Back to Multiple platform build/check report for BioC 3.15
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This page was generated on 2022-10-19 13:20:55 -0400 (Wed, 19 Oct 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 20.04.5 LTS)x86_644.2.1 (2022-06-23) -- "Funny-Looking Kid" 4386
palomino3Windows Server 2022 Datacenterx644.2.1 (2022-06-23 ucrt) -- "Funny-Looking Kid" 4138
merida1macOS 10.14.6 Mojavex86_644.2.1 (2022-06-23) -- "Funny-Looking Kid" 4205
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

CHECK results for spiky on nebbiolo1


To the developers/maintainers of the spiky package:
- Please 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 How and When does the builder pull? When will my changes propagate? for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 1907/2140HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
spiky 1.2.0  (landing page)
Tim Triche
Snapshot Date: 2022-10-18 13:55:19 -0400 (Tue, 18 Oct 2022)
git_url: https://git.bioconductor.org/packages/spiky
git_branch: RELEASE_3_15
git_last_commit: 9300a49
git_last_commit_date: 2022-04-26 12:16:37 -0400 (Tue, 26 Apr 2022)
nebbiolo1Linux (Ubuntu 20.04.5 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino3Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: spiky
Version: 1.2.0
Command: /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD check --install=check:spiky.install-out.txt --library=/home/biocbuild/bbs-3.15-bioc/R/library --no-vignettes --timings spiky_1.2.0.tar.gz
StartedAt: 2022-10-18 21:58:20 -0400 (Tue, 18 Oct 2022)
EndedAt: 2022-10-18 22:02:31 -0400 (Tue, 18 Oct 2022)
EllapsedTime: 251.1 seconds
RetCode: 0
Status:   OK  
CheckDir: spiky.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD check --install=check:spiky.install-out.txt --library=/home/biocbuild/bbs-3.15-bioc/R/library --no-vignettes --timings spiky_1.2.0.tar.gz
###
##############################################################################
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* using log directory ‘/home/biocbuild/bbs-3.15-bioc/meat/spiky.Rcheck’
* using R version 4.2.1 (2022-06-23)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘spiky/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘spiky’ version ‘1.2.0’
* 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 ... OK
* 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 ... OK
* 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 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
bin_pmol     5.993  2.758   9.113
predict_pmol 5.054  2.551   7.606
* 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: OK


Installation output

spiky.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD INSTALL spiky
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.15-bioc/R/library’
* installing *source* package ‘spiky’ ...
** using staged installation
** R
** data
** 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)

Tests output


Example timings

spiky.Rcheck/spiky-Ex.timings

nameusersystemelapsed
add_frag_info0.1530.0240.177
bam_to_bins0.1410.0000.141
bin_pmol5.9932.7589.113
covg_to_df1.1140.1391.254
find_spike_contigs0.0520.0050.058
generate_spike_fasta0.1200.0040.124
get_base_name0.0060.0030.009
get_binned_coverage0.2220.0040.227
get_merged_gr0.0660.0000.066
get_spike_depth0.2550.0160.270
get_spiked_coverage0.220.020.24
kmax0.0720.0000.072
kmers0.0590.0000.059
methylation_specificity0.1820.0040.186
model_bam_standards4.5710.1804.751
model_glm_pmol0.1610.0000.161
predict_pmol5.0542.5517.606
process_spikes0.2390.0010.240
scan_genomic_contigs0.1640.0000.164
scan_methylation_specificity0.0450.0000.046
scan_spike_contigs0.2870.0000.288
scan_spike_counts0.0640.0040.069
scan_spiked_bam0.4680.0150.484
seqinfo_from_header0.1000.0240.123
spike_bland_altman_plot0.1720.0240.196
spike_counts0.0610.0220.084
tile_bins0.0370.0120.050