| Back to Multiple platform build/check report for BioC 3.17 | 
  | 
This page was generated on 2023-01-25 10:57:06 -0500 (Wed, 25 Jan 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs | 
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 22.04.1 LTS) | x86_64 | R Under development (unstable) (2023-01-10 r83596) -- "Unsuffered Consequences" | 4464 | 
| nebbiolo2 | Linux (Ubuntu 20.04.5 LTS) | x86_64 | R 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 | ||||
| 
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.  | 
| Package 1910/2162 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| spatialDE 1.5.1  (landing page) Gabriele Sales 
  | nebbiolo1 | Linux (Ubuntu 22.04.1 LTS) / x86_64 | OK | OK | OK | |||||||||
| nebbiolo2 | Linux (Ubuntu 20.04.5 LTS) / x86_64 | OK | OK | ERROR | ||||||||||
| 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 | 
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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.
spatialDE.Rcheck/00install.out
############################################################################## ############################################################################## ### ### 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)
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