Back to Multiple platform build/check report for BioC 3.19:   simplified   long
ABCDEFGHIJK[L]MNOPQRSTUVWXYZ

This page was generated on 2024-05-04 11:38:01 -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 1133/2300HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
lute 1.0.0  (landing page)
Sean K Maden
Snapshot Date: 2024-05-03 14:00:19 -0400 (Fri, 03 May 2024)
git_url: https://git.bioconductor.org/packages/lute
git_branch: RELEASE_3_19
git_last_commit: 7a503f8
git_last_commit_date: 2024-04-30 11:52:55 -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 lute on palomino3


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.

raw results


Summary

Package: lute
Version: 1.0.0
Command: F:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:lute.install-out.txt --library=F:\biocbuild\bbs-3.19-bioc\R\library --no-vignettes --timings lute_1.0.0.tar.gz
StartedAt: 2024-05-04 04:55:48 -0400 (Sat, 04 May 2024)
EndedAt: 2024-05-04 04:59:57 -0400 (Sat, 04 May 2024)
EllapsedTime: 249.1 seconds
RetCode: 0
Status:   OK  
CheckDir: lute.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:lute.install-out.txt --library=F:\biocbuild\bbs-3.19-bioc\R\library --no-vignettes --timings lute_1.0.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'F:/biocbuild/bbs-3.19-bioc/meat/lute.Rcheck'
* using R version 4.4.0 beta (2024-04-15 r86425 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 'lute/DESCRIPTION' ... OK
* this is package 'lute' 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 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 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 ... 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 files in 'vignettes' ... NOTE
The following files look like leftovers/mistakes:
  'lute_algorithm_classes.log'
Please remove them from your package.
* 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
  'F:/biocbuild/bbs-3.19-bioc/meat/lute.Rcheck/00check.log'
for details.


Installation output

lute.Rcheck/00install.out

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


* installing to library 'F:/biocbuild/bbs-3.19-bioc/R/library'
* installing *source* package 'lute' ...
** 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
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (lute)

Tests output


Example timings

lute.Rcheck/lute-Ex.timings

nameusersystemelapsed
bisqueParam-class3.550.133.85
bisqueParam2.230.052.29
cellProportionsPredictions-class0.030.000.03
cellProportionsPredictions000
deconvolution-bisqueParam-method2.510.202.72
deconvolution-deconvolutionParam-method000
deconvolution-independentbulkParam-method000
deconvolution-nnlsParam-method0.000.010.02
deconvolution-referencebasedParam-method000
deconvolution0.020.000.02
deconvolutionParam-class000
eset_to_sce0.590.000.59
eset_to_se0.470.030.50
findmarkersParam-class1.170.051.23
findmarkersParam0.860.000.86
getDeconvolutionExampleData000
getDeconvolutionExampleDataBisque0.450.000.46
getDeconvolutionExampleDataSCDC0.210.000.20
get_celltypes_from_sce000
get_csf_reference000
get_eset_from_matrix000
independentbulkParam-class000
independentbulkParam000
lute0.240.000.23
luteSupportedDeconvolutionAlgorithms000
new_workflow_table000
nnlsParam-class000
nnlsParam000
parseDeconvolutionPredictionsResults000
proportionsVectorsList000
randomMarkersVectorsList000
randomSingleCellExperiment0.110.000.11
referenceFromSingleCellExperiment000
referencebasedParam-class000
referencebasedParam000
rmse000
rmseTest000
sce_to_eset0.140.010.15
sce_to_se0.130.000.13
se_to_eset0.150.000.15
se_to_sce0.160.020.18
show-bisqueParam-method0.700.010.71
show-cellProportionsPredictions-method000
show-deconvolutionParam-method000
show-findmarkersParam-method0.850.040.88
show-independentbulkParam-method000
show-nnlsParam-method000
show-referencebasedParam-method000
show-typemarkersParam-method0.010.000.02
sub-sub-deconvolutionParam-ANY-ANY-method000
sub-sub-typemarkersParam-ANY-ANY-method000
typemarkers-findmarkersParam-method0.940.000.93
typemarkers-typemarkersParam-method000
typemarkers000
typemarkersParam-class000
typemarkersParam000
ypb_from_sce0.120.000.13
z_matrix_from_sce0.130.000.13