Back to Multiple platform build/check report for BioC 3.13 |
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This page was generated on 2021-10-15 15:05:36 -0400 (Fri, 15 Oct 2021).
To the developers/maintainers of the BUSpaRse package: - Please 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 How and When does the builder pull? When will my changes propagate? here for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
Package 227/2041 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
BUSpaRse 1.6.1 (landing page) Lambda Moses
| nebbiolo1 | Linux (Ubuntu 20.04.2 LTS) / x86_64 | OK | OK | OK | |||||||||
tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | |||||||||
machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | |||||||||
Package: BUSpaRse |
Version: 1.6.1 |
Command: /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD check --install=check:BUSpaRse.install-out.txt --library=/home/biocbuild/bbs-3.13-bioc/R/library --no-vignettes --timings BUSpaRse_1.6.1.tar.gz |
StartedAt: 2021-10-14 09:06:55 -0400 (Thu, 14 Oct 2021) |
EndedAt: 2021-10-14 09:14:41 -0400 (Thu, 14 Oct 2021) |
EllapsedTime: 465.6 seconds |
RetCode: 0 |
Status: OK |
CheckDir: BUSpaRse.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD check --install=check:BUSpaRse.install-out.txt --library=/home/biocbuild/bbs-3.13-bioc/R/library --no-vignettes --timings BUSpaRse_1.6.1.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.13-bioc/meat/BUSpaRse.Rcheck’ * using R version 4.1.1 (2021-08-10) * using platform: x86_64-pc-linux-gnu (64-bit) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘BUSpaRse/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘BUSpaRse’ version ‘1.6.1’ * 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 * 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 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 28.195 4.443 32.708 knee_plot 26.687 2.751 36.545 dl_transcriptome 10.688 0.493 18.465 transcript2gene 6.840 0.057 63.709 tr2g_EnsDb 3.905 2.072 5.978 tr2g_ensembl 2.642 0.064 16.520 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘testthat.R’ OK * checking for unstated dependencies in vignettes ... OK * checking package vignettes in ‘inst/doc’ ... OK * checking running R code from vignettes ... SKIPPED * checking re-building of vignette outputs ... SKIPPED * checking PDF version of manual ... OK * DONE Status: 1 NOTE See ‘/home/biocbuild/bbs-3.13-bioc/meat/BUSpaRse.Rcheck/00check.log’ for details.
BUSpaRse.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD INSTALL BUSpaRse ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.13-bioc/R/library’ * installing *source* package ‘BUSpaRse’ ... ** using staged installation ** libs g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/RcppArmadillo/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/RcppProgress/include' -I'/home/biocbuild/bbs-3.13-bioc/R/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-3.13-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/RcppArmadillo/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/RcppProgress/include' -I'/home/biocbuild/bbs-3.13-bioc/R/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-3.13-bioc/R/library/BH/include/boost/mpl/aux_/na_assert.hpp:23, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/arg.hpp:25, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/placeholders.hpp:24, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/iterator/iterator_categories.hpp:16, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/iterator/iterator_adaptor.hpp:14, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/token_iterator.hpp:22, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/tokenizer.hpp:20, from fill_cell_gene.cpp:16: /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of ‘assert_arg’ [-Wparentheses] 194 | failed ************ (Pred::************ | ^ /home/biocbuild/bbs-3.13-bioc/R/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>::************ | ^ g++ -std=gnu++11 -shared -L/home/biocbuild/bbs-3.13-bioc/R/lib -L/usr/local/lib -o BUSpaRse.so RcppExports.o fill_cell_gene.o -L/home/biocbuild/bbs-3.13-bioc/R/lib -lRlapack -L/home/biocbuild/bbs-3.13-bioc/R/lib -lRblas -lgfortran -lm -lquadmath -L/home/biocbuild/bbs-3.13-bioc/R/lib -lR installing to /home/biocbuild/bbs-3.13-bioc/R/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 4.1.1 (2021-08-10) -- "Kick Things" Copyright (C) 2021 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 0 | WARN 0 | SKIP 0 | PASS 102 ] > > proc.time() user system elapsed 47.661 1.207 54.805
BUSpaRse.Rcheck/BUSpaRse-Ex.timings
name | user | system | elapsed | |
EC2gene | 0.079 | 0.004 | 0.084 | |
annots_from_fa_df | 0.166 | 0.004 | 0.170 | |
dl_transcriptome | 10.688 | 0.493 | 18.465 | |
get_velocity_files | 1.533 | 0.209 | 1.742 | |
knee_plot | 26.687 | 2.751 | 36.545 | |
make_sparse_matrix | 0.003 | 0.000 | 0.003 | |
read_count_output | 0.008 | 0.000 | 0.007 | |
read_velocity_output | 0.004 | 0.000 | 0.004 | |
save_tr2g_bustools | 0.427 | 0.012 | 0.438 | |
sort_tr2g | 0.306 | 0.008 | 0.314 | |
species2dataset | 0 | 0 | 0 | |
subset_annot | 1.147 | 0.217 | 1.374 | |
tr2g_EnsDb | 3.905 | 2.072 | 5.978 | |
tr2g_TxDb | 28.195 | 4.443 | 32.708 | |
tr2g_ensembl | 2.642 | 0.064 | 16.520 | |
tr2g_fasta | 0.017 | 0.004 | 0.022 | |
tr2g_gff3 | 1.088 | 0.040 | 1.128 | |
tr2g_gtf | 0.639 | 0.012 | 0.651 | |
transcript2gene | 6.840 | 0.057 | 63.709 | |