* using log directory ‘/data/gannet/ripley/R/packages/tests-Suggests/BiSEp.Rcheck’
* using R Under development (unstable) (2024-04-19 r86451)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc-13 (GCC) 13.2.0
    GNU Fortran (GCC) 13.2.0
* running under: Fedora Linux 36 (Workstation Edition)
* using session charset: UTF-8
* using option ‘--no-stop-on-test-error’
* checking for file ‘BiSEp/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘BiSEp’ version ‘2.2’
* 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 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 ‘BiSEp’ can be installed ... [28s/38s] 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 code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... [8s/10s] OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... [9s/12s] OK
* checking whether the namespace can be loaded with stated dependencies ... [8s/11s] OK
* checking whether the namespace can be unloaded cleanly ... [9s/11s] OK
* checking loading without being on the library search path ... OK
* checking use of S3 registration ... 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 ... [40s/67s] OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd line widths ... 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [10s/15s] OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... [11s/27s] ERROR
Error(s) in re-building vignettes:
--- re-building ‘BiSEp.Snw’ using Sweave
Loading required package: BiSEp
Loading required package: mclust
Package 'mclust' version 6.1
Type 'citation("mclust")' for citing this R package in publications.
Loading required package: GOSemSim

GOSemSim v2.29.2  For help: https://yulab-smu.top/biomedical-knowledge-mining-book/

If you use GOSemSim in published research, please cite:
- Guangchuang Yu. Gene Ontology Semantic Similarity Analysis Using GOSemSim. In: Kidder B. (eds) Stem Cell Transcriptional Networks. Methods in Molecular Biology, 2020, 2117:207-215. Humana, New York, NY. doi:10.1007/978-1-0716-0301-7_11
- Guangchuang Yu, Fei Li, Yide Qin, Xiaochen Bo, Yibo Wu, Shengqi Wang. GOSemSim: an R package for measuring semantic similarity among GO terms and gene products Bioinformatics 2010, 26(7):976-978. doi:10.1093/bioinformatics/btq064



Error: processing vignette 'BiSEp.Snw' failed with diagnostics:
 chunk 16 (label = packages) 
Error in (function (cond)  : 
  error in evaluating the argument 'x' in selecting a method for function 'toTable': there is no package called ‘org.Hs.eg.db’

--- failed re-building ‘BiSEp.Snw’

SUMMARY: processing the following file failed:
  ‘BiSEp.Snw’

Error: Vignette re-building failed.
Execution halted

* checking PDF version of manual ... [7s/12s] OK
* checking HTML version of manual ... OK
* checking for non-standard things in the check directory ... OK
* checking for detritus in the temp directory ... OK
* DONE

Status: 1 ERROR
See
  ‘/data/gannet/ripley/R/packages/tests-Suggests/BiSEp.Rcheck/00check.log’
for details.

Command exited with non-zero status 1
Time 6:13.27, 232.94 + 26.50