Back to Multiple platform build/check report for BioC 3.18:   simplified   long
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This page was generated on 2024-01-27 11:35:34 -0500 (Sat, 27 Jan 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 22.04.2 LTS)x86_644.3.2 Patched (2023-11-13 r85521) -- "Eye Holes" 4690
palomino4Windows Server 2022 Datacenterx644.3.2 (2023-10-31 ucrt) -- "Eye Holes" 4443
lconwaymacOS 12.7.1 Montereyx86_644.3.2 Patched (2023-11-01 r85457) -- "Eye Holes" 4462
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

Package 254/2266HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
BUSpaRse 1.16.0  (landing page)
Lambda Moses
Snapshot Date: 2024-01-26 14:05:07 -0500 (Fri, 26 Jan 2024)
git_url: https://git.bioconductor.org/packages/BUSpaRse
git_branch: RELEASE_3_18
git_last_commit: 3f91189
git_last_commit_date: 2023-10-24 11:15:59 -0500 (Tue, 24 Oct 2023)
nebbiolo2Linux (Ubuntu 22.04.2 LTS) / x86_64  OK    OK    ERROR  
palomino4Windows Server 2022 Datacenter / x64  OK    OK    ERROR    OK  
lconwaymacOS 12.7.1 Monterey / x86_64  OK    ERROR  skippedskipped
kjohnson1macOS 13.6.1 Ventura / arm64see weekly results here

CHECK results for BUSpaRse on nebbiolo2


To the developers/maintainers of the BUSpaRse package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/BUSpaRse.git to reflect on this report. See Troubleshooting Build Report for more information.
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results


Summary

Package: BUSpaRse
Version: 1.16.0
Command: /home/biocbuild/bbs-3.18-bioc/R/bin/R CMD check --install=check:BUSpaRse.install-out.txt --library=/home/biocbuild/bbs-3.18-bioc/R/site-library --timings BUSpaRse_1.16.0.tar.gz
StartedAt: 2024-01-26 20:35:58 -0500 (Fri, 26 Jan 2024)
EndedAt: 2024-01-26 20:45:56 -0500 (Fri, 26 Jan 2024)
EllapsedTime: 598.2 seconds
RetCode: 1
Status:   ERROR  
CheckDir: BUSpaRse.Rcheck
Warnings: NA

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.18-bioc/R/bin/R CMD check --install=check:BUSpaRse.install-out.txt --library=/home/biocbuild/bbs-3.18-bioc/R/site-library --timings BUSpaRse_1.16.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.18-bioc/meat/BUSpaRse.Rcheck’
* using R version 4.3.2 Patched (2023-11-13 r85521)
* using platform: x86_64-pc-linux-gnu (64-bit)
* R was compiled by
    gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
    GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
* running under: Ubuntu 22.04.3 LTS
* using session charset: UTF-8
* checking for file ‘BUSpaRse/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘BUSpaRse’ version ‘1.16.0’
* 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 11.4.0-1ubuntu1~22.04) 11.4.0’
* checking C++ specification ... NOTE
  Specified C++11: please drop specification unless essential
* 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 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 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 ... 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 ... NOTE
Note: information on .o files is not available
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                   user system elapsed
tr2g_TxDb        31.458  2.120  33.581
knee_plot        21.691  2.851  30.164
dl_transcriptome  8.772  0.569  27.820
transcript2gene   2.924  0.269   8.402
tr2g_ensembl      1.257  0.096  21.261
* 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:
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test_tr2g.R:34:3'): Sensible results from biomart query ─────────────
  Error in `if (biomart == "ensembl" & grepl(x = host, pattern = "ensembl.org")) {
      biomart = "ENSEMBL_MART_ENSEMBL"
  }`: argument is of length zero
  Backtrace:
      ▆
   1. └─BUSpaRse::tr2g_ensembl(...) at test_tr2g.R:34:3
   2.   └─BUSpaRse:::my_useMart(ensembl_version, mart_use, ds_name, host_use)
   3.     └─biomaRt::useMart(biomart = mart_use, dataset = ds_name, host = host_use)
   4.       └─biomaRt:::.useMart(...)
  
  [ 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 ... OK
* checking PDF version of manual ... OK
* DONE

Status: 1 ERROR, 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.18-bioc/meat/BUSpaRse.Rcheck/00check.log’
for details.


Installation output

BUSpaRse.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.18-bioc/R/bin/R CMD INSTALL BUSpaRse
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.18-bioc/R/site-library’
* installing *source* package ‘BUSpaRse’ ...
** using staged installation
** libs
using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’
using C++11
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/RcppArmadillo/include' -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/RcppProgress/include' -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/BH/include' -I/usr/local/include    -fpic  -g -O2  -Wall -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/RcppArmadillo/include' -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/RcppProgress/include' -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/BH/include' -I/usr/local/include    -fpic  -g -O2  -Wall -c fill_cell_gene.cpp -o fill_cell_gene.o
In file included from /home/biocbuild/bbs-3.18-bioc/R/site-library/BH/include/boost/mpl/aux_/na_assert.hpp:23,
                 from /home/biocbuild/bbs-3.18-bioc/R/site-library/BH/include/boost/mpl/arg.hpp:25,
                 from /home/biocbuild/bbs-3.18-bioc/R/site-library/BH/include/boost/mpl/placeholders.hpp:24,
                 from /home/biocbuild/bbs-3.18-bioc/R/site-library/BH/include/boost/iterator/iterator_categories.hpp:16,
                 from /home/biocbuild/bbs-3.18-bioc/R/site-library/BH/include/boost/iterator/iterator_adaptor.hpp:14,
                 from /home/biocbuild/bbs-3.18-bioc/R/site-library/BH/include/boost/token_iterator.hpp:22,
                 from /home/biocbuild/bbs-3.18-bioc/R/site-library/BH/include/boost/tokenizer.hpp:20,
                 from fill_cell_gene.cpp:16:
/home/biocbuild/bbs-3.18-bioc/R/site-library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of ‘assert_arg’ [-Wparentheses]
  194 | failed ************ (Pred::************
      |                     ^~~~~~~~~~~~~~~~~~~
  195 |       assert_arg( void (*)(Pred), typename assert_arg_pred<Pred>::type )
      |       ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  196 |     );
      |     ~                
/home/biocbuild/bbs-3.18-bioc/R/site-library/BH/include/boost/mpl/assert.hpp:194:21: note: remove parentheses
  194 | failed ************ (Pred::************
      |                     ^~~~~~~~~~~~~~~~~~~
      |                     -
  195 |       assert_arg( void (*)(Pred), typename assert_arg_pred<Pred>::type )
      |       ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  196 |     );
      |     ~                
      |     -
/home/biocbuild/bbs-3.18-bioc/R/site-library/BH/include/boost/mpl/assert.hpp:199:21: warning: unnecessary parentheses in declaration of ‘assert_not_arg’ [-Wparentheses]
  199 | failed ************ (boost::mpl::not_<Pred>::************
      |                     ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  200 |       assert_not_arg( void (*)(Pred), typename assert_arg_pred_not<Pred>::type )
      |       ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  201 |     );
      |     ~                
/home/biocbuild/bbs-3.18-bioc/R/site-library/BH/include/boost/mpl/assert.hpp:199:21: note: remove parentheses
  199 | failed ************ (boost::mpl::not_<Pred>::************
      |                     ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
      |                     -
  200 |       assert_not_arg( void (*)(Pred), typename assert_arg_pred_not<Pred>::type )
      |       ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  201 |     );
      |     ~                
      |     -
g++ -std=gnu++11 -shared -L/home/biocbuild/bbs-3.18-bioc/R/lib -L/usr/local/lib -o BUSpaRse.so RcppExports.o fill_cell_gene.o -llapack -L/home/biocbuild/bbs-3.18-bioc/R/lib -lRblas -lgfortran -lm -lquadmath -L/home/biocbuild/bbs-3.18-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.18-bioc/R/site-library/00LOCK-BUSpaRse/00new/BUSpaRse/libs
** R
** data
*** moving datasets to lazyload DB
** 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
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (BUSpaRse)

Tests output

BUSpaRse.Rcheck/tests/testthat.Rout.fail


R version 4.3.2 Patched (2023-11-13 r85521) -- "Eye Holes"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(testthat)
> library(BUSpaRse)
> 
> test_check("BUSpaRse")
[ FAIL 1 | WARN 0 | SKIP 0 | PASS 95 ]

══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test_tr2g.R:34:3'): Sensible results from biomart query ─────────────
Error in `if (biomart == "ensembl" & grepl(x = host, pattern = "ensembl.org")) {
    biomart = "ENSEMBL_MART_ENSEMBL"
}`: argument is of length zero
Backtrace:
    ▆
 1. └─BUSpaRse::tr2g_ensembl(...) at test_tr2g.R:34:3
 2.   └─BUSpaRse:::my_useMart(ensembl_version, mart_use, ds_name, host_use)
 3.     └─biomaRt::useMart(biomart = mart_use, dataset = ds_name, host = host_use)
 4.       └─biomaRt:::.useMart(...)

[ FAIL 1 | WARN 0 | SKIP 0 | PASS 95 ]
Error: Test failures
Execution halted

Example timings

BUSpaRse.Rcheck/BUSpaRse-Ex.timings

nameusersystemelapsed
EC2gene0.0520.0000.053
annots_from_fa_df0.1810.0240.206
dl_transcriptome 8.772 0.56927.820
get_velocity_files1.3220.1881.511
knee_plot21.691 2.85130.164
make_sparse_matrix0.0020.0000.003
read_count_output0.0120.0000.013
read_velocity_output0.0000.0030.004
save_tr2g_bustools0.3930.0010.394
sort_tr2g0.2950.0160.312
species2dataset000
subset_annot1.0780.0991.181
tr2g_EnsDb2.8170.3843.200
tr2g_TxDb31.458 2.12033.581
tr2g_ensembl 1.257 0.09621.261
tr2g_fasta0.0200.0030.023
tr2g_gff30.7680.1080.876
tr2g_gtf0.7460.1160.862
transcript2gene2.9240.2698.402