Back to Multiple platform build/check report for BioC 3.19: simplified long |
|
This page was generated on 2024-08-27 17:43 -0400 (Tue, 27 Aug 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4757 |
palomino7 | Windows Server 2022 Datacenter | x64 | 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" | 4494 |
merida1 | macOS 12.7.5 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4523 |
kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4472 |
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 2050/2300 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
spiky 1.10.0 (landing page) Tim Triche
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | |||||||||
palomino7 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | |||||||||
merida1 | macOS 12.7.5 Monterey / x86_64 | OK | OK | OK | OK | |||||||||
kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | OK | OK | NA | |||||||||
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. |
Package: spiky |
Version: 1.10.0 |
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:spiky.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings spiky_1.10.0.tar.gz |
StartedAt: 2024-08-26 12:42:59 -0400 (Mon, 26 Aug 2024) |
EndedAt: 2024-08-26 12:54:11 -0400 (Mon, 26 Aug 2024) |
EllapsedTime: 672.7 seconds |
RetCode: 0 |
Status: OK |
CheckDir: spiky.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:spiky.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings spiky_1.10.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.19-bioc/meat/spiky.Rcheck’ * using R version 4.4.1 (2024-06-14) * using platform: x86_64-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 Monterey 12.7.5 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘spiky/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘spiky’ version ‘1.10.0’ * 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 16.3Mb 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 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_bedpe 29.794 0.863 34.487 scan_genomic_contigs 22.493 1.966 27.443 bin_pmol 10.237 4.499 17.155 model_bam_standards 13.110 0.268 15.011 scan_spike_bedpe 10.449 0.108 11.816 predict_pmol 5.723 2.046 9.237 * 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 ‘/Users/biocbuild/bbs-3.19-bioc/meat/spiky.Rcheck/00check.log’ for details.
spiky.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL spiky ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/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 | 0.284 | 0.071 | 0.395 | |
bam_to_bins | 0.327 | 0.008 | 0.360 | |
bin_pmol | 10.237 | 4.499 | 17.155 | |
covg_to_df | 0.179 | 0.004 | 0.211 | |
find_spike_contigs | 0.049 | 0.006 | 0.062 | |
generate_spike_fasta | 0.243 | 0.009 | 0.281 | |
get_base_name | 0.025 | 0.003 | 0.032 | |
get_binned_coverage | 0.452 | 0.016 | 0.528 | |
get_merged_gr | 0.135 | 0.007 | 0.162 | |
get_spike_depth | 0.633 | 0.021 | 0.719 | |
get_spiked_coverage | 0.389 | 0.013 | 0.446 | |
kmax | 0.090 | 0.005 | 0.107 | |
kmers | 0.058 | 0.004 | 0.070 | |
methylation_specificity | 0.184 | 0.008 | 0.219 | |
model_bam_standards | 13.110 | 0.268 | 15.011 | |
model_glm_pmol | 0.123 | 0.006 | 0.147 | |
predict_pmol | 5.723 | 2.046 | 9.237 | |
process_spikes | 0.402 | 0.019 | 0.455 | |
read_bedpe | 0.001 | 0.000 | 0.000 | |
scan_genomic_bedpe | 29.794 | 0.863 | 34.487 | |
scan_genomic_contigs | 22.493 | 1.966 | 27.443 | |
scan_methylation_specificity | 0.067 | 0.005 | 0.081 | |
scan_spike_bedpe | 10.449 | 0.108 | 11.816 | |
scan_spike_contigs | 0.832 | 0.101 | 1.055 | |
scan_spike_counts | 0.120 | 0.011 | 0.145 | |
scan_spiked_bam | 1.013 | 0.107 | 1.246 | |
seqinfo_from_header | 0.225 | 0.021 | 0.299 | |
spike_bland_altman_plot | 0.215 | 0.011 | 0.265 | |
spike_counts | 0.126 | 0.006 | 0.151 | |
tile_bins | 0.086 | 0.004 | 0.099 | |