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### Running command:
###
###   /home/biocbuild/bbs-3.18-bioc/R/bin/R CMD check --install=check:pcxnData.install-out.txt --library=/home/biocbuild/bbs-3.18-bioc/R/site-library --timings pcxnData_2.24.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.18-data-experiment/meat/pcxnData.Rcheck’
* using R version 4.3.3 (2024-02-29)
* using platform: x86_64-pc-linux-gnu (64-bit)
* R was compiled by
    gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
    GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
* running under: Ubuntu 22.04.4 LTS
* using session charset: UTF-8
* checking for file ‘pcxnData/DESCRIPTION’ ... OK
* this is package ‘pcxnData’ version ‘2.24.0’
* 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:
  .BBSoptions
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 ‘pcxnData’ can be installed ... OK
* checking installed package size ... NOTE
  installed size is 40.4Mb
  sub-directories of 1Mb or more:
    data  40.3Mb
* 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 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 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 ... WARNING
File ‘data/datalist’ contains malformed line(s):
  ‘cp_gs_v5.1:cp_gs_v5.1’ ‘gobp_gs_v5.1:gobp_gs_v5.1’
  ‘h_gs_v5.1:h_gs_v5.1’ ‘pathprint.Hs.gs:pathprint.Hs.gs’
  ‘pathCor_CPv5.1_dframe:pathCor_CPv5.1_dframe’
  ‘pathCor_GOBPv5.1_dframe:pathCor_GOBPv5.1_dframe’
  ‘pathCor_Hv5.1_dframe:pathCor_Hv5.1_dframe’
  ‘pathCor_pathprint_v1.2.3_dframe:pathCor_pathprint_v1.2.3_dframe’
  ‘pathCor_CPv5.1_unadjusted_dframe:pathCor_CPv5.1_unadjusted_dframe’
  ‘pathCor_GOBPv5.1_unadjusted_dframe:pathCor_GOBPv5.1_unadjusted_dframe’
  ‘pathCor_Hv5.1_unadjusted_dframe:pathCor_Hv5.1_unadjusted_dframe’
  ‘pathCor_pathprint_v1.2.3_unadjusted_dframe:pathCor_pathprint_v1.2.3_unadjusted_dframe’
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ...
  ‘usingpcxnData.Rnw’ using ‘UTF-8’... failed
 WARNING
Errors in running code in vignettes:
when running code in ‘usingpcxnData.Rnw’
  ...
+     phenotype_0_genesets = c("ABC transporters (KEGG)", "ACE Inhibitor Pathway (Wikipathways)" .... [TRUNCATED] 
[1] "Successful analyzing: Based on phenotype 0 [ABC transporters (KEGG), ACE Inhibitor Pathway (Wikipathways), AR down reg. targets (Netpath)], phenotype 1 [DNA Repair (Reactome)] and 10 top correlated genesets, 55 correlation pairs were found."

> hm <- pcxn_heatmap(pcxn.obj, cluster_method = "complete")

> gene_members <- pcxn_gene_members(pathway_name = "Alzheimer's disease (KEGG)")

  When sourcing ‘usingpcxnData.R’:
Error: there is no package called ‘org.Hs.eg.db’
Execution halted

* checking re-building of vignette outputs ... NOTE
Error(s) in re-building vignettes:
  ...
--- re-building ‘usingpcxnData.Rnw’ using Sweave
Loading required package: pcxnData

Error: processing vignette 'usingpcxnData.Rnw' failed with diagnostics:
 chunk 1 
Error in loadNamespace(name) : there is no package called ‘org.Hs.eg.db’

--- failed re-building ‘usingpcxnData.Rnw’

SUMMARY: processing the following file failed:
  ‘usingpcxnData.Rnw’

Error: Vignette re-building failed.
Execution halted

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

Status: 2 WARNINGs, 3 NOTEs
See
  ‘/home/biocbuild/bbs-3.18-data-experiment/meat/pcxnData.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /home/biocbuild/bbs-3.18-bioc/R/bin/R CMD INSTALL pcxnData
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* installing to library ‘/home/biocbuild/bbs-3.18-bioc/R/site-library’
* installing *source* package ‘pcxnData’ ...
** using staged installation
** data
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (pcxnData)