Back to Multiple platform build/check report for BioC 3.19: simplified long |
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This page was generated on 2024-05-10 11:37:24 -0400 (Fri, 10 May 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4751 |
palomino3 | Windows Server 2022 Datacenter | x64 | 4.4.0 (2024-04-24 ucrt) -- "Puppy Cup" | 4485 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4515 |
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 | |||||||||
palomino3 | 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 | see weekly results here | ||||||||||||
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: F:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:spiky.install-out.txt --library=F:\biocbuild\bbs-3.19-bioc\R\library --no-vignettes --timings spiky_1.10.0.tar.gz |
StartedAt: 2024-05-10 06:41:46 -0400 (Fri, 10 May 2024) |
EndedAt: 2024-05-10 06:47:45 -0400 (Fri, 10 May 2024) |
EllapsedTime: 358.7 seconds |
RetCode: 0 |
Status: OK |
CheckDir: spiky.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:spiky.install-out.txt --library=F:\biocbuild\bbs-3.19-bioc\R\library --no-vignettes --timings spiky_1.10.0.tar.gz ### ############################################################################## ############################################################################## * using log directory 'F:/biocbuild/bbs-3.19-bioc/meat/spiky.Rcheck' * using R version 4.4.0 (2024-04-24 ucrt) * using platform: x86_64-w64-mingw32 * R was compiled by gcc.exe (GCC) 13.2.0 GNU Fortran (GCC) 13.2.0 * running under: Windows Server 2022 x64 (build 20348) * 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 whether package 'spiky' can be installed ... OK * checking installed package size ... NOTE installed size is 16.3Mb sub-directories of 1Mb or more: data 3.1Mb 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 20.78 0.74 21.91 scan_genomic_contigs 17.18 2.59 22.31 bin_pmol 9.26 2.77 12.22 model_bam_standards 7.45 0.25 7.72 predict_pmol 5.52 1.35 6.86 scan_spike_bedpe 5.81 0.22 6.03 * 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 'F:/biocbuild/bbs-3.19-bioc/meat/spiky.Rcheck/00check.log' for details.
spiky.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD INSTALL spiky ### ############################################################################## ############################################################################## * installing to library 'F:/biocbuild/bbs-3.19-bioc/R/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 | 0.14 | 0.01 | 0.16 | |
bam_to_bins | 0.16 | 0.00 | 0.17 | |
bin_pmol | 9.26 | 2.77 | 12.22 | |
covg_to_df | 0.11 | 0.02 | 0.13 | |
find_spike_contigs | 0.03 | 0.01 | 0.04 | |
generate_spike_fasta | 0.17 | 0.02 | 0.19 | |
get_base_name | 0.02 | 0.00 | 0.01 | |
get_binned_coverage | 0.30 | 0.05 | 0.59 | |
get_merged_gr | 0.11 | 0.00 | 0.13 | |
get_spike_depth | 0.46 | 0.03 | 0.50 | |
get_spiked_coverage | 0.27 | 0.02 | 0.30 | |
kmax | 0.06 | 0.01 | 0.07 | |
kmers | 0.05 | 0.00 | 0.05 | |
methylation_specificity | 0.11 | 0.03 | 0.14 | |
model_bam_standards | 7.45 | 0.25 | 7.72 | |
model_glm_pmol | 0.06 | 0.00 | 0.06 | |
predict_pmol | 5.52 | 1.35 | 6.86 | |
process_spikes | 0.18 | 0.00 | 0.19 | |
read_bedpe | 0 | 0 | 0 | |
scan_genomic_bedpe | 20.78 | 0.74 | 21.91 | |
scan_genomic_contigs | 17.18 | 2.59 | 22.31 | |
scan_methylation_specificity | 0.01 | 0.02 | 0.03 | |
scan_spike_bedpe | 5.81 | 0.22 | 6.03 | |
scan_spike_contigs | 0.52 | 0.02 | 0.54 | |
scan_spike_counts | 0.07 | 0.01 | 0.09 | |
scan_spiked_bam | 0.55 | 0.05 | 0.61 | |
seqinfo_from_header | 0.14 | 0.00 | 0.18 | |
spike_bland_altman_plot | 0.12 | 0.00 | 0.13 | |
spike_counts | 0.08 | 0.00 | 0.08 | |
tile_bins | 0.06 | 0.00 | 0.06 | |