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This page was generated on 2025-10-04 12:07 -0400 (Sat, 04 Oct 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" 4853
lconwaymacOS 12.7.1 Montereyx86_644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4640
kjohnson3macOS 13.7.7 Venturaarm644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4585
taishanLinux (openEuler 24.03 LTS)aarch644.5.0 (2025-04-11) -- "How About a Twenty-Six" 4576
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 1154/2341HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
lute 1.5.1  (landing page)
Sean K Maden
Snapshot Date: 2025-10-03 13:45 -0400 (Fri, 03 Oct 2025)
git_url: https://git.bioconductor.org/packages/lute
git_branch: devel
git_last_commit: 46c2ab0
git_last_commit_date: 2025-09-22 09:54:51 -0400 (Mon, 22 Sep 2025)
nebbiolo2Linux (Ubuntu 24.04.3 LTS) / x86_64  OK    OK    ERROR  
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    ERROR    OK  
kjohnson3macOS 13.7.7 Ventura / arm64  OK    OK    ERROR    OK  
taishanLinux (openEuler 24.03 LTS) / aarch64  OK    OK    OK  


CHECK results for lute on taishan

To the developers/maintainers of the lute package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/lute.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: lute
Version: 1.5.1
Command: /home/biocbuild/R/R/bin/R CMD check --install=check:lute.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings lute_1.5.1.tar.gz
StartedAt: 2025-10-03 08:35:53 -0000 (Fri, 03 Oct 2025)
EndedAt: 2025-10-03 08:40:10 -0000 (Fri, 03 Oct 2025)
EllapsedTime: 256.5 seconds
RetCode: 0
Status:   OK  
CheckDir: lute.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD check --install=check:lute.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings lute_1.5.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/lute.Rcheck’
* using R version 4.5.0 (2025-04-11)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
    aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0
    GNU Fortran (GCC) 14.2.0
* running under: openEuler 24.03 (LTS)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘lute/DESCRIPTION’ ... OK
* this is package ‘lute’ version ‘1.5.1’
* 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 ‘lute’ 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 ... NOTE
The following files look like leftovers:
  ‘lute/NEWS.Rd’
Please remove them from your package.
* 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 whether startup messages can be suppressed ... OK
* checking dependencies in R code ... NOTE
Namespace in Imports field not imported from: ‘ggplot2’
  All declared Imports should be used.
* 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 ... NOTE
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  lute.Rd: SummarizedExperiment-class
  nnlsParam.Rd: ExpressionSet-class
  ypb_from_sce.Rd: SingleCellExperiment-class
  z_matrix_from_sce.Rd: SingleCellExperiment-class
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
* 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 files in ‘vignettes’ ... OK
* checking examples ... 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: 3 NOTEs
See
  ‘/home/biocbuild/bbs-3.22-bioc/meat/lute.Rcheck/00check.log’
for details.


Installation output

lute.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD INSTALL lute
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/R/R-4.5.0/site-library’
* installing *source* package ‘lute’ ...
** this is package ‘lute’ version ‘1.5.1’
** using staged installation
** R
** 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
Warning in fun(libname, pkgname) :
  Package 'lute' is deprecated and will be removed from Bioconductor
  version 3.23
** testing if installed package can be loaded from final location
Warning in fun(libname, pkgname) :
  Package 'lute' is deprecated and will be removed from Bioconductor
  version 3.23
** testing if installed package keeps a record of temporary installation path
* DONE (lute)

Tests output


Example timings

lute.Rcheck/lute-Ex.timings

nameusersystemelapsed
bisqueParam-class3.3100.0283.347
bisqueParam2.4580.0122.476
cellProportionsPredictions-class0.0140.0010.015
cellProportionsPredictions0.0000.0000.001
deconvolution-bisqueParam-method2.4100.0072.424
deconvolution-deconvolutionParam-method0.0010.0000.000
deconvolution-independentbulkParam-method0.0020.0000.002
deconvolution-nnlsParam-method0.0140.0000.014
deconvolution-referencebasedParam-method0.0040.0000.003
deconvolution0.0040.0000.004
deconvolutionParam-class0.0000.0000.001
eset_to_sce0.4850.0000.486
eset_to_se0.3830.0000.383
findmarkersParam-class0.9060.0150.923
findmarkersParam0.7350.0000.737
getDeconvolutionExampleData0.0000.0000.001
getDeconvolutionExampleDataBisque0.3650.0000.366
getDeconvolutionExampleDataSCDC0.1540.0000.154
get_celltypes_from_sce000
get_csf_reference000
get_eset_from_matrix000
independentbulkParam-class0.0010.0000.000
independentbulkParam0.0000.0000.001
lute0.1570.0000.158
luteSupportedDeconvolutionAlgorithms0.0070.0000.008
new_workflow_table0.0010.0000.001
nnlsParam-class0.0070.0000.007
nnlsParam0.0070.0000.007
parseDeconvolutionPredictionsResults0.0010.0000.000
proportionsVectorsList0.0010.0000.000
randomMarkersVectorsList0.0000.0000.001
randomSingleCellExperiment0.0720.0040.076
referenceFromSingleCellExperiment0.0010.0000.000
referencebasedParam-class0.0020.0000.002
referencebasedParam0.0020.0000.001
rmse0.0010.0000.001
rmseTest0.0000.0000.001
sce_to_eset0.1210.0000.122
sce_to_se0.1050.0000.110
se_to_eset0.1360.0000.137
se_to_sce0.1240.0000.124
show-bisqueParam-method0.5080.0000.509
show-cellProportionsPredictions-method0.0010.0000.001
show-deconvolutionParam-method000
show-findmarkersParam-method0.7270.0000.729
show-independentbulkParam-method0.0010.0000.001
show-nnlsParam-method0.0020.0000.002
show-referencebasedParam-method0.0020.0000.002
show-typemarkersParam-method000
sub-sub-deconvolutionParam-ANY-ANY-method0.0000.0000.001
sub-sub-typemarkersParam-ANY-ANY-method0.0010.0000.001
typemarkers-findmarkersParam-method0.7220.0000.724
typemarkers-typemarkersParam-method0.0000.0000.001
typemarkers0.0000.0000.001
typemarkersParam-class0.0000.0000.001
typemarkersParam0.0000.0000.001
ypb_from_sce0.1070.0000.108
z_matrix_from_sce0.0980.0000.099