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### Running command:
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###   /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD check --install=check:GSVAdata.install-out.txt --library=/home/biocbuild/bbs-3.23-bioc/R/site-library --timings GSVAdata_1.47.2.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.23-data-experiment/meat/GSVAdata.Rcheck’
* using R version 4.6.0 alpha (2026-04-05 r89794)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.3.0-6ubuntu2~24.04.1) 13.3.0
    GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04.1) 13.3.0
* running under: Ubuntu 24.04.4 LTS
* using session charset: UTF-8
* current time: 2026-04-16 16:26:14 UTC
* checking for file ‘GSVAdata/DESCRIPTION’ ... OK
* this is package ‘GSVAdata’ version ‘1.47.2’
* 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 ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘GSVAdata’ can be installed ... OK
* checking installed package size ... INFO
  installed size is 16.0Mb
  sub-directories of 1Mb or more:
    data     11.6Mb
    extdata   4.3Mb
* checking package directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Packages listed in more than one of Depends, Imports, Suggests, Enhances:
  ‘Biobase’ ‘GSEABase’ ‘SummarizedExperiment’
A package should be listed in only one of these fields.
* 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 dependencies in R code ... NOTE
Namespaces in Imports field not imported from:
  ‘Biobase’ ‘GSEABase’ ‘SummarizedExperiment’
  All declared Imports should be used.
Packages in Depends field not imported from:
  ‘Biobase’ ‘GSEABase’ ‘SummarizedExperiment’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
* 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 ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... NOTE
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  GSVAdata-package.Rd: leukemia
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
* 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 examples ... ERROR
Running examples in ‘GSVAdata-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: HumanCerebellumNormSubset
> ### Title: HumanCerebellumSubset
> ### Aliases: HumanCerebellumNormSubset
> 
> ### ** Examples
> 
> 
> spe <- HumanCerebellumNormSubset()
Warning in open.connection(file) :
  cannot open compressed file '/human_cerebellum_norm_logcounts_250x4816.mtx.gz', probable reason 'No such file or directory'
Error in open.connection(file) : cannot open the connection
Calls: HumanCerebellumNormSubset -> as -> .class1 -> readMM -> open -> open.connection
Execution halted
* checking PDF version of manual ... OK
* DONE

Status: 1 ERROR, 3 NOTEs
See
  ‘/home/biocbuild/bbs-3.23-data-experiment/meat/GSVAdata.Rcheck/00check.log’
for details.

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### Running command:
###
###   /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD INSTALL GSVAdata
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* installing to library ‘/home/biocbuild/bbs-3.23-bioc/R/site-library’
* installing *source* package ‘GSVAdata’ ...
** this is package ‘GSVAdata’ version ‘1.47.2’
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** 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 (GSVAdata)