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This page was generated on 2024-07-12 17:38 -0400 (Fri, 12 Jul 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_644.4.1 (2024-06-14) -- "Race for Your Life" 4741
palomino7Windows Server 2022 Datacenterx644.4.1 (2024-06-14 ucrt) -- "Race for Your Life" 4483
merida1macOS 12.7.4 Montereyx86_644.4.1 (2024-06-14) -- "Race for Your Life" 4512
kjohnson1macOS 13.6.6 Venturaarm644.4.1 (2024-06-14) -- "Race for Your Life" 4461
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: 2024-07-10 14:00 -0400 (Wed, 10 Jul 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
palomino7Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  
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 nebbiolo1

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: /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:lute.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings lute_1.0.0.tar.gz
StartedAt: 2024-07-11 00:28:03 -0400 (Thu, 11 Jul 2024)
EndedAt: 2024-07-11 00:32:15 -0400 (Thu, 11 Jul 2024)
EllapsedTime: 251.7 seconds
RetCode: 0
Status:   OK  
CheckDir: lute.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:lute.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings lute_1.0.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/lute.Rcheck’
* using R version 4.4.1 (2024-06-14)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
    GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
* running under: Ubuntu 22.04.4 LTS
* using session charset: UTF-8
* 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 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 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 re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 3 NOTEs
See
  ‘/home/biocbuild/bbs-3.19-bioc/meat/lute.Rcheck/00check.log’
for details.


Installation output

lute.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD INSTALL lute
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.19-bioc/R/site-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-class2.9360.1723.108
bisqueParam1.8770.0161.893
cellProportionsPredictions-class0.0150.0000.015
cellProportionsPredictions000
deconvolution-bisqueParam-method2.0670.0962.163
deconvolution-deconvolutionParam-method0.0010.0000.000
deconvolution-independentbulkParam-method0.0020.0000.001
deconvolution-nnlsParam-method0.0130.0000.013
deconvolution-referencebasedParam-method0.0030.0000.003
deconvolution0.0040.0000.004
deconvolutionParam-class000
eset_to_sce0.5910.0230.615
eset_to_se0.3820.0130.393
findmarkersParam-class0.7360.0440.779
findmarkersParam0.5940.0280.622
getDeconvolutionExampleData0.0000.0000.001
getDeconvolutionExampleDataBisque0.3610.0000.361
getDeconvolutionExampleDataSCDC0.1670.0000.166
get_celltypes_from_sce0.0000.0000.001
get_csf_reference000
get_eset_from_matrix0.0010.0000.000
independentbulkParam-class0.0010.0000.001
independentbulkParam0.0010.0000.001
lute0.1890.0000.189
luteSupportedDeconvolutionAlgorithms0.0000.0060.007
new_workflow_table0.0000.0000.001
nnlsParam-class0.0050.0000.005
nnlsParam0.0040.0000.005
parseDeconvolutionPredictionsResults000
proportionsVectorsList0.0000.0000.001
randomMarkersVectorsList0.0000.0010.000
randomSingleCellExperiment0.1190.0030.121
referenceFromSingleCellExperiment0.0000.0000.001
referencebasedParam-class0.0020.0000.001
referencebasedParam0.0020.0000.002
rmse0.0010.0000.001
rmseTest000
sce_to_eset0.1630.0080.171
sce_to_se0.1280.0080.136
se_to_eset0.1490.0030.153
se_to_sce0.1480.0040.151
show-bisqueParam-method0.5130.0010.513
show-cellProportionsPredictions-method000
show-deconvolutionParam-method000
show-findmarkersParam-method0.5930.0080.600
show-independentbulkParam-method0.0010.0000.001
show-nnlsParam-method0.0020.0000.002
show-referencebasedParam-method0.0010.0000.001
show-typemarkersParam-method000
sub-sub-deconvolutionParam-ANY-ANY-method0.0000.0000.001
sub-sub-typemarkersParam-ANY-ANY-method0.0000.0010.000
typemarkers-findmarkersParam-method0.5780.0150.593
typemarkers-typemarkersParam-method0.0010.0000.001
typemarkers0.0010.0000.001
typemarkersParam-class0.0010.0000.000
typemarkersParam0.0010.0000.000
ypb_from_sce0.1430.0040.147
z_matrix_from_sce0.1300.0000.131