Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-12-23 12:03 -0500 (Mon, 23 Dec 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4744 |
palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" | 4487 |
merida1 | macOS 12.7.5 Monterey | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4515 |
kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4467 |
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 259/2289 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
BUSpaRse 1.20.0 (landing page) Lambda Moses
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | |||||||||
palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | |||||||||
merida1 | macOS 12.7.5 Monterey / x86_64 | OK | OK | OK | OK | |||||||||
kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | OK | OK | OK | |||||||||
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. |
Package: BUSpaRse |
Version: 1.20.0 |
Command: /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:BUSpaRse.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings BUSpaRse_1.20.0.tar.gz |
StartedAt: 2024-12-19 20:56:18 -0500 (Thu, 19 Dec 2024) |
EndedAt: 2024-12-19 21:08:29 -0500 (Thu, 19 Dec 2024) |
EllapsedTime: 730.5 seconds |
RetCode: 0 |
Status: OK |
CheckDir: BUSpaRse.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:BUSpaRse.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings BUSpaRse_1.20.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/BUSpaRse.Rcheck’ * using R version 4.4.2 (2024-10-31) * using platform: x86_64-pc-linux-gnu * R was compiled by gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0 GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0 * running under: Ubuntu 24.04.1 LTS * using session charset: UTF-8 * checking for file ‘BUSpaRse/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘BUSpaRse’ version ‘1.20.0’ * package encoding: UTF-8 * checking package namespace information ... OK * checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib: cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES' 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 13.3.0-6ubuntu2~24.04) 13.3.0’ * 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 ... NOTE License stub is invalid DCF. Package listed in more than one of Depends, Imports, Suggests, Enhances: ‘txdbmaker’ 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 ... 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 27.500 1.464 28.976 knee_plot 19.057 3.696 26.897 dl_transcriptome 8.695 0.457 14.018 transcript2gene 4.084 0.084 8.472 tr2g_ensembl 1.455 0.039 6.429 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘testthat.R’ OK * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking re-building of vignette outputs ... OK * checking PDF version of manual ... OK * DONE Status: 3 NOTEs See ‘/home/biocbuild/bbs-3.20-bioc/meat/BUSpaRse.Rcheck/00check.log’ for details.
BUSpaRse.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD INSTALL BUSpaRse ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.20-bioc/R/site-library’ * installing *source* package ‘BUSpaRse’ ... ** using staged installation ** libs using C++ compiler: ‘g++ (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’ using C++11 g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/RcppArmadillo/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/RcppProgress/include' -I'/home/biocbuild/bbs-3.20-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-3.20-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/RcppArmadillo/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/RcppProgress/include' -I'/home/biocbuild/bbs-3.20-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-3.20-bioc/R/site-library/BH/include/boost/mpl/aux_/na_assert.hpp:23, from /home/biocbuild/bbs-3.20-bioc/R/site-library/BH/include/boost/mpl/arg.hpp:25, from /home/biocbuild/bbs-3.20-bioc/R/site-library/BH/include/boost/mpl/placeholders.hpp:24, from /home/biocbuild/bbs-3.20-bioc/R/site-library/BH/include/boost/iterator/iterator_categories.hpp:16, from /home/biocbuild/bbs-3.20-bioc/R/site-library/BH/include/boost/iterator/iterator_adaptor.hpp:14, from /home/biocbuild/bbs-3.20-bioc/R/site-library/BH/include/boost/token_iterator.hpp:22, from /home/biocbuild/bbs-3.20-bioc/R/site-library/BH/include/boost/tokenizer.hpp:20, from fill_cell_gene.cpp:16: /home/biocbuild/bbs-3.20-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-3.20-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-3.20-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-3.20-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-3.20-bioc/R/lib -L/usr/local/lib -o BUSpaRse.so RcppExports.o fill_cell_gene.o -llapack -L/home/biocbuild/bbs-3.20-bioc/R/lib -lRblas -lgfortran -lm -lquadmath -L/home/biocbuild/bbs-3.20-bioc/R/lib -lR installing to /home/biocbuild/bbs-3.20-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)
BUSpaRse.Rcheck/tests/testthat.Rout
R version 4.4.2 (2024-10-31) -- "Pile of Leaves" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: x86_64-pc-linux-gnu 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 0 | WARN 0 | SKIP 0 | PASS 102 ] > > proc.time() user system elapsed 35.281 3.007 43.461
BUSpaRse.Rcheck/BUSpaRse-Ex.timings
name | user | system | elapsed | |
EC2gene | 0.039 | 0.001 | 0.040 | |
annots_from_fa_df | 0.139 | 0.005 | 0.144 | |
dl_transcriptome | 8.695 | 0.457 | 14.018 | |
get_velocity_files | 1.252 | 0.206 | 1.458 | |
knee_plot | 19.057 | 3.696 | 26.897 | |
make_sparse_matrix | 0.002 | 0.000 | 0.034 | |
read_count_output | 0.010 | 0.002 | 0.029 | |
read_velocity_output | 0.004 | 0.000 | 0.004 | |
save_tr2g_bustools | 0.348 | 0.048 | 0.466 | |
sort_tr2g | 0.275 | 0.023 | 0.299 | |
species2dataset | 0 | 0 | 0 | |
subset_annot | 1.882 | 0.258 | 2.142 | |
tr2g_EnsDb | 2.501 | 0.356 | 2.857 | |
tr2g_TxDb | 27.500 | 1.464 | 28.976 | |
tr2g_ensembl | 1.455 | 0.039 | 6.429 | |
tr2g_fasta | 0.018 | 0.000 | 0.018 | |
tr2g_gff3 | 0.784 | 0.021 | 0.804 | |
tr2g_gtf | 0.522 | 0.006 | 0.528 | |
transcript2gene | 4.084 | 0.084 | 8.472 | |