Back to Mac ARM64 build report for BioC 3.18 |
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This page was generated on 2024-03-28 11:32:32 -0400 (Thu, 28 Mar 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
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kjohnson1 | macOS 13.6.1 Ventura | arm64 | 4.3.3 (2024-02-29) -- "Angel Food Cake" | 4376 |
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
| kjohnson1 | macOS 13.6.1 Ventura / arm64 | OK | OK | OK | OK | ||||||||
To the developers/maintainers of the spiky package: - 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: /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_1.8.0.tar.gz |
StartedAt: 2024-03-28 03:59:57 -0400 (Thu, 28 Mar 2024) |
EndedAt: 2024-03-28 04:06:19 -0400 (Thu, 28 Mar 2024) |
EllapsedTime: 381.5 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_1.8.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.18-bioc-mac-arm64/meat/spiky.Rcheck’ * using R version 4.3.3 (2024-02-29) * using platform: aarch64-apple-darwin20 (64-bit) * R was compiled by Apple clang version 14.0.0 (clang-1400.0.29.202) GNU Fortran (GCC) 12.2.0 * running under: macOS Ventura 13.6.1 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘spiky/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘spiky’ version ‘1.8.0’ * 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 16.3Mb 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 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 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 21.009 0.432 21.562 scan_genomic_contigs 19.764 1.518 21.495 bin_pmol 6.610 1.724 8.695 model_bam_standards 5.924 0.142 6.172 scan_spike_bedpe 5.596 0.097 5.743 * checking for unstated dependencies in vignettes ... OK * checking package vignettes in ‘inst/doc’ ... 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-3.18-bioc-mac-arm64/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/4.3-arm64/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 | 0.178 | 0.032 | 0.213 | |
bam_to_bins | 0.160 | 0.015 | 0.178 | |
bin_pmol | 6.610 | 1.724 | 8.695 | |
covg_to_df | 0.094 | 0.002 | 0.097 | |
find_spike_contigs | 0.031 | 0.003 | 0.035 | |
generate_spike_fasta | 0.162 | 0.005 | 0.170 | |
get_base_name | 0.011 | 0.002 | 0.013 | |
get_binned_coverage | 0.252 | 0.008 | 0.262 | |
get_merged_gr | 0.070 | 0.003 | 0.075 | |
get_spike_depth | 0.394 | 0.012 | 0.410 | |
get_spiked_coverage | 0.206 | 0.006 | 0.213 | |
kmax | 0.061 | 0.003 | 0.064 | |
kmers | 0.047 | 0.003 | 0.051 | |
methylation_specificity | 0.091 | 0.006 | 0.098 | |
model_bam_standards | 5.924 | 0.142 | 6.172 | |
model_glm_pmol | 0.067 | 0.004 | 0.072 | |
predict_pmol | 3.541 | 1.182 | 4.981 | |
process_spikes | 0.244 | 0.013 | 0.258 | |
read_bedpe | 0.000 | 0.001 | 0.000 | |
scan_genomic_bedpe | 21.009 | 0.432 | 21.562 | |
scan_genomic_contigs | 19.764 | 1.518 | 21.495 | |
scan_methylation_specificity | 0.043 | 0.006 | 0.049 | |
scan_spike_bedpe | 5.596 | 0.097 | 5.743 | |
scan_spike_contigs | 0.410 | 0.029 | 0.442 | |
scan_spike_counts | 0.069 | 0.007 | 0.076 | |
scan_spiked_bam | 0.463 | 0.023 | 0.488 | |
seqinfo_from_header | 0.111 | 0.016 | 0.132 | |
spike_bland_altman_plot | 0.130 | 0.011 | 0.141 | |
spike_counts | 0.068 | 0.007 | 0.074 | |
tile_bins | 0.037 | 0.004 | 0.042 | |