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### Running command:
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###   /home/biocbuild/R/R-4.3.1/bin/R CMD check --install=check:ccmap.install-out.txt --library=/home/biocbuild/R/R-4.3.1/site-library --timings ccmap_1.27.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.18-bioc/meat/ccmap.Rcheck’
* using R version 4.3.1 (2023-06-16)
* using platform: aarch64-unknown-linux-gnu (64-bit)
* R was compiled by
    gcc (GCC) 10.3.1
    GNU Fortran (GCC) 10.3.1
* running under: openEuler 22.03 (LTS-SP1)
* using session charset: UTF-8
* checking for file ‘ccmap/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘ccmap’ version ‘1.27.0’
* 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 ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘ccmap’ 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 ... 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 ... NOTE
Namespace in Imports field not imported from: ‘lsa’
  All declared Imports should be used.
Unexported object imported by a ':::' call: ‘xgboost:::predict.xgb.Booster’
  See the note in ?`:::` about the use of this operator.
* 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 ... WARNING
Missing link or links in documentation object 'query_drugs.Rd':
  ‘[crossmeta]{diff_path}’ ‘[crossmeta]{path_meta}’

See section 'Cross-references' in the 'Writing R Extensions' manual.
* 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 ... ERROR
Running examples in ‘ccmap-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: query_combos
> ### Title: Get overlap between query and predicted drug combination
> ###   signatures.
> ### Aliases: query_combos
> 
> ### ** Examples
> 
> library(lydata)
> library(crossmeta)
> 
> # location of data
> data_dir <- system.file("extdata", package = "lydata")
> 
> # gather GSE names
> gse_names  <- c("GSE9601", "GSE15069", "GSE50841", "GSE34817", "GSE29689")
> 
> # load previous analysis
> anals <- load_diff(gse_names, data_dir)
> 
> # perform meta-analysis
> es <- es_meta(anals)
> 
> # get dprimes
> dprimes <- get_dprimes(es)
> 
> # query combinations of metformin and all other cmap drugs
> top_met_combos <- query_combos(dprimes$all$meta, include = 'metformin', ncores = 1)
* 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 ...
  ‘ccmap-vignette.Rmd’ using ‘UTF-8’... OK
 NONE
* checking re-building of vignette outputs ... ERROR
Error(s) in re-building vignettes:
  ...
--- re-building ‘ccmap-vignette.Rmd’ using rmarkdown

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

Status: 2 ERRORs, 1 WARNING, 1 NOTE
See
  ‘/home/biocbuild/bbs-3.18-bioc/meat/ccmap.Rcheck/00check.log’
for details.