Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-11-20 12:08 -0500 (Wed, 20 Nov 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
teran2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4481 |
nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4479 |
palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" | 4359 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4539 |
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4493 |
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 2035/2289 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
spiky 1.12.0 (landing page) Tim Triche
| teran2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | |||||||||
nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | ||||||||||
palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | |||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | |||||||||
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | OK | ||||||||||
To the developers/maintainers of the spiky package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/spiky.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. - See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host. |
Package: spiky |
Version: 1.12.0 |
Command: /home/biocbuild/R/R/bin/R CMD check --install=check:spiky.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings spiky_1.12.0.tar.gz |
StartedAt: 2024-11-20 12:49:34 -0000 (Wed, 20 Nov 2024) |
EndedAt: 2024-11-20 12:56:13 -0000 (Wed, 20 Nov 2024) |
EllapsedTime: 399.7 seconds |
RetCode: 0 |
Status: OK |
CheckDir: spiky.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R/bin/R CMD check --install=check:spiky.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings spiky_1.12.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/spiky.Rcheck’ * using R version 4.4.1 (2024-06-14) * using platform: aarch64-unknown-linux-gnu * R was compiled by gcc (GCC) 12.2.1 20220819 (openEuler 12.2.1-14) GNU Fortran (GCC) 10.3.1 * running under: openEuler 22.03 (LTS-SP1) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘spiky/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘spiky’ version ‘1.12.0’ * 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 ‘spiky’ can be installed ... OK * checking installed package size ... NOTE installed size is 16.4Mb sub-directories of 1Mb or more: data 3.2Mb extdata 12.9Mb * 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 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 ... NOTE .toGRs: warning in grep("(chrom|seqnames|start|end)1", colnames(x), val = TRUE): partial argument match of 'val' to 'value' .toGRs: warning in grep("(chrom|seqnames|start|end)2", colnames(x), val = TRUE): partial argument match of 'val' to 'value' * 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 files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed scan_genomic_contigs 24.087 0.699 24.874 scan_genomic_bedpe 21.446 0.606 22.097 model_bam_standards 9.357 0.455 9.833 scan_spike_bedpe 5.898 0.164 6.074 * 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: 2 NOTEs See ‘/home/biocbuild/bbs-3.20-bioc/meat/spiky.Rcheck/00check.log’ for details.
spiky.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R/bin/R CMD INSTALL spiky ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/R/R-4.4.1/site-library’ * installing *source* package ‘spiky’ ... ** using staged installation ** 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 ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (spiky)
spiky.Rcheck/spiky-Ex.timings
name | user | system | elapsed | |
add_frag_info | 0.161 | 0.008 | 0.170 | |
bam_to_bins | 0.198 | 0.008 | 0.206 | |
bin_pmol | 3.976 | 0.435 | 4.539 | |
covg_to_df | 0.109 | 0.000 | 0.108 | |
find_spike_contigs | 0.027 | 0.004 | 0.033 | |
generate_spike_fasta | 0.135 | 0.004 | 0.142 | |
get_base_name | 0.015 | 0.000 | 0.015 | |
get_binned_coverage | 0.274 | 0.012 | 0.288 | |
get_merged_gr | 0.115 | 0.008 | 0.122 | |
get_spike_depth | 0.326 | 0.012 | 0.339 | |
get_spiked_coverage | 0.231 | 0.000 | 0.232 | |
kmax | 0.104 | 0.000 | 0.104 | |
kmers | 0.037 | 0.004 | 0.042 | |
methylation_specificity | 0.105 | 0.000 | 0.106 | |
model_bam_standards | 9.357 | 0.455 | 9.833 | |
model_glm_pmol | 0.074 | 0.000 | 0.074 | |
predict_pmol | 2.607 | 0.395 | 3.008 | |
process_spikes | 0.221 | 0.024 | 0.246 | |
read_bedpe | 0 | 0 | 0 | |
scan_genomic_bedpe | 21.446 | 0.606 | 22.097 | |
scan_genomic_contigs | 24.087 | 0.699 | 24.874 | |
scan_methylation_specificity | 0.043 | 0.000 | 0.044 | |
scan_spike_bedpe | 5.898 | 0.164 | 6.074 | |
scan_spike_contigs | 0.466 | 0.044 | 0.511 | |
scan_spike_counts | 0.070 | 0.003 | 0.073 | |
scan_spiked_bam | 0.806 | 0.012 | 0.819 | |
seqinfo_from_header | 0.125 | 0.001 | 0.125 | |
spike_bland_altman_plot | 0.125 | 0.000 | 0.126 | |
spike_counts | 0.073 | 0.000 | 0.074 | |
tile_bins | 0.050 | 0.000 | 0.049 | |