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### Running command:
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### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:recount.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings recount_1.30.2.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.19-bioc/meat/recount.Rcheck’
* using R version 4.4.1 (2024-06-14)
* using platform: aarch64-apple-darwin20
* R was compiled by
Apple clang version 14.0.0 (clang-1400.0.29.202)
GNU Fortran (GCC) 12.2.0
* running under: macOS Ventura 13.6.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘recount/DESCRIPTION’ ... OK
* this is package ‘recount’ version ‘1.30.2’
* 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 ‘recount’ can be installed ... OK
* checking installed package size ... NOTE
installed size is 6.1Mb
sub-directories of 1Mb or more:
data 5.8Mb
* 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 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 ... 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 ... NOTE
Note: found 347 marked UTF-8 strings
* checking LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking line endings in Makefiles ... OK
* checking for GNU extensions in Makefiles ... OK
* checking include directives in Makefiles ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... ERROR
Running examples in ‘recount-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: find_geo
> ### Title: Find the GEO accession id for a given SRA run
> ### Aliases: find_geo
>
> ### ** Examples
>
> ## Find the GEO accession id for for SRX110461
> find_geo("SRX110461")
Error: HTTP failure: 500
NCBI/eutils101 - WWW Error 500 Diagnostic
Server Error
Your request could not be processed due to a problem on
our Web server. This could be a transient problem, please
try the query again. If it doesn't clear up within a
reasonable period of time, e-mail a short description of your
query and the diagnostic information shown below to:
pubmed@nlm.nih.gov - for problems with PubMed
webadmin@ncbi.nlm.nih.gov - for problems with other services
Thank you for your assistance. We will try to fix the
problem as soon as possible.
Diagnostic Information:
Error: 500
URL: h t t p : / / e x t - h t t p - e u t i l s . l
Execution halted
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘test-all.R’
ERROR
Running the tests in ‘tests/test-all.R’ failed.
Last 13 lines of output:
Backtrace:
▆
1. ├─testthat::expect_equal(find_geo("SRX110461"), "GSM836270") at test-misc.R:16:5
2. │ └─testthat::quasi_label(enquo(object), label, arg = "object")
3. │ └─rlang::eval_bare(expr, quo_get_env(quo))
4. └─recount::find_geo("SRX110461")
5. └─rentrez::entrez_summary(db = "gds", i)
6. ├─base::do.call(make_entrez_query, args)
7. └─rentrez (local) ``(...)
8. └─rentrez:::entrez_check(response)
[ FAIL 1 | WARN 2 | SKIP 0 | PASS 44 ]
Error: Test failures
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: 2 ERRORs, 2 NOTEs
See
‘/Users/biocbuild/bbs-3.19-bioc/meat/recount.Rcheck/00check.log’
for details.