biocbuild@kunpeng1 ~/git> R CMD build --keep-empty-dirs --no-resave-data BUSpaRse
* checking for file ‘BUSpaRse/DESCRIPTION’ ... OK
* preparing ‘BUSpaRse’:
* checking DESCRIPTION meta-information ... OK
* cleaning src
* installing the package to build vignettes
* creating vignettes ... OK
* cleaning src
* checking for LF line-endings in source and make files and shell scripts
* checking for empty or unneeded directories
* building ‘BUSpaRse_1.13.0.tar.gz’
biocbuild@kunpeng1 ~/git> R CMD check BUSpaRse_1.13.0.tar.gz
* using log directory ‘/home/biocbuild/git/BUSpaRse.Rcheck’
* using R Under development (unstable) (2023-03-12 r83975)
* using platform: aarch64-unknown-linux-gnu (64-bit)
* R was compiled by
gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
* running under: Ubuntu 22.04.2 LTS
* using session charset: UTF-8
* checking for file ‘BUSpaRse/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘BUSpaRse’ version ‘1.13.0’
* 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 ‘BUSpaRse’ can be installed ... OK
* used C++ compiler: ‘g++ (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0’
* checking C++ specification ... NOTE
Specified C++11: please drop specification unless essential
* checking installed package size ... NOTE
installed size is 5.2Mb
sub-directories of 1Mb or more:
doc 1.4Mb
libs 3.2Mb
* 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 R 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 ... OK
* checking LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking use of PKG_*FLAGS in Makefiles ... OK
* checking compiled code ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’
ERROR
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
3. └─biomaRt::useMart(biomart = mart_use, dataset = ds_name, host = host_use)
4. └─biomaRt:::.useMart(...)
5. └─biomaRt::useDataset(mart = mart, dataset = dataset, verbose = verbose)
6. └─biomaRt:::.getFilters(mart, verbose = verbose)
7. └─biomaRt:::.getAttrFilt(mart = mart, verbose = verbose, type = "filters")
8. └─biomaRt:::bmRequest(...)
9. └─httr::GET(...)
10. └─httr:::request_perform(req, hu$handle$handle)
11. ├─httr:::request_fetch(req$output, req$url, handle)
12. └─httr:::request_fetch.write_memory(req$output, req$url, handle)
13. └─curl::curl_fetch_memory(url, handle = handle)
[ FAIL 1 | WARN 0 | SKIP 0 | PASS 95 ]
Error: Test failures
Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ...
‘sparse-matrix.Rmd’ using ‘UTF-8’... OK
‘tr2g.Rmd’ using ‘UTF-8’... OK
NONE
* checking re-building of vignette outputs ... ERROR
Error(s) in re-building vignettes:
...
--- re-building ‘sparse-matrix.Rmd’ using rmarkdown
Quitting from lines 43-46 (sparse-matrix.Rmd)
Error: processing vignette 'sparse-matrix.Rmd' failed with diagnostics:
Timeout was reached: [jan2020.archive.ensembl.org:443] Operation timed out after 10000 milliseconds with 368729 bytes received
--- failed re-building ‘sparse-matrix.Rmd’
--- re-building ‘tr2g.Rmd’ using rmarkdown
Quitting from lines 38-42 (tr2g.Rmd)
Error: processing vignette 'tr2g.Rmd' failed with diagnostics:
Timeout was reached: [www.ensembl.org:80] Operation timed out after 10000 milliseconds with 0 bytes received
--- failed re-building ‘tr2g.Rmd’
SUMMARY: processing the following files failed:
‘sparse-matrix.Rmd’ ‘tr2g.Rmd’
Error: Vignette re-building failed.
Execution halted
* checking PDF version of manual ... OK
* DONE
Status: 2 ERRORs, 2 NOTEs
See
‘/home/biocbuild/git/BUSpaRse.Rcheck/00check.log’
for details.
martin-g
commented
1 year ago