Back to Multiple platform build/check report for BioC 3.15
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This page was generated on 2022-06-24 12:06:50 -0400 (Fri, 24 Jun 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 20.04.4 LTS)x86_644.2.0 (2022-04-22) -- "Vigorous Calisthenics" 4380
palomino3Windows Server 2022 Datacenterx644.2.0 (2022-04-22 ucrt) -- "Vigorous Calisthenics" 4156
merida1macOS 10.14.6 Mojavex86_644.2.0 (2022-04-22) -- "Vigorous Calisthenics" 4221
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 palomino3


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 1907/2140HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
spiky 1.2.0  (landing page)
Tim Triche
Snapshot Date: 2022-06-23 13:55:15 -0400 (Thu, 23 Jun 2022)
git_url: https://git.bioconductor.org/packages/spiky
git_branch: RELEASE_3_15
git_last_commit: 9300a49
git_last_commit_date: 2022-04-26 12:16:37 -0400 (Tue, 26 Apr 2022)
nebbiolo1Linux (Ubuntu 20.04.4 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
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    NA  

Summary

Package: spiky
Version: 1.2.0
Command: F:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:spiky.install-out.txt --library=F:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings spiky_1.2.0.tar.gz
StartedAt: 2022-06-24 05:11:40 -0400 (Fri, 24 Jun 2022)
EndedAt: 2022-06-24 05:16:20 -0400 (Fri, 24 Jun 2022)
EllapsedTime: 280.0 seconds
RetCode: 0
Status:   OK  
CheckDir: spiky.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:spiky.install-out.txt --library=F:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings spiky_1.2.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'F:/biocbuild/bbs-3.15-bioc/meat/spiky.Rcheck'
* using R version 4.2.0 (2022-04-22 ucrt)
* using platform: x86_64-w64-mingw32 (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 '1.2.0'
* 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  5.0Mb
  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            11.86   2.84   15.11
predict_pmol         8.34   1.81   10.16
model_bam_standards  6.76   0.16    6.95
* 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
  'F:/biocbuild/bbs-3.15-bioc/meat/spiky.Rcheck/00check.log'
for details.



Installation output

spiky.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL spiky
###
##############################################################################
##############################################################################


* installing to library 'F:/biocbuild/bbs-3.15-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_info0.250.030.28
bam_to_bins0.170.050.24
bin_pmol11.86 2.8415.11
covg_to_df0.250.020.27
find_spike_contigs0.100.000.09
generate_spike_fasta0.340.000.34
get_base_name0.020.000.02
get_binned_coverage0.290.010.42
get_merged_gr0.110.000.11
get_spike_depth0.320.050.36
get_spiked_coverage0.200.010.21
kmax0.080.000.08
kmers0.090.000.10
methylation_specificity0.220.000.22
model_bam_standards6.760.166.95
model_glm_pmol0.140.000.14
predict_pmol 8.34 1.8110.16
process_spikes0.290.030.31
scan_genomic_contigs0.200.010.22
scan_methylation_specificity0.030.020.04
scan_spike_contigs0.300.020.32
scan_spike_counts0.060.000.07
scan_spiked_bam0.550.010.56
seqinfo_from_header0.120.000.12
spike_bland_altman_plot0.140.020.16
spike_counts0.100.000.09
tile_bins0.110.010.13