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This page was generated on 2024-06-11 15:40 -0400 (Tue, 11 Jun 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 22.04.3 LTS)x86_644.4.0 RC (2024-04-16 r86468) -- "Puppy Cup" 4679
palomino4Windows Server 2022 Datacenterx644.4.0 RC (2024-04-16 r86468 ucrt) -- "Puppy Cup" 4414
merida1macOS 12.7.4 Montereyx86_644.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup" 4441
kjohnson1macOS 13.6.6 Venturaarm644.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup" 4394
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 1101/2239HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
lute 1.1.0  (landing page)
Sean K Maden
Snapshot Date: 2024-06-09 14:00 -0400 (Sun, 09 Jun 2024)
git_url: https://git.bioconductor.org/packages/lute
git_branch: devel
git_last_commit: 0986a8b
git_last_commit_date: 2024-04-30 11:52:55 -0400 (Tue, 30 Apr 2024)
nebbiolo2Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino4Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 12.7.4 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.6 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published


CHECK results for lute on palomino4

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: 1.1.0
Command: F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:lute.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings lute_1.1.0.tar.gz
StartedAt: 2024-06-10 04:38:59 -0400 (Mon, 10 Jun 2024)
EndedAt: 2024-06-10 04:45:16 -0400 (Mon, 10 Jun 2024)
EllapsedTime: 377.2 seconds
RetCode: 0
Status:   OK  
CheckDir: lute.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:lute.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings lute_1.1.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'F:/biocbuild/bbs-3.20-bioc/meat/lute.Rcheck'
* using R version 4.4.0 RC (2024-04-16 r86468 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 '1.1.0'
* 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-3.20-bioc/meat/lute.Rcheck/00check.log'
for details.


Installation output

lute.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD INSTALL lute
###
##############################################################################
##############################################################################


* installing to library 'F:/biocbuild/bbs-3.20-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-class2.960.193.30
bisqueParam2.000.082.08
cellProportionsPredictions-class0.020.000.01
cellProportionsPredictions000
deconvolution-bisqueParam-method1.530.151.69
deconvolution-deconvolutionParam-method000
deconvolution-independentbulkParam-method000
deconvolution-nnlsParam-method0.000.020.01
deconvolution-referencebasedParam-method000
deconvolution000
deconvolutionParam-class000
eset_to_sce1.420.011.44
eset_to_se0.500.020.51
findmarkersParam-class0.690.120.83
findmarkersParam0.630.040.66
getDeconvolutionExampleData000
getDeconvolutionExampleDataBisque0.360.010.37
getDeconvolutionExampleDataSCDC0.150.020.17
get_celltypes_from_sce000
get_csf_reference000
get_eset_from_matrix000
independentbulkParam-class000
independentbulkParam000
lute0.190.010.20
luteSupportedDeconvolutionAlgorithms0.000.000.02
new_workflow_table000
nnlsParam-class0.010.000.01
nnlsParam000
parseDeconvolutionPredictionsResults000
proportionsVectorsList000
randomMarkersVectorsList000
randomSingleCellExperiment0.090.010.11
referenceFromSingleCellExperiment000
referencebasedParam-class000
referencebasedParam000
rmse0.020.000.02
rmseTest000
sce_to_eset0.160.000.15
sce_to_se0.120.020.16
se_to_eset0.140.000.14
se_to_sce0.230.000.24
show-bisqueParam-method0.580.020.59
show-cellProportionsPredictions-method000
show-deconvolutionParam-method000
show-findmarkersParam-method0.700.030.74
show-independentbulkParam-method000
show-nnlsParam-method000
show-referencebasedParam-method000
show-typemarkersParam-method000
sub-sub-deconvolutionParam-ANY-ANY-method000
sub-sub-typemarkersParam-ANY-ANY-method000
typemarkers-findmarkersParam-method0.690.010.70
typemarkers-typemarkersParam-method000
typemarkers000
typemarkersParam-class000
typemarkersParam000
ypb_from_sce0.130.020.14
z_matrix_from_sce0.120.010.14