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###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD check --install=check:GEOmetadb.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings GEOmetadb_1.69.2.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/GEOmetadb.Rcheck’
* using R Under development (unstable) (2024-11-24 r87369)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
    aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0
    GNU Fortran (GCC) 14.2.0
* running under: openEuler 24.03 (LTS)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘GEOmetadb/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘GEOmetadb’ version ‘1.69.2’
* 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:
  .travis.yml
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 ‘GEOmetadb’ 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 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 ... NOTE
getSQLiteFile: no visible global function definition for
  ‘download.file’
Undefined global functions or variables:
  download.file
Consider adding
  importFrom("utils", "download.file")
to your NAMESPACE file.
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... WARNING
Codoc mismatches from Rd file 'getSQLiteFile.Rd':
getSQLiteFile
  Code: function(destdir = getwd(), destfile = "GEOmetadb.sqlite.gz",
                 type = "full")
  Docs: function(destdir = getwd(), destfile = "GEOmetadb.sqlite.gz",
                 type = "normal")
  Mismatches in argument default values:
    Name: 'type' Code: "full" Docs: "normal"

* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... ERROR
Running examples in ‘GEOmetadb-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: GEOmetadb-package
> ### Title: Query NCBI GEO metadata from a local SQLite database
> ### Aliases: GEOmetadb-package GEOmetadb
> ### Keywords: package
> 
> ### ** Examples
> 
> ## Use the demo GEOmetadb database:
> if( !file.exists("GEOmetadb.sqlite") ) {
+     demo_sqlfile <- getSQLiteFile(destdir = getwd(), destfile = "GEOmetadb.sqlite.gz", type = "demo")
+ } else {
+     demo_sqlfile <- "GEOmetadb.sqlite"
+ }
trying URL 'https://gbnci.cancer.gov/geo/GEOmetadb_demo.sqlite.gz'
Content type 'application/x-gzip' length 20889492 bytes (19.9 MB)
======================
downloaded 9.2 MB

Warning in download.file(url_geo, destfile = localfile, mode = "wb") :
  downloaded length 9607859 != reported length 20889492
Warning in download.file(url_geo, destfile = localfile, mode = "wb") :
  URL 'https://gbnci.cancer.gov/geo/GEOmetadb_demo.sqlite.gz': status was 'Transferred a partial file'
Error in download.file(url_geo, destfile = localfile, mode = "wb") : 
  download from 'https://gbnci.cancer.gov/geo/GEOmetadb_demo.sqlite.gz' failed
Calls: getSQLiteFile -> download.file
Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 1 ERROR, 1 WARNING, 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.21-bioc/meat/GEOmetadb.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD INSTALL GEOmetadb
###
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* installing to library ‘/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library’
* installing *source* package ‘GEOmetadb’ ...
** using staged installation
** R
** 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
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (GEOmetadb)