Back to Multiple platform build/check report for BioC 3.18: simplified long |
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This page was generated on 2024-04-17 11:36:25 -0400 (Wed, 17 Apr 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.3.3 (2024-02-29) -- "Angel Food Cake" | 4676 |
palomino4 | Windows Server 2022 Datacenter | x64 | 4.3.3 (2024-02-29 ucrt) -- "Angel Food Cake" | 4414 |
merida1 | macOS 12.7.1 Monterey | x86_64 | 4.3.3 (2024-02-29) -- "Angel Food Cake" | 4437 |
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 2027/2266 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
spiky 1.8.0 (landing page) Tim Triche
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | ERROR | |||||||||
palomino4 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | |||||||||
merida1 | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | |||||||||
kjohnson1 | macOS 13.6.1 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: 1.8.0 |
Command: /home/biocbuild/bbs-3.18-bioc/R/bin/R CMD check --install=check:spiky.install-out.txt --library=/home/biocbuild/bbs-3.18-bioc/R/site-library --timings spiky_1.8.0.tar.gz |
StartedAt: 2024-04-16 04:18:25 -0400 (Tue, 16 Apr 2024) |
EndedAt: 2024-04-16 04:24:09 -0400 (Tue, 16 Apr 2024) |
EllapsedTime: 344.0 seconds |
RetCode: 1 |
Status: ERROR |
CheckDir: spiky.Rcheck |
Warnings: NA |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.18-bioc/R/bin/R CMD check --install=check:spiky.install-out.txt --library=/home/biocbuild/bbs-3.18-bioc/R/site-library --timings spiky_1.8.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.18-bioc/meat/spiky.Rcheck’ * using R version 4.3.3 (2024-02-29) * using platform: x86_64-pc-linux-gnu (64-bit) * 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 ‘spiky/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘spiky’ version ‘1.8.0’ * 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 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 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 13.356 1.688 15.046 scan_genomic_bedpe 13.434 0.912 14.346 model_bam_standards 6.313 0.576 6.889 * checking for unstated dependencies in vignettes ... OK * checking package vignettes in ‘inst/doc’ ... OK * checking running R code from vignettes ... ‘spiky_vignette.Rmd’ using ‘UTF-8’... failed ERROR Errors in running code in vignettes: when running code in ‘spiky_vignette.Rmd’ ... Loading required package: usethis > load_all("./") When sourcing ‘spiky_vignette.R’: Error: Could not find a root 'DESCRIPTION' file that starts with '^Package' in '/tmp/RtmpL4urW8/file2ce2527b73010c/vignettes'. ℹ Are you in your project directory and does your project have a 'DESCRIPTION' file? Execution halted * checking re-building of vignette outputs ... OK * checking PDF version of manual ... OK * DONE Status: 1 ERROR, 2 NOTEs See ‘/home/biocbuild/bbs-3.18-bioc/meat/spiky.Rcheck/00check.log’ for details.
spiky.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.18-bioc/R/bin/R CMD INSTALL spiky ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.18-bioc/R/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 | 0.111 | 0.028 | 0.139 | |
bam_to_bins | 0.137 | 0.008 | 0.145 | |
bin_pmol | 3.167 | 0.472 | 3.764 | |
covg_to_df | 0.077 | 0.000 | 0.077 | |
find_spike_contigs | 0.023 | 0.000 | 0.023 | |
generate_spike_fasta | 0.090 | 0.000 | 0.091 | |
get_base_name | 0.005 | 0.004 | 0.009 | |
get_binned_coverage | 0.204 | 0.012 | 0.216 | |
get_merged_gr | 0.075 | 0.012 | 0.087 | |
get_spike_depth | 0.233 | 0.008 | 0.242 | |
get_spiked_coverage | 0.172 | 0.020 | 0.192 | |
kmax | 0.086 | 0.008 | 0.095 | |
kmers | 0.032 | 0.000 | 0.033 | |
methylation_specificity | 0.075 | 0.000 | 0.075 | |
model_bam_standards | 6.313 | 0.576 | 6.889 | |
model_glm_pmol | 0.075 | 0.000 | 0.075 | |
predict_pmol | 1.852 | 0.336 | 2.187 | |
process_spikes | 0.189 | 0.012 | 0.201 | |
read_bedpe | 0 | 0 | 0 | |
scan_genomic_bedpe | 13.434 | 0.912 | 14.346 | |
scan_genomic_contigs | 13.356 | 1.688 | 15.046 | |
scan_methylation_specificity | 0.026 | 0.004 | 0.030 | |
scan_spike_bedpe | 3.783 | 0.060 | 3.843 | |
scan_spike_contigs | 1.218 | 0.140 | 1.359 | |
scan_spike_counts | 0.049 | 0.000 | 0.049 | |
scan_spiked_bam | 0.4 | 0.0 | 0.4 | |
seqinfo_from_header | 0.086 | 0.000 | 0.087 | |
spike_bland_altman_plot | 0.094 | 0.008 | 0.103 | |
spike_counts | 0.050 | 0.004 | 0.054 | |
tile_bins | 0.033 | 0.000 | 0.033 | |