Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-06-04 14:36:42 -0400 (Tue, 04 Jun 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.0 RC (2024-04-16 r86468) -- "Puppy Cup" | 4669 |
palomino4 | Windows Server 2022 Datacenter | x64 | 4.4.0 RC (2024-04-16 r86468 ucrt) -- "Puppy Cup" | 4404 |
merida1 | macOS 12.7.4 Monterey | x86_64 | 4.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup" | 4431 |
kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup" | 4384 |
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 252/2233 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
BUSpaRse 1.19.0 (landing page) Lambda Moses
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | ERROR | |||||||||
palomino4 | Windows Server 2022 Datacenter / x64 | OK | OK | ERROR | OK | |||||||||
merida1 | macOS 12.7.4 Monterey / x86_64 | OK | OK | ERROR | OK | |||||||||
kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | OK | ERROR | 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: 1.19.0 |
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:BUSpaRse.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings BUSpaRse_1.19.0.tar.gz |
StartedAt: 2024-06-03 12:27:34 -0400 (Mon, 03 Jun 2024) |
EndedAt: 2024-06-03 12:35:16 -0400 (Mon, 03 Jun 2024) |
EllapsedTime: 462.2 seconds |
RetCode: 1 |
Status: ERROR |
CheckDir: BUSpaRse.Rcheck |
Warnings: NA |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:BUSpaRse.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings BUSpaRse_1.19.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/BUSpaRse.Rcheck’ * using R version 4.4.0 Patched (2024-04-24 r86482) * 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 ‘BUSpaRse/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘BUSpaRse’ version ‘1.19.0’ * 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: ‘Apple clang version 15.0.0 (clang-1500.0.40.1)’ * used SDK: ‘MacOSX11.3.sdk’ * 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. * 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 ... 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 40.023 5.410 46.400 knee_plot 28.870 2.104 33.603 dl_transcriptome 12.220 0.535 13.888 tr2g_EnsDb 4.647 1.274 6.012 transcript2gene 5.431 0.252 6.485 tr2g_ensembl 1.312 0.067 14.237 * 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 ... 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, 3 NOTEs See ‘/Users/biocbuild/bbs-3.20-bioc/meat/BUSpaRse.Rcheck/00check.log’ for details.
BUSpaRse.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL BUSpaRse ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library’ * installing *source* package ‘BUSpaRse’ ... ** using staged installation ** libs using C++ compiler: ‘Apple clang version 15.0.0 (clang-1500.0.40.1)’ using C++11 using SDK: ‘MacOSX11.3.sdk’ clang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppArmadillo/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppProgress/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/BH/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c RcppExports.cpp -o RcppExports.o clang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppArmadillo/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppProgress/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/BH/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c fill_cell_gene.cpp -o fill_cell_gene.o clang++ -arch arm64 -std=gnu++11 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/arm64/lib -o BUSpaRse.so RcppExports.o fill_cell_gene.o -L/Library/Frameworks/R.framework/Resources/lib -lRlapack -L/Library/Frameworks/R.framework/Resources/lib -lRblas -L/opt/gfortran/lib/gcc/aarch64-apple-darwin20.0/12.2.0 -L/opt/gfortran/lib -lgfortran -lemutls_w -lquadmath -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation installing to /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/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.fail
R version 4.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: aarch64-apple-darwin20 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
BUSpaRse.Rcheck/BUSpaRse-Ex.timings
name | user | system | elapsed | |
EC2gene | 0.058 | 0.003 | 0.062 | |
annots_from_fa_df | 0.181 | 0.007 | 0.189 | |
dl_transcriptome | 12.220 | 0.535 | 13.888 | |
get_velocity_files | 1.491 | 0.105 | 1.597 | |
knee_plot | 28.870 | 2.104 | 33.603 | |
make_sparse_matrix | 0.002 | 0.001 | 0.004 | |
read_count_output | 0.012 | 0.002 | 0.014 | |
read_velocity_output | 0.004 | 0.001 | 0.005 | |
save_tr2g_bustools | 0.428 | 0.028 | 0.457 | |
sort_tr2g | 0.347 | 0.028 | 0.376 | |
species2dataset | 0.001 | 0.000 | 0.001 | |
subset_annot | 1.803 | 0.158 | 2.078 | |
tr2g_EnsDb | 4.647 | 1.274 | 6.012 | |
tr2g_TxDb | 40.023 | 5.410 | 46.400 | |
tr2g_ensembl | 1.312 | 0.067 | 14.237 | |
tr2g_fasta | 0.021 | 0.004 | 0.026 | |
tr2g_gff3 | 0.984 | 0.075 | 1.099 | |
tr2g_gtf | 0.704 | 0.055 | 0.760 | |
transcript2gene | 5.431 | 0.252 | 6.485 | |