Back to Multiple platform build/check report for BioC 3.14
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This page was generated on 2022-04-13 12:06:00 -0400 (Wed, 13 Apr 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.1.3 (2022-03-10) -- "One Push-Up" 4324
tokay2Windows Server 2012 R2 Standardx644.1.3 (2022-03-10) -- "One Push-Up" 4077
machv2macOS 10.14.6 Mojavex86_644.1.3 (2022-03-10) -- "One Push-Up" 4137
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 nebbiolo2


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 1859/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
spiky 1.0.0  (landing page)
Tim Triche
Snapshot Date: 2022-04-12 01:55:07 -0400 (Tue, 12 Apr 2022)
git_url: https://git.bioconductor.org/packages/spiky
git_branch: RELEASE_3_14
git_last_commit: 1b25b68
git_last_commit_date: 2021-10-26 13:10:41 -0400 (Tue, 26 Oct 2021)
nebbiolo2Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: spiky
Version: 1.0.0
Command: /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD check --install=check:spiky.install-out.txt --library=/home/biocbuild/bbs-3.14-bioc/R/library --no-vignettes --timings spiky_1.0.0.tar.gz
StartedAt: 2022-04-12 09:30:18 -0400 (Tue, 12 Apr 2022)
EndedAt: 2022-04-12 09:34:07 -0400 (Tue, 12 Apr 2022)
EllapsedTime: 228.6 seconds
RetCode: 0
Status:   OK  
CheckDir: spiky.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD check --install=check:spiky.install-out.txt --library=/home/biocbuild/bbs-3.14-bioc/R/library --no-vignettes --timings spiky_1.0.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.14-bioc/meat/spiky.Rcheck’
* using R version 4.1.3 (2022-03-10)
* 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 ‘1.0.0’
* 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  5.1Mb
  sub-directories of 1Mb or more:
    data      1.8Mb
    extdata   3.0Mb
* 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 5.581  0.991   6.813
* 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: 1 NOTE
See
  ‘/home/biocbuild/bbs-3.14-bioc/meat/spiky.Rcheck/00check.log’
for details.



Installation output

spiky.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD INSTALL spiky
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.14-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_info1.1540.1811.334
bam_to_bins0.1490.0000.149
bin_pmol5.5810.9916.813
covg_to_df0.2430.0080.251
find_spike_contigs0.0610.0000.062
generate_spike_fasta0.1110.0240.135
get_base_name0.0060.0040.010
get_binned_coverage0.2380.0280.266
get_merged_gr0.0840.0040.088
get_spike_depth0.3510.0240.375
get_spiked_coverage0.2380.0440.283
kmax0.0680.0000.068
kmers0.0560.0000.056
methylation_specificity0.2280.0000.228
model_bam_standards4.5510.1364.688
model_glm_pmol0.1680.0140.182
predict_pmol4.0540.5604.614
process_spikes0.2450.0080.253
scan_genomic_contigs0.1530.0200.171
scan_methylation_specificity0.0470.0000.047
scan_spike_contigs0.3790.0160.395
scan_spike_counts0.0660.0040.070
scan_spiked_bam0.5250.0320.557
seqinfo_from_header0.1080.0040.112
spike_bland_altman_plot0.1910.0000.191
spike_counts0.080.000.08
tile_bins0.0550.0000.056