visible binding for global variable ‘Direction’
splineHVG: no visible binding for global variable ‘logMean’
splineHVG: no visible binding for global variable ‘logCV’
splineHVG: no visible binding for global variable ‘spliney’
splineHVG: no visible binding for global variable ‘Distance’
Undefined global functions or variables:
  CV1 CV2 Direction Distance FDR Pval X_dvecx X_dvecy X_dvecz X_splinex
  X_spliney X_splinez Y_dvecx Y_dvecy Y_dvecz Y_splinex Y_spliney
  Y_splinez Z dist1 dist2 drop1 drop2 genes logCV logMean mu1 mu2
  spliney vectorDist
Consider adding
  importFrom("stats", "drop1")
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
Examples with CPU (user + system) or elapsed time > 5s
          user system elapsed
DVPlot   6.794  0.247   7.312
splineDV 4.848  0.100   5.079
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.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: 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.21-bioc/meat/SplineDV.Rcheck/00check.log’
for details.


Installation output

SplineDV.Rcheck/00install.out

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


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

Tests output

SplineDV.Rcheck/tests/testthat.Rout


R Under development (unstable) (2024-11-24 r87369) -- "Unsuffered Consequences"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: aarch64-unknown-linux-gnu

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.

> # This file is part of the standard setup for testthat.
> # It is recommended that you do not modify it.
> #
> # Where should you do additional test configuration?
> # Learn more about the roles of various files in:
> # * https://r-pkgs.org/testing-design.html#sec-tests-files-overview
> # * https://testthat.r-lib.org/articles/special-files.html
> 
> library(testthat)
> library(SplineDV)
> 
> test_check("SplineDV")
Computing distances for Data 1
Performing normalization...
Computing distances...
HVG computed
Computing distances for Data 2
Performing normalization...
Computing distances...
HVG computed
QC done
Performing normalization...
Computing distances...
HVG computed
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 4 ]
> 
> proc.time()
   user  system elapsed 
 19.470   0.648  21.321 

Example timings

SplineDV.Rcheck/SplineDV-Ex.timings

nameusersystemelapsed
DVPlot6.7940.2477.312
HVGPlot2.3910.0512.798
hvgQC0.4030.0080.412
splineDV4.8480.1005.079
splineHVG2.3050.0082.590