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This page was generated on 2024-12-23 12:08 -0500 (Mon, 23 Dec 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.1 LTS)x86_644.4.2 (2024-10-31) -- "Pile of Leaves" 4744
palomino8Windows Server 2022 Datacenterx644.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" 4487
merida1macOS 12.7.5 Montereyx86_644.4.2 (2024-10-31) -- "Pile of Leaves" 4515
kjohnson1macOS 13.6.6 Venturaarm644.4.2 (2024-10-31) -- "Pile of Leaves" 4467
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 2035/2289HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
spiky 1.12.0  (landing page)
Tim Triche
Snapshot Date: 2024-12-19 13:00 -0500 (Thu, 19 Dec 2024)
git_url: https://git.bioconductor.org/packages/spiky
git_branch: RELEASE_3_20
git_last_commit: a179df8
git_last_commit_date: 2024-10-29 11:01:11 -0500 (Tue, 29 Oct 2024)
nebbiolo2Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino8Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 12.7.5 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.6 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published


CHECK results for spiky on kjohnson1

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.

raw results


Summary

Package: spiky
Version: 1.12.0
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_1.12.0.tar.gz
StartedAt: 2024-12-21 10:32:06 -0500 (Sat, 21 Dec 2024)
EndedAt: 2024-12-21 10:38:07 -0500 (Sat, 21 Dec 2024)
EllapsedTime: 361.5 seconds
RetCode: 0
Status:   OK  
CheckDir: spiky.Rcheck
Warnings: 0

Command output

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### 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_1.12.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/spiky.Rcheck’
* using R version 4.4.2 (2024-10-31)
* using platform: aarch64-apple-darwin20
* 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 13.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘spiky/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘spiky’ version ‘1.12.0’
* 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 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_contigs 21.053  1.481  22.669
scan_genomic_bedpe   20.479  0.407  21.073
bin_pmol              6.138  1.796   8.081
predict_pmol          4.650  1.153   5.841
scan_spike_bedpe      5.558  0.118   5.693
* 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
  ‘/Users/biocbuild/bbs-3.20-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/4.4-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)

Tests output


Example timings

spiky.Rcheck/spiky-Ex.timings

nameusersystemelapsed
add_frag_info0.1670.0370.205
bam_to_bins0.1520.0130.166
bin_pmol6.1381.7968.081
covg_to_df0.0880.0020.090
find_spike_contigs0.0290.0030.032
generate_spike_fasta0.1140.0050.119
get_base_name0.0090.0010.011
get_binned_coverage0.2920.0100.308
get_merged_gr0.0660.0030.070
get_spike_depth0.3830.0110.395
get_spiked_coverage0.1960.0070.203
kmax0.0580.0030.060
kmers0.0400.0020.043
methylation_specificity0.0810.0050.086
model_bam_standards4.5850.1154.744
model_glm_pmol0.0610.0040.066
predict_pmol4.6501.1535.841
process_spikes0.2190.0110.230
read_bedpe000
scan_genomic_bedpe20.479 0.40721.073
scan_genomic_contigs21.053 1.48122.669
scan_methylation_specificity0.0370.0040.040
scan_spike_bedpe5.5580.1185.693
scan_spike_contigs0.4230.0570.484
scan_spike_counts0.0630.0100.074
scan_spiked_bam0.5130.0620.597
seqinfo_from_header0.0960.0080.103
spike_bland_altman_plot0.1070.0050.112
spike_counts0.0580.0040.062
tile_bins0.0330.0010.034