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This page was generated on 2023-01-25 10:57:06 -0500 (Wed, 25 Jan 2023).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.1 LTS)x86_64R Under development (unstable) (2023-01-10 r83596) -- "Unsuffered Consequences" 4464
nebbiolo2Linux (Ubuntu 20.04.5 LTS)x86_64R Under development (unstable) (2022-12-12 r83438) -- "Unsuffered Consequences" 4248
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 spatialDE on nebbiolo2


To the developers/maintainers of the spatialDE package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/spatialDE.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 1910/2162HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
spatialDE 1.5.1  (landing page)
Gabriele Sales
Snapshot Date: 2023-01-24 14:00:21 -0500 (Tue, 24 Jan 2023)
git_url: https://git.bioconductor.org/packages/spatialDE
git_branch: master
git_last_commit: 18009cb
git_last_commit_date: 2023-01-23 12:44:09 -0500 (Mon, 23 Jan 2023)
nebbiolo1Linux (Ubuntu 22.04.1 LTS) / x86_64  OK    OK    OK  
nebbiolo2Linux (Ubuntu 20.04.5 LTS) / x86_64  OK    OK    ERROR  

Summary

Package: spatialDE
Version: 1.5.1
Command: /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:spatialDE.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/library --timings spatialDE_1.5.1.tar.gz
StartedAt: 2023-01-25 06:34:47 -0500 (Wed, 25 Jan 2023)
EndedAt: 2023-01-25 06:37:48 -0500 (Wed, 25 Jan 2023)
EllapsedTime: 180.8 seconds
RetCode: 1
Status:   ERROR  
CheckDir: spatialDE.Rcheck
Warnings: NA

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:spatialDE.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/library --timings spatialDE_1.5.1.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/spatialDE.Rcheck’
* using R Under development (unstable) (2022-12-12 r83438)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* checking for file ‘spatialDE/DESCRIPTION’ ... OK
* this is package ‘spatialDE’ version ‘1.5.1’
* 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 ‘spatialDE’ can be installed ... NOTE
Found the following notes/warnings:
  Non-staged installation was used
See ‘/home/biocbuild/bbs-3.17-bioc/meat/spatialDE.Rcheck/00install.out’ for details.
* 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 ... WARNING
Invalid citation information in ‘inst/CITATION’:
  Warning message:
  In utils::packageDescription(basename(dir), dirname(dir)) :
    no package 'spatialDE' was found
* 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 loading without being on the library search path ... WARNING
Error in library(spatialDE, lib.loc = "/home/biocbuild/bbs-3.17-bioc/R/library") : 
  there is no package called ‘spatialDE’
Execution halted

It looks like this package has a loading problem when not on .libPaths:
see the messages for details.
* 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 ... OK
* 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 data for ASCII and uncompressed saves ... OK
* checking line endings in shell scripts ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... SKIPPED
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 ERROR
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(spatialDE)
  Error in library(spatialDE) : there is no package called 'spatialDE'
  Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ...
  ‘spatialDE.Rmd’ using ‘UTF-8’... OK
 NONE
* checking re-building of vignette outputs ... ERROR
Error(s) in re-building vignettes:
  ...
--- re-building ‘spatialDE.Rmd’ using rmarkdown
Quitting from lines 62-64 (spatialDE.Rmd) 
Error: processing vignette 'spatialDE.Rmd' failed with diagnostics:
there is no package called 'spatialDE'
--- failed re-building ‘spatialDE.Rmd’

SUMMARY: processing the following file failed:
  ‘spatialDE.Rmd’

Error: Vignette re-building failed.
Execution halted

* checking PDF version of manual ... OK
* DONE

Status: 2 ERRORs, 2 WARNINGs, 1 NOTE
See
  ‘/home/biocbuild/bbs-3.17-bioc/meat/spatialDE.Rcheck/00check.log’
for details.


Installation output

spatialDE.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL spatialDE
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.17-bioc/R/site-library’
* installing *source* package ‘spatialDE’ ...
** using non-staged installation via StagedInstall field
** R
** data
** 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
* DONE (spatialDE)

Tests output

spatialDE.Rcheck/tests/testthat.Rout.fail


R Under development (unstable) (2022-12-12 r83438) -- "Unsuffered Consequences"
Copyright (C) 2022 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (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.

> library(testthat)
> library(spatialDE)
Error in library(spatialDE) : there is no package called 'spatialDE'
Execution halted

Example timings