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### Running command:
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###   /home/biocbuild/bbs-3.16-bioc/R/bin/R CMD check --install=check:DEComplexDisease.install-out.txt --library=/home/biocbuild/bbs-3.16-bioc/R/site-library --timings DEComplexDisease_1.18.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.16-bioc/meat/DEComplexDisease.Rcheck’
* using R version 4.2.3 (2023-03-15)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* checking for file ‘DEComplexDisease/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘DEComplexDisease’ version ‘1.18.0’
* 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 ‘DEComplexDisease’ can be installed ... WARNING
Found the following significant warnings:
  Warning: Package 'DEComplexDisease' is deprecated and will be removed from
See ‘/home/biocbuild/bbs-3.16-bioc/meat/DEComplexDisease.Rcheck/00install.out’ for details.
* 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 ... 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 ... NOTE
prepare_Rd: Plot.cluster.module.Rd:53-55: Dropping empty section \references
prepare_Rd: Plot.deg.specific.test.Rd:43-45: Dropping empty section \references
prepare_Rd: module.curve.Rd:27-29: Dropping empty section \references
prepare_Rd: summarize.cluster.module.Rd:30-32: Dropping empty section \references
prepare_Rd: summarize.seed.module.Rd:31-33: Dropping empty section \references
* 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 ... OK
* checking LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
              user system elapsed
bi.deg      19.841  1.659  21.502
seed.module  5.155  0.076   5.231
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ...
  ‘decd.Rmd’... OK
 NONE
* checking re-building of vignette outputs ... ERROR
Error(s) in re-building vignettes:
  ...
--- re-building ‘decd.Rmd’ using knitr
Quitting from lines 261-262 (decd.Rmd) 
Error: processing vignette 'decd.Rmd' failed with diagnostics:
need finite 'ylim' values
--- failed re-building ‘decd.Rmd’

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

Error: Vignette re-building failed.
Execution halted

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

Status: 1 ERROR, 1 WARNING, 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.16-bioc/meat/DEComplexDisease.Rcheck/00check.log’
for details.

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### Running command:
###
###   /home/biocbuild/bbs-3.16-bioc/R/bin/R CMD INSTALL DEComplexDisease
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* installing to library ‘/home/biocbuild/bbs-3.16-bioc/R/site-library’
* installing *source* package ‘DEComplexDisease’ ...
** using staged installation
** libs
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c sig.cpp -o sig.o
g++ -std=gnu++14 -shared -L/home/biocbuild/bbs-3.16-bioc/R/lib -L/usr/local/lib -o DEComplexDisease.so RcppExports.o sig.o -L/home/biocbuild/bbs-3.16-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.16-bioc/R/site-library/00LOCK-DEComplexDisease/00new/DEComplexDisease/libs
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
Warning: Package 'DEComplexDisease' is deprecated and will be removed from
  Bioconductor version 3.17
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
Warning: Package 'DEComplexDisease' is deprecated and will be removed from
  Bioconductor version 3.17
** testing if installed package keeps a record of temporary installation path
* DONE (DEComplexDisease)