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This page was generated on 2024-02-28 11:37:22 -0500 (Wed, 28 Feb 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 22.04.3 LTS)x86_644.3.2 Patched (2023-11-13 r85521) -- "Eye Holes" 4692
palomino4Windows Server 2022 Datacenterx644.3.2 (2023-10-31 ucrt) -- "Eye Holes" 4445
lconwaymacOS 12.7.1 Montereyx86_644.3.2 Patched (2023-11-01 r85457) -- "Eye Holes" 4466
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 2027/2266HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
spiky 1.8.0  (landing page)
Tim Triche
Snapshot Date: 2024-02-27 14:05:07 -0500 (Tue, 27 Feb 2024)
git_url: https://git.bioconductor.org/packages/spiky
git_branch: RELEASE_3_18
git_last_commit: 9732d52
git_last_commit_date: 2023-10-24 11:34:17 -0500 (Tue, 24 Oct 2023)
nebbiolo2Linux (Ubuntu 22.04.3 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 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.1 Ventura / arm64see weekly results here

CHECK results for spiky on palomino4


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: 1.8.0
Command: F:\biocbuild\bbs-3.18-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:spiky.install-out.txt --library=F:\biocbuild\bbs-3.18-bioc\R\library --no-vignettes --timings spiky_1.8.0.tar.gz
StartedAt: 2024-02-28 06:52:40 -0500 (Wed, 28 Feb 2024)
EndedAt: 2024-02-28 06:57:41 -0500 (Wed, 28 Feb 2024)
EllapsedTime: 301.3 seconds
RetCode: 0
Status:   OK  
CheckDir: spiky.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.18-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:spiky.install-out.txt --library=F:\biocbuild\bbs-3.18-bioc\R\library --no-vignettes --timings spiky_1.8.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'F:/biocbuild/bbs-3.18-bioc/meat/spiky.Rcheck'
* using R version 4.3.2 (2023-10-31 ucrt)
* using platform: x86_64-w64-mingw32 (64-bit)
* R was compiled by
    gcc.exe (GCC) 12.3.0
    GNU Fortran (GCC) 12.3.0
* running under: Windows Server 2022 x64 (build 20348)
* 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 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   15.81   0.39   16.36
scan_genomic_contigs 13.42   0.73   15.73
bin_pmol              8.02   2.49   10.73
predict_pmol          5.18   1.50    6.68
model_bam_standards   5.83   0.17    6.02
* 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
  'F:/biocbuild/bbs-3.18-bioc/meat/spiky.Rcheck/00check.log'
for details.



Installation output

spiky.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.18-bioc\R\bin\R.exe CMD INSTALL spiky
###
##############################################################################
##############################################################################


* installing to library 'F:/biocbuild/bbs-3.18-bioc/R/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_info0.170.020.19
bam_to_bins0.120.040.18
bin_pmol 8.02 2.4910.73
covg_to_df0.090.000.10
find_spike_contigs0.030.000.03
generate_spike_fasta0.110.000.11
get_base_name0.010.000.02
get_binned_coverage0.310.000.42
get_merged_gr0.070.010.08
get_spike_depth0.210.070.28
get_spiked_coverage0.270.000.28
kmax0.070.010.09
kmers0.040.000.03
methylation_specificity0.070.000.08
model_bam_standards5.830.176.02
model_glm_pmol0.060.020.07
predict_pmol5.181.506.68
process_spikes0.230.020.25
read_bedpe000
scan_genomic_bedpe15.81 0.3916.36
scan_genomic_contigs13.42 0.7315.73
scan_methylation_specificity0.040.020.05
scan_spike_bedpe4.340.004.34
scan_spike_contigs0.330.010.34
scan_spike_counts0.060.000.07
scan_spiked_bam0.410.000.42
seqinfo_from_header0.110.020.14
spike_bland_altman_plot0.060.040.11
spike_counts0.060.020.08
tile_bins0.030.000.03