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### Running command:
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###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:signatureSearch.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/site-library --timings signatureSearch_1.14.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/signatureSearch.Rcheck’
* using R version 4.3.1 (2023-06-16)
* using platform: x86_64-pc-linux-gnu (64-bit)
* R was compiled by
    gcc (Ubuntu 11.3.0-1ubuntu1~22.04.1) 11.3.0
    GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04.1) 11.3.0
* running under: Ubuntu 22.04.3 LTS
* using session charset: UTF-8
* checking for file ‘signatureSearch/DESCRIPTION’ ... OK
* this is package ‘signatureSearch’ version ‘1.14.0’
* 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 ... NOTE
Found the following hidden files and directories:
  inst/extdata/.batchtools.conf.R
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘signatureSearch’ can be installed ... OK
* used C compiler: ‘gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’
* used C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’
* checking C++ specification ... NOTE
  Specified C++11: please drop specification unless essential
* checking installed package size ... NOTE
  installed size is 87.9Mb
  sub-directories of 1Mb or more:
    R        82.6Mb
    data      2.9Mb
    extdata   1.3Mb
* 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 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 ... 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 ... NOTE
  Note: found 147 marked UTF-8 strings
* checking LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking R/sysdata.rda ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
* checking files in ‘vignettes’ ... OK
* checking examples ... ERROR
Running examples in ‘signatureSearch-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: addGESSannot
> ### Title: Add Compound Annotation Info to GESS Result Table
> ### Aliases: addGESSannot
> 
> ### ** Examples
> 
> gess_tb <- data.frame(pert=c("vorinostat", "sirolimus", "estradiol"),
+                   cell=c("SKB", "SKB", "MCF7"),
+                   NCS=runif(3))
> cmp_annot_tb <- data.frame(pert_name=c("vorinostat", "sirolimus", "estradiol"),
+                            prop1=c("a", "b", "c"),
+                            prop2=1:3)
> addGESSannot(gess_tb, "custom", cmp_annot_tb, by="pert_name", 
+              cmp_name_col="pert")
Warning: download failed
  web resource path: ‘https://experimenthub.bioconductor.org/fetch/3244’
  local file path: ‘/home/biocbuild/.cache/R/ExperimentHub/filed78af2757abe2’
  reason: Internal Server Error (HTTP 500).
Warning: bfcdownload() failed
  rid: BFC376
  file: ‘https://experimenthub.bioconductor.org/fetch/3244’
  reason: download failed
Warning: download failed
  hub path: ‘https://experimenthub.bioconductor.org/fetch/3244’
  cache resource: ‘EH3228 : 3244’
  reason: download failed; see warnings()
Error: failed to load resource
  name: EH3228
  title: dtlink_db_clue_sti
  reason: 1 resources failed to download
Execution halted
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ...
  ‘signatureSearch.Rmd’ using ‘UTF-8’... OK
 NONE
* checking re-building of vignette outputs ... ERROR
Error(s) in re-building vignettes:
  ...
--- re-building ‘signatureSearch.Rmd’ using rmarkdown

Quitting from lines 520-523 [gess_gcmap] (signatureSearch.Rmd)
Error: processing vignette 'signatureSearch.Rmd' failed with diagnostics:
file is not a database
--- failed re-building ‘signatureSearch.Rmd’

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

Error: Vignette re-building failed.
Execution halted

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

Status: 2 ERRORs, 5 NOTEs
See
  ‘/home/biocbuild/bbs-3.17-bioc/meat/signatureSearch.Rcheck/00check.log’
for details.