Back to Multiple platform build/check report for BioC 3.11 |
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This page was generated on 2020-10-17 11:54:30 -0400 (Sat, 17 Oct 2020).
TO THE DEVELOPERS/MAINTAINERS OF THE BUSpaRse PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page. |
Package 216/1905 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
BUSpaRse 1.2.2 Lambda Moses
| malbec2 | Linux (Ubuntu 18.04.4 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: 1.2.2 |
Command: /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD check --install=check:BUSpaRse.install-out.txt --library=/home/biocbuild/bbs-3.11-bioc/R/library --no-vignettes --timings BUSpaRse_1.2.2.tar.gz |
StartedAt: 2020-10-16 23:29:01 -0400 (Fri, 16 Oct 2020) |
EndedAt: 2020-10-16 23:37:48 -0400 (Fri, 16 Oct 2020) |
EllapsedTime: 527.4 seconds |
RetCode: 0 |
Status: OK |
CheckDir: BUSpaRse.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD check --install=check:BUSpaRse.install-out.txt --library=/home/biocbuild/bbs-3.11-bioc/R/library --no-vignettes --timings BUSpaRse_1.2.2.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.11-bioc/meat/BUSpaRse.Rcheck’ * using R version 4.0.3 (2020-10-10) * 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 ‘1.2.2’ * 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 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 36.660 1.743 41.517 knee_plot 31.531 1.783 42.989 dl_transcriptome 15.706 0.313 25.300 transcript2gene 7.775 0.005 15.504 tr2g_EnsDb 4.976 0.760 5.850 tr2g_ensembl 3.571 0.020 8.843 * 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-3.11-bioc/meat/BUSpaRse.Rcheck/00check.log’ for details.
BUSpaRse.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD INSTALL BUSpaRse ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.11-bioc/R/library’ * installing *source* package ‘BUSpaRse’ ... ** using staged installation ** libs g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.11-bioc/R/library/RcppArmadillo/include' -I'/home/biocbuild/bbs-3.11-bioc/R/library/RcppProgress/include' -I'/home/biocbuild/bbs-3.11-bioc/R/library/BH/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -c RcppExports.cpp -o RcppExports.o g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.11-bioc/R/library/RcppArmadillo/include' -I'/home/biocbuild/bbs-3.11-bioc/R/library/RcppProgress/include' -I'/home/biocbuild/bbs-3.11-bioc/R/library/BH/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -c fill_cell_gene.cpp -o fill_cell_gene.o g++ -std=gnu++11 -shared -L/home/biocbuild/bbs-3.11-bioc/R/lib -L/usr/local/lib -o BUSpaRse.so RcppExports.o fill_cell_gene.o -fopenmp -L/home/biocbuild/bbs-3.11-bioc/R/lib -lRlapack -L/home/biocbuild/bbs-3.11-bioc/R/lib -lRblas -lgfortran -lm -lquadmath -L/home/biocbuild/bbs-3.11-bioc/R/lib -lR installing to /home/biocbuild/bbs-3.11-bioc/R/library/00LOCK-BUSpaRse/00new/BUSpaRse/libs ** R ** data ** 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 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out" Copyright (C) 2020 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") ══ testthat results ═══════════════════════════════════════════════════════════ [ OK: 104 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 0 ] > > proc.time() user system elapsed 52.151 0.714 64.521
BUSpaRse.Rcheck/BUSpaRse-Ex.timings
name | user | system | elapsed | |
EC2gene | 0.153 | 0.000 | 0.394 | |
annots_from_fa_df | 0.195 | 0.004 | 0.265 | |
dl_transcriptome | 15.706 | 0.313 | 25.300 | |
get_velocity_files | 1.966 | 0.060 | 2.064 | |
knee_plot | 31.531 | 1.783 | 42.989 | |
make_sparse_matrix | 0.002 | 0.000 | 0.018 | |
read_count_output | 0.008 | 0.001 | 0.014 | |
read_velocity_output | 0.004 | 0.000 | 0.004 | |
save_tr2g_bustools | 0.386 | 0.012 | 0.398 | |
sort_tr2g | 0.352 | 0.004 | 0.356 | |
species2dataset | 0.000 | 0.000 | 0.001 | |
subset_annot | 1.335 | 0.072 | 1.622 | |
tr2g_EnsDb | 4.976 | 0.760 | 5.850 | |
tr2g_TxDb | 36.660 | 1.743 | 41.517 | |
tr2g_ensembl | 3.571 | 0.020 | 8.843 | |
tr2g_fasta | 0.032 | 0.004 | 0.035 | |
tr2g_gff3 | 1.258 | 0.012 | 1.280 | |
tr2g_gtf | 0.688 | 0.012 | 0.699 | |
transcript2gene | 7.775 | 0.005 | 15.504 | |