Back to Multiple platform build/check report for BioC 3.19:   simplified   long
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This page was generated on 2024-05-22 11:35:34 -0400 (Wed, 22 May 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_644.4.0 (2024-04-24) -- "Puppy Cup" 4751
palomino3Windows Server 2022 Datacenterx644.4.0 (2024-04-24 ucrt) -- "Puppy Cup" 4485
lconwaymacOS 12.7.1 Montereyx86_644.4.0 (2024-04-24) -- "Puppy Cup" 3444
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 518/2300HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
dearseq 1.16.0  (landing page)
Boris P. Hejblum
Snapshot Date: 2024-05-21 14:00:15 -0400 (Tue, 21 May 2024)
git_url: https://git.bioconductor.org/packages/dearseq
git_branch: RELEASE_3_19
git_last_commit: 7ebc2c8
git_last_commit_date: 2024-04-30 11:19:52 -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    ERROR  skippedskipped
kjohnson3macOS 13.6.5 Ventura / arm64see weekly results here

CHECK results for dearseq on palomino3


To the developers/maintainers of the dearseq package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/dearseq.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: dearseq
Version: 1.16.0
Command: F:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:dearseq.install-out.txt --library=F:\biocbuild\bbs-3.19-bioc\R\library --no-vignettes --timings dearseq_1.16.0.tar.gz
StartedAt: 2024-05-22 00:58:16 -0400 (Wed, 22 May 2024)
EndedAt: 2024-05-22 00:59:49 -0400 (Wed, 22 May 2024)
EllapsedTime: 93.4 seconds
RetCode: 0
Status:   OK  
CheckDir: dearseq.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:dearseq.install-out.txt --library=F:\biocbuild\bbs-3.19-bioc\R\library --no-vignettes --timings dearseq_1.16.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'F:/biocbuild/bbs-3.19-bioc/meat/dearseq.Rcheck'
* using R version 4.4.0 (2024-04-24 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 13.2.0
    GNU Fortran (GCC) 13.2.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'dearseq/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'dearseq' version '1.16.0'
* 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 'dearseq' can be installed ... OK
* checking installed package size ... OK
* 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 ... OK
* checking Rd files ... NOTE
checkRd: (-1) plot.dearseq.Rd:12: Lost braces; missing escapes or markup?
    12 | \item{signif_threshold}{a value between \code{0} and {1} specifying the 
       |                                                      ^
checkRd: (-1) plot_ord_pvals.Rd:13: Lost braces; missing escapes or markup?
    13 | \item{signif_threshold}{a value between \code{0} and {1} specifying the 
       |                                                      ^
checkRd: (-1) summary.dearseq.Rd:15: Lost braces; missing escapes or markup?
    15 | \item{signif_threshold}{a value between \code{0} and {1} specifying the 
       |                                                      ^
* 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
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
  Running 'testthat.R'
 OK
* 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: 1 NOTE
See
  'F:/biocbuild/bbs-3.19-bioc/meat/dearseq.Rcheck/00check.log'
for details.


Installation output

dearseq.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD INSTALL dearseq
###
##############################################################################
##############################################################################


* installing to library 'F:/biocbuild/bbs-3.19-bioc/R/library'
* installing *source* package 'dearseq' ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
*** copying figures
** 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 (dearseq)

Tests output

dearseq.Rcheck/tests/testthat.Rout


R version 4.4.0 (2024-04-24 ucrt) -- "Puppy Cup"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(testthat)
> library(dearseq)
> 
> test_check("dearseq")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 5 ]
> 
> proc.time()
   user  system elapsed 
   2.95    0.54    3.50 

Example timings

dearseq.Rcheck/dearseq-Ex.timings

nameusersystemelapsed
PBT_gmt0.000.020.02
baduel_5gs000
dear_seq0.560.010.58
dgsa_seq0.220.030.25
permPvals000
plot_hist_pvals0.390.020.41
plot_ord_pvals0.600.090.68
plot_weights0.040.000.05
sp_weights0.140.000.14
spaghettiPlot1GS1.570.051.63
vc_score0.010.000.01
vc_score_h0.050.000.05
vc_score_h_perm0.110.000.11
vc_score_perm0.170.080.25
vc_test_asym0.060.000.06
vc_test_perm0.020.010.03
voom_weights1.610.051.65