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This page was generated on 2024-05-04 11:41:17 -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 2278/2300HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
weitrix 1.16.0  (landing page)
Paul Harrison
Snapshot Date: 2024-05-03 14:00:19 -0400 (Fri, 03 May 2024)
git_url: https://git.bioconductor.org/packages/weitrix
git_branch: RELEASE_3_19
git_last_commit: b1d9a3f
git_last_commit_date: 2024-04-30 11:23:57 -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 weitrix on kunpeng2


To the developers/maintainers of the weitrix package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/weitrix.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.
- See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host.

raw results


Summary

Package: weitrix
Version: 1.16.0
Command: /home/biocbuild/R/R-beta-2024-04-15_r86425/bin/R CMD check --install=check:weitrix.install-out.txt --library=/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library --no-vignettes --timings weitrix_1.16.0.tar.gz
StartedAt: 2024-05-04 13:12:11 -0000 (Sat, 04 May 2024)
EndedAt: 2024-05-04 13:17:49 -0000 (Sat, 04 May 2024)
EllapsedTime: 338.2 seconds
RetCode: 0
Status:   OK  
CheckDir: weitrix.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/R/R-beta-2024-04-15_r86425/bin/R CMD check --install=check:weitrix.install-out.txt --library=/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library --no-vignettes --timings weitrix_1.16.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/weitrix.Rcheck’
* using R version 4.4.0 beta (2024-04-15 r86425)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
    gcc (GCC) 10.3.1
    GNU Fortran (GCC) 10.3.1
* running under: openEuler 22.03 (LTS-SP1)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘weitrix/DESCRIPTION’ ... OK
* this is package ‘weitrix’ 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 for sufficient/correct file permissions ... OK
* checking whether package ‘weitrix’ 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 loading without being on the library search path ... 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) weitrix_calibrate_trend.Rd:27: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) weitrix_calibrate_trend.Rd:28: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) weitrix_calibrate_trend.Rd:29: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) weitrix_calibrate_trend.Rd:30: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) weitrix_components.Rd:64-68: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) weitrix_components.Rd:69-73: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) weitrix_components.Rd:74-76: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) weitrix_components.Rd:77-80: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) weitrix_components.Rd:81: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) weitrix_components.Rd:82: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) weitrix_confects.Rd:51: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) weitrix_confects.Rd:52: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) weitrix_confects.Rd:53: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) weitrix_confects.Rd:54: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) weitrix_confects.Rd:55: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) weitrix_sd_confects.Rd:33: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) weitrix_sd_confects.Rd:34: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) weitrix_sd_confects.Rd:35: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) weitrix_sd_confects.Rd:36: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) weitrix_sd_confects.Rd:37: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) weitrix_sd_confects.Rd:38: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) weitrix_sd_confects.Rd:39: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) weitrix_sd_confects.Rd:40: Lost braces in \itemize; \value handles \item{}{} directly
* 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 line endings in Makefiles ... OK
* checking for GNU extensions in Makefiles ... OK
* checking include directives in Makefiles ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                          user system elapsed
components_seq_scree    37.180  4.206  30.697
weitrix_calplot          9.408  4.904  11.964
weitrix_calibrate_trend 10.233  3.809  10.293
weitrix_calibrate        8.594  2.562   7.456
weitrix_dispersions      6.073  2.108  10.035
weitrix_elist            3.910  1.757   0.065
* 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
  ‘/home/biocbuild/bbs-3.19-bioc/meat/weitrix.Rcheck/00check.log’
for details.


Installation output

weitrix.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R-beta-2024-04-15_r86425/bin/R CMD INSTALL weitrix
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library’
* installing *source* package ‘weitrix’ ...
** 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 (weitrix)

Tests output

weitrix.Rcheck/tests/testthat.Rout


R version 4.4.0 beta (2024-04-15 r86425) -- "Puppy Cup"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: aarch64-unknown-linux-gnu

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(weitrix)
Loading required package: SummarizedExperiment
Loading required package: MatrixGenerics
Loading required package: matrixStats

Attaching package: 'MatrixGenerics'

The following objects are masked from 'package:matrixStats':

    colAlls, colAnyNAs, colAnys, colAvgsPerRowSet, colCollapse,
    colCounts, colCummaxs, colCummins, colCumprods, colCumsums,
    colDiffs, colIQRDiffs, colIQRs, colLogSumExps, colMadDiffs,
    colMads, colMaxs, colMeans2, colMedians, colMins, colOrderStats,
    colProds, colQuantiles, colRanges, colRanks, colSdDiffs, colSds,
    colSums2, colTabulates, colVarDiffs, colVars, colWeightedMads,
    colWeightedMeans, colWeightedMedians, colWeightedSds,
    colWeightedVars, rowAlls, rowAnyNAs, rowAnys, rowAvgsPerColSet,
    rowCollapse, rowCounts, rowCummaxs, rowCummins, rowCumprods,
    rowCumsums, rowDiffs, rowIQRDiffs, rowIQRs, rowLogSumExps,
    rowMadDiffs, rowMads, rowMaxs, rowMeans2, rowMedians, rowMins,
    rowOrderStats, rowProds, rowQuantiles, rowRanges, rowRanks,
    rowSdDiffs, rowSds, rowSums2, rowTabulates, rowVarDiffs, rowVars,
    rowWeightedMads, rowWeightedMeans, rowWeightedMedians,
    rowWeightedSds, rowWeightedVars

Loading required package: GenomicRanges
Loading required package: stats4
Loading required package: BiocGenerics

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append,
    as.data.frame, basename, cbind, colnames, dirname, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
    pmin.int, rank, rbind, rownames, sapply, setdiff, table, tapply,
    union, unique, unsplit, which.max, which.min

Loading required package: S4Vectors

Attaching package: 'S4Vectors'

The following object is masked from 'package:utils':

    findMatches

The following objects are masked from 'package:base':

    I, expand.grid, unname

Loading required package: IRanges
Loading required package: GenomeInfoDb
Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.


Attaching package: 'Biobase'

The following object is masked from 'package:MatrixGenerics':

    rowMedians

The following objects are masked from 'package:matrixStats':

    anyMissing, rowMedians

> 
> test_check("weitrix")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 15 ]
> 
> proc.time()
   user  system elapsed 
 22.054   5.256  24.533 

Example timings

weitrix.Rcheck/weitrix-Ex.timings

nameusersystemelapsed
as_weitrix0.0930.0000.093
bless_weitrix0.0260.0000.026
components_seq_scree37.180 4.20630.697
counts_proportions0.0810.0040.086
counts_shift0.0560.0080.064
matrix_long0.0250.0000.025
weitrix_calibrate8.5942.5627.456
weitrix_calibrate_all1.3650.8411.802
weitrix_calibrate_trend10.233 3.80910.293
weitrix_calplot 9.408 4.90411.964
weitrix_components2.8471.1083.423
weitrix_confects1.6040.8971.447
weitrix_dispersions 6.073 2.10810.035
weitrix_elist3.9101.7570.065
weitrix_hill0.0420.0040.047
weitrix_randomize0.0360.0080.044
weitrix_sd_confects2.6121.8543.812
weitrix_weights0.0000.0070.007
weitrix_x0.0750.0630.039
well_knotted_spline1.2830.2351.527