Back to Multiple platform build/check report for BioC 3.16:   simplified   long
ABCDEFGHIJKLMNOPQR[S]TUVWXYZ

This page was generated on 2023-04-12 11:06:27 -0400 (Wed, 12 Apr 2023).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.5 LTS)x86_644.2.3 (2023-03-15) -- "Shortstop Beagle" 4502
palomino4Windows Server 2022 Datacenterx644.2.3 (2023-03-15 ucrt) -- "Shortstop Beagle" 4282
lconwaymacOS 12.5.1 Montereyx86_644.2.3 (2023-03-15) -- "Shortstop Beagle" 4310
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 lconway


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 1942/2183HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
spiky 1.4.0  (landing page)
Tim Triche
Snapshot Date: 2023-04-10 14:00:05 -0400 (Mon, 10 Apr 2023)
git_url: https://git.bioconductor.org/packages/spiky
git_branch: RELEASE_3_16
git_last_commit: ca789a4
git_last_commit_date: 2022-11-01 11:25:11 -0400 (Tue, 01 Nov 2022)
nebbiolo2Linux (Ubuntu 20.04.5 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino4Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.5.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: spiky
Version: 1.4.0
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_1.4.0.tar.gz
StartedAt: 2023-04-10 22:52:02 -0400 (Mon, 10 Apr 2023)
EndedAt: 2023-04-10 22:56:37 -0400 (Mon, 10 Apr 2023)
EllapsedTime: 275.0 seconds
RetCode: 0
Status:   OK  
CheckDir: spiky.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### 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_1.4.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.16-bioc/meat/spiky.Rcheck’
* using R version 4.2.3 (2023-03-15)
* using platform: x86_64-apple-darwin17.0 (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 ‘1.4.0’
* 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   19.095  0.666  19.790
scan_genomic_contigs 12.966  1.304  14.322
bin_pmol              5.023  2.032   7.209
scan_spike_bedpe      5.615  0.096   5.725
model_bam_standards   4.785  0.256   5.054
* 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-3.16-bioc/meat/spiky.Rcheck/00check.log’
for details.



Installation output

spiky.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL spiky
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.2/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)

Tests output


Example timings

spiky.Rcheck/spiky-Ex.timings

nameusersystemelapsed
add_frag_info0.1270.0240.152
bam_to_bins0.1240.0030.129
bin_pmol5.0232.0327.209
covg_to_df0.0680.0020.070
find_spike_contigs0.0420.0030.046
generate_spike_fasta0.1100.0040.116
get_base_name0.0090.0010.011
get_binned_coverage0.2500.0100.262
get_merged_gr0.0570.0030.061
get_spike_depth0.2560.0080.265
get_spiked_coverage0.1810.0080.190
kmax0.0380.0020.041
kmers0.0300.0020.031
methylation_specificity0.0730.0030.077
model_bam_standards4.7850.2565.054
model_glm_pmol0.0550.0030.058
predict_pmol3.3570.8564.249
process_spikes0.1900.0080.199
read_bedpe000
scan_genomic_bedpe19.095 0.66619.790
scan_genomic_contigs12.966 1.30414.322
scan_methylation_specificity0.0320.0040.037
scan_spike_bedpe5.6150.0965.725
scan_spike_contigs0.3190.0620.381
scan_spike_counts0.0590.0080.068
scan_spiked_bam0.4360.0990.541
seqinfo_from_header0.0870.0100.098
spike_bland_altman_plot0.1000.0030.104
spike_counts0.0450.0020.046
tile_bins0.0280.0040.031