##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:mammaPrintData.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings mammaPrintData_1.45.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.22-data-experiment/meat/mammaPrintData.Rcheck’
* using R version 4.5.1 Patched (2025-08-23 r88802)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
    GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.3 LTS
* using session charset: UTF-8
* checking for file ‘mammaPrintData/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘mammaPrintData’ version ‘1.45.0’
* 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 ‘mammaPrintData’ can be installed ... OK
* checking installed package size ... INFO
  installed size is 216.0Mb
  sub-directories of 1Mb or more:
    data      10.4Mb
    extdata  205.4Mb
* 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 ... OK
* 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 ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: OK

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD INSTALL mammaPrintData
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.22-bioc/R/site-library’
* installing *source* package ‘mammaPrintData’ ...
** this is package ‘mammaPrintData’ version ‘1.45.0’
** using staged installation
** data
** inst
** help
*** installing help indices
** building package indices
# Bootstrapping renv 0.17.3 --------------------------------------------------
* Downloading renv 0.17.3 ... OK
* Installing renv 0.17.3 ... Done!
Error installing renv:
======================
* installing *source* package ‘renv’ ...
** this is package ‘renv’ version ‘0.17.3’
** package ‘renv’ successfully unpacked and MD5 sums checked
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
*** copying figures
** 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
ERROR: hard-coded installation path: please report to the package maintainer and use ‘--no-staged-install’
* removing ‘/home/biocbuild/.cache/R/renv/library/mammaPrintData-4827d13d/R-4.5/x86_64-pc-linux-gnu/renv’
Warning messages:
1: In system2(r, args, stdout = TRUE, stderr = TRUE) :
  running command ''/home/biocbuild/bbs-3.22-bioc/R/bin/R' --vanilla CMD INSTALL --no-multiarch -l '/home/biocbuild/.cache/R/renv/library/mammaPrintData-4827d13d/R-4.5/x86_64-pc-linux-gnu' '/tmp/RtmpUjS3dV/renv_0.17.3.tar.gz' 2>&1' had status 1
2: Failed to find an renv installation: the project will not be loaded.
Use `renv::activate()` to re-initialize the project. 
** installing vignettes
** testing if installed package can be loaded from temporary location
# Bootstrapping renv 0.17.3 --------------------------------------------------
* Downloading renv 0.17.3 ... OK
* Installing renv 0.17.3 ... Done!
Error installing renv:
======================
* installing *source* package ‘renv’ ...
** this is package ‘renv’ version ‘0.17.3’
** package ‘renv’ successfully unpacked and MD5 sums checked
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
*** copying figures
** 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
ERROR: hard-coded installation path: please report to the package maintainer and use ‘--no-staged-install’
* removing ‘/home/biocbuild/.cache/R/renv/library/mammaPrintData-4827d13d/R-4.5/x86_64-pc-linux-gnu/renv’
Warning messages:
1: In system2(r, args, stdout = TRUE, stderr = TRUE) :
  running command ''/home/biocbuild/bbs-3.22-bioc/R/bin/R' --vanilla CMD INSTALL --no-multiarch -l '/home/biocbuild/.cache/R/renv/library/mammaPrintData-4827d13d/R-4.5/x86_64-pc-linux-gnu' '/tmp/RtmpRGZ5oa/renv_0.17.3.tar.gz' 2>&1' had status 1
2: Failed to find an renv installation: the project will not be loaded.
Use `renv::activate()` to re-initialize the project. 
** testing if installed package can be loaded from final location
# Bootstrapping renv 0.17.3 --------------------------------------------------
* Downloading renv 0.17.3 ... OK
* Installing renv 0.17.3 ... Done!
* Successfully installed and loaded renv 0.17.3.
ℹ Using R 4.5.1 (lockfile was generated with R 4.2.3)
Retrieving 'http://lib.stat.cmu.edu/R/CRAN/src/contrib/BiocManager_1.30.26.tar.gz' ...
	OK [downloaded 580.6 Kb in 0.36 seconds]
Installing BiocManager [1.30.26] ...
	OK [built from source in 2 seconds]
Moving BiocManager [1.30.26] into the cache ...
	OK [moved to cache in 4.7 milliseconds]
* Installed 1 package in 3.9 seconds.
Warning message:
This project is configured to use Bioconductor 3.15, which is not compatible with R 4.5.1.
Use 'renv::init(bioconductor = "3.15")' to re-initialize this project with the appropriate Bioconductor release.
 
** testing if installed package keeps a record of temporary installation path
* DONE (mammaPrintData)