Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-07-02 11:39 -0400 (Tue, 02 Jul 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" | 4693 |
palomino6 | Windows Server 2022 Datacenter | x64 | 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" | 4413 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.1 RC (2024-06-06 r86719) -- "Race for Your Life" | 4407 |
kjohnson3 | macOS 13.6.5 Ventura | arm64 | 4.4.1 RC (2024-06-06 r86719) -- "Race for Your Life" | 4356 |
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4407 |
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 2136/2243 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
transite 1.23.0 (landing page) Konstantin Krismer
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | ![]() | ||||||||
palomino6 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | |||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | ![]() | ||||||||
kjohnson3 | macOS 13.6.5 Ventura / arm64 | OK | OK | OK | OK | ![]() | ||||||||
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | OK | ||||||||||
To the developers/maintainers of the transite package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/transite.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: transite |
Version: 1.23.0 |
Command: /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:transite.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings transite_1.23.0.tar.gz |
StartedAt: 2024-07-02 05:01:51 -0400 (Tue, 02 Jul 2024) |
EndedAt: 2024-07-02 05:08:26 -0400 (Tue, 02 Jul 2024) |
EllapsedTime: 394.7 seconds |
RetCode: 0 |
Status: OK |
CheckDir: transite.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:transite.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings transite_1.23.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/transite.Rcheck’ * using R version 4.4.0 RC (2024-04-16 r86468) * using platform: x86_64-pc-linux-gnu * 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 22.04.4 LTS * using session charset: UTF-8 * checking for file ‘transite/DESCRIPTION’ ... OK * this is package ‘transite’ version ‘1.23.0’ * 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 ‘transite’ 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 ... 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 loading without being on the library search path ... OK * checking whether startup messages can be suppressed ... 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 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 run_kmer_tsma 40.408 0.180 44.293 run_kmer_spma 35.082 0.379 37.637 classify_spectrum 4.591 0.231 5.604 compute_kmer_enrichment 4.014 0.053 5.107 run_matrix_spma 3.067 0.052 5.123 * 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/transite.Rcheck/00check.log’ for details.
transite.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD INSTALL transite ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.20-bioc/R/site-library’ * installing *source* package ‘transite’ ... ** 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-3.20-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/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/usr/local/include -fpic -g -O2 -Wall -c scoring.cpp -o scoring.o g++ -std=gnu++11 -shared -L/home/biocbuild/bbs-3.20-bioc/R/lib -L/usr/local/lib -o transite.so RcppExports.o scoring.o -L/home/biocbuild/bbs-3.20-bioc/R/lib -lR installing to /home/biocbuild/bbs-3.20-bioc/R/site-library/00LOCK-transite/00new/transite/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 (transite)
transite.Rcheck/tests/testthat.Rout
R version 4.4.0 RC (2024-04-16 r86468) -- "Puppy Cup" 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(transite) > > test_check("transite") [ FAIL 0 | WARN 6 | SKIP 0 | PASS 95 ] [ FAIL 0 | WARN 6 | SKIP 0 | PASS 95 ] > > proc.time() user system elapsed 73.842 2.214 175.511
transite.Rcheck/transite-Ex.timings
name | user | system | elapsed | |
RBPMotif-class | 0.004 | 0.001 | 0.004 | |
SpectrumScore-class | 0.001 | 0.000 | 0.001 | |
calculate_kmer_enrichment | 3.846 | 0.020 | 3.866 | |
calculate_local_consistency | 0.486 | 0.011 | 0.498 | |
calculate_motif_enrichment | 1.410 | 0.049 | 1.458 | |
calculate_transcript_mc | 0.009 | 0.000 | 0.009 | |
check_kmers | 0.001 | 0.000 | 0.001 | |
classify_spectrum | 4.591 | 0.231 | 5.604 | |
compute_kmer_enrichment | 4.014 | 0.053 | 5.107 | |
create_kmer_motif | 0.004 | 0.000 | 0.005 | |
create_matrix_motif | 0.005 | 0.000 | 0.005 | |
draw_volcano_plot | 0.746 | 0.052 | 1.038 | |
estimate_significance_core | 0.005 | 0.000 | 0.004 | |
generate_iupac_by_kmers | 0.001 | 0.000 | 0.001 | |
generate_iupac_by_matrix | 0.004 | 0.000 | 0.004 | |
generate_kmers | 0.281 | 0.012 | 0.397 | |
generate_kmers_from_iupac | 0.006 | 0.000 | 0.021 | |
geometric_mean | 0.001 | 0.000 | 0.000 | |
get_motif_by_id | 0.008 | 0.000 | 0.008 | |
get_motif_by_rbp | 0.011 | 0.000 | 0.010 | |
get_motifs | 0 | 0 | 0 | |
get_motifs_meta_info | 0.019 | 0.008 | 0.027 | |
get_ppm | 0.010 | 0.000 | 0.011 | |
init_iupac_lookup_table | 0.004 | 0.000 | 0.005 | |
p_combine | 0.002 | 0.000 | 0.001 | |
run_kmer_spma | 35.082 | 0.379 | 37.637 | |
run_kmer_tsma | 40.408 | 0.180 | 44.293 | |
run_matrix_spma | 3.067 | 0.052 | 5.123 | |
run_matrix_tsma | 0.019 | 0.000 | 0.019 | |
score_sequences | 0.004 | 0.000 | 0.004 | |
score_spectrum | 2.190 | 0.012 | 2.202 | |
score_transcripts | 0.006 | 0.000 | 0.006 | |
set_motifs | 0.002 | 0.000 | 0.001 | |
subdivide_data | 0.004 | 0.000 | 0.004 | |