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### Running command:
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###   /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:STROMA4.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings STROMA4_1.27.1.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/STROMA4.Rcheck’
* using R Under development (unstable) (2024-03-18 r86148)
* using platform: x86_64-pc-linux-gnu
* 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 ‘STROMA4/DESCRIPTION’ ... OK
* this is package ‘STROMA4’ version ‘1.27.1’
* 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 ‘STROMA4’ 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 code 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 whether startup messages can be suppressed ... 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
checkRd: (-1) B.stroma.property.Rd:9: Lost braces in \itemize; meant \describe ?
checkRd: (-1) B.stroma.property.Rd:10: Lost braces in \itemize; meant \describe ?
checkRd: (-1) BL1.property.Rd:9: Lost braces in \itemize; meant \describe ?
checkRd: (-1) BL1.property.Rd:10: Lost braces in \itemize; meant \describe ?
checkRd: (-1) BL2.property.Rd:9: Lost braces in \itemize; meant \describe ?
checkRd: (-1) BL2.property.Rd:10: Lost braces in \itemize; meant \describe ?
checkRd: (-1) D.stroma.property.Rd:9: Lost braces in \itemize; meant \describe ?
checkRd: (-1) D.stroma.property.Rd:10: Lost braces in \itemize; meant \describe ?
checkRd: (-1) E.stroma.property.Rd:9: Lost braces in \itemize; meant \describe ?
checkRd: (-1) E.stroma.property.Rd:10: Lost braces in \itemize; meant \describe ?
checkRd: (-1) IM.property.Rd:9: Lost braces in \itemize; meant \describe ?
checkRd: (-1) IM.property.Rd:10: Lost braces in \itemize; meant \describe ?
checkRd: (-1) LAR.property.Rd:9: Lost braces in \itemize; meant \describe ?
checkRd: (-1) LAR.property.Rd:10: Lost braces in \itemize; meant \describe ?
checkRd: (-1) M.property.Rd:9: Lost braces in \itemize; meant \describe ?
checkRd: (-1) M.property.Rd:10: Lost braces in \itemize; meant \describe ?
checkRd: (-1) MSL.property.Rd:9: Lost braces in \itemize; meant \describe ?
checkRd: (-1) MSL.property.Rd:10: Lost braces in \itemize; meant \describe ?
checkRd: (-1) T.stroma.property.Rd:9: Lost braces in \itemize; meant \describe ?
checkRd: (-1) T.stroma.property.Rd:10: Lost braces in \itemize; meant \describe ?
* 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                   user system elapsed
assign.properties 7.314  0.525  37.868
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... ERROR
Error(s) in re-building vignettes:
  ...
--- re-building ‘STROMA4-vignette.Rnw’ using Sweave
Installing package into ‘/tmp/RtmpIJjs57/RLIBS_31fe5145b72460’
(as ‘lib’ is unspecified)

Error: processing vignette 'STROMA4-vignette.Rnw' failed with diagnostics:
 chunk 1 
Error in contrib.url(repos, type) : 
  trying to use CRAN without setting a mirror

--- failed re-building ‘STROMA4-vignette.Rnw’

SUMMARY: processing the following file failed:
  ‘STROMA4-vignette.Rnw’

Error: Vignette re-building failed.
Execution halted

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

Status: 1 ERROR, 1 NOTE
See
  ‘/home/biocbuild/bbs-3.19-bioc/meat/STROMA4.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD INSTALL STROMA4
###
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* installing to library ‘/home/biocbuild/bbs-3.19-bioc/R/site-library’
* installing *source* package ‘STROMA4’ ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** 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 in fun(libname, pkgname) :
  Package 'STROMA4' is deprecated and will be removed from Bioconductor
  version 3.20
** testing if installed package can be loaded from final location
Warning in fun(libname, pkgname) :
  Package 'STROMA4' is deprecated and will be removed from Bioconductor
  version 3.20
** testing if installed package keeps a record of temporary installation path
* DONE (STROMA4)