* using log directory '/scratch/th798/data.table-revdeps/2022-11-12/tasks/753/OmicNavigator.Rcheck'
* using R version 4.2.2 (2022-10-31)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: ASCII
* checking for file 'OmicNavigator/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'OmicNavigator' version '1.11.5'
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Packages suggested but not available for checking:
  'faviconPlease', 'opencpu', 'plotly', 'tinytest', 'ttdo', 'UpSetR'
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for executable files ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package 'OmicNavigator' can be installed ... OK
* checking installed package size ... OK
* checking package 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 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 ... 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 ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... NOTE
Packages unavailable to check Rd xrefs: 'UpSetR', 'opencpu'
* 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 LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ... ERROR
Running examples in 'OmicNavigator-Ex.R' failed
The error most likely occurred in:

> ### Name: getFavicons
> ### Title: Get favicon URLs for table linkouts
> ### Aliases: getFavicons
> 
> ### ** Examples
> 
>   getFavicons("https://reactome.org/content/detail/")
Error in loadNamespace(x) : there is no package called 'faviconPlease'
Calls: getFavicons ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted
* checking for unstated dependencies in 'tests' ... OK
* checking tests ... OK
  Running 'tinytest.R'
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in 'inst/doc' ... OK
* checking running R code from vignettes ... ERROR
Errors in running code in vignettes:
when running code in 'OmicNavigatorAPI.Rnw'
  ...
+     plots <- OmicN .... [TRUNCATED] 
Installing study "ABC" in /tmp/RtmpilXIPL/file24243a4c1cac28
Exporting study "ABC" as an R package
Note: No maintainer email was specified. Using the placeholder: Unknown <unknown@unknown>
Calculating pairwise overlaps. This may take a while...
Exported study to /tmp/RtmpilXIPL/ONstudyABC

  When sourcing 'OmicNavigatorAPI.R':
Error: (converted from warning) installation of package '/tmp/RtmpilXIPL/ONstudyABC' had non-zero exit status
Execution halted

  'OmicNavigatorAPI.Rnw' using 'UTF-8'... failed
  'OmicNavigatorUsersGuide.Rnw' using 'UTF-8'... OK
* checking re-building of vignette outputs ... NOTE
Error(s) in re-building vignettes:
--- re-building 'OmicNavigatorAPI.Rnw' using Sweave
OmicNavigator R package version: 1.11.5
The app is not installed. Install it with installApp()
Installing study "ABC" in /tmp/RtmpTIGZHn/file2425db4819e0a2
Exporting study "ABC" as an R package
Note: No maintainer email was specified. Using the placeholder: Unknown <unknown@unknown>
Calculating pairwise overlaps. This may take a while...
Exported study to /tmp/RtmpTIGZHn/ONstudyABC

Error: processing vignette 'OmicNavigatorAPI.Rnw' failed with diagnostics:
 chunk 3 (label = test-data) 
Error in utils::install.packages(tmpPkgDir, lib = library, repos = NULL,  : 
  (converted from warning) installation of package '/tmp/RtmpTIGZHn/ONstudyABC' had non-zero exit status

--- failed re-building 'OmicNavigatorAPI.Rnw'

--- re-building 'OmicNavigatorUsersGuide.Rnw' using Sweave
Installing study "vignetteExample" in /tmp/RtmpTIGZHn/file2425db2973b83
Exporting study "vignetteExample" as an R package
Note: No maintainer email was specified. Using the placeholder: Unknown <unknown@unknown>
Calculating pairwise overlaps. This may take a while...
Exported study to /tmp/RtmpTIGZHn/ONstudyvignetteExample
Success!
Returning "default" features for modelID "modelThatDoesntExistYet"
--- finished re-building 'OmicNavigatorUsersGuide.Rnw'

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

Error: Vignette re-building failed.
Execution halted

* checking PDF version of manual ... OK
* DONE
Status: 2 ERRORs, 3 NOTEs