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This page was generated on 2024-05-04 11:40:03 -0400 (Sat, 04 May 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_644.4.0 beta (2024-04-15 r86425) -- "Puppy Cup" 4753
palomino3Windows Server 2022 Datacenterx644.4.0 beta (2024-04-15 r86425 ucrt) -- "Puppy Cup" 4486
lconwaymacOS 12.7.1 Montereyx86_644.4.0 beta (2024-04-14 r86421) -- "Puppy Cup" 4519
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch644.4.0 beta (2024-04-15 r86425) -- "Puppy Cup" 4479
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 2050/2300HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
spiky 1.10.0  (landing page)
Tim Triche
Snapshot Date: 2024-05-03 14:00:19 -0400 (Fri, 03 May 2024)
git_url: https://git.bioconductor.org/packages/spiky
git_branch: RELEASE_3_19
git_last_commit: 76e2d10
git_last_commit_date: 2024-04-30 11:35:17 -0400 (Tue, 30 Apr 2024)
nebbiolo1Linux (Ubuntu 22.04.3 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
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kunpeng2Linux (openEuler 22.03 LTS-SP1) / aarch64  OK    OK    OK  
kjohnson3macOS 13.6.5 Ventura / arm64see weekly results here

CHECK results for spiky on lconway


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: 1.10.0
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_1.10.0.tar.gz
StartedAt: 2024-05-04 01:08:41 -0400 (Sat, 04 May 2024)
EndedAt: 2024-05-04 01:14:41 -0400 (Sat, 04 May 2024)
EllapsedTime: 359.9 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_1.10.0.tar.gz
###
##############################################################################
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* using log directory ‘/Users/biocbuild/bbs-3.19-bioc/meat/spiky.Rcheck’
* using R version 4.4.0 beta (2024-04-14 r86421)
* using platform: x86_64-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 Monterey 12.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘spiky/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘spiky’ version ‘1.10.0’
* 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_bedpe   20.262  0.593  20.995
scan_genomic_contigs 18.067  1.662  19.873
bin_pmol              6.250  2.202   8.730
scan_spike_bedpe      6.220  0.166   6.435
model_bam_standards   5.586  0.168   5.785
predict_pmol          4.201  1.099   5.442
* 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-3.19-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-x86_64/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_info1.0020.0361.044
bam_to_bins0.1780.0050.186
bin_pmol6.2502.2028.730
covg_to_df0.0820.0020.085
find_spike_contigs0.0220.0030.026
generate_spike_fasta0.1160.0050.121
get_base_name0.0140.0020.016
get_binned_coverage0.2460.0120.261
get_merged_gr0.0710.0060.078
get_spike_depth0.2940.0180.315
get_spiked_coverage0.2450.0240.270
kmax0.0540.0030.058
kmers0.0380.0020.041
methylation_specificity0.1020.0050.108
model_bam_standards5.5860.1685.785
model_glm_pmol0.0900.0110.102
predict_pmol4.2011.0995.442
process_spikes0.2340.0110.247
read_bedpe000
scan_genomic_bedpe20.262 0.59320.995
scan_genomic_contigs18.067 1.66219.873
scan_methylation_specificity0.0380.0050.043
scan_spike_bedpe6.2200.1666.435
scan_spike_contigs0.4210.0850.511
scan_spike_counts0.0580.0060.063
scan_spiked_bam0.5140.0890.613
seqinfo_from_header0.1260.0130.141
spike_bland_altman_plot0.1130.0060.122
spike_counts0.0650.0020.067
tile_bins0.0460.0030.051