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This page was generated on 2024-12-24 11:45 -0500 (Tue, 24 Dec 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.1 LTS)x86_64R Under development (unstable) (2024-10-21 r87258) -- "Unsuffered Consequences" 4754
palomino7Windows Server 2022 Datacenterx64R Under development (unstable) (2024-10-26 r87273 ucrt) -- "Unsuffered Consequences" 4472
lconwaymacOS 12.7.1 Montereyx86_64R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" 4426
kjohnson3macOS 13.7.1 Venturaarm64R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" 4381
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch64R Under development (unstable) (2024-11-24 r87369) -- "Unsuffered Consequences" 4373
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 1119/2274HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
lute 1.3.0  (landing page)
Sean K Maden
Snapshot Date: 2024-12-23 13:40 -0500 (Mon, 23 Dec 2024)
git_url: https://git.bioconductor.org/packages/lute
git_branch: devel
git_last_commit: 449b0aa
git_last_commit_date: 2024-10-29 11:25:42 -0500 (Tue, 29 Oct 2024)
nebbiolo1Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino7Windows 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
kjohnson3macOS 13.7.1 Ventura / arm64  OK    OK    OK    OK  NO, package depends on 'scran' which is only available as a source package that needs compilation
kunpeng2Linux (openEuler 22.03 LTS-SP1) / aarch64  OK    OK    OK  


CHECK results for lute on kjohnson3

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: 1.3.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:lute.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings lute_1.3.0.tar.gz
StartedAt: 2024-12-23 19:57:48 -0500 (Mon, 23 Dec 2024)
EndedAt: 2024-12-23 19:59:06 -0500 (Mon, 23 Dec 2024)
EllapsedTime: 78.1 seconds
RetCode: 0
Status:   OK  
CheckDir: lute.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:lute.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings lute_1.3.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/lute.Rcheck’
* using R Under development (unstable) (2024-11-20 r87352)
* using platform: aarch64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Ventura 13.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘lute/DESCRIPTION’ ... OK
* this is package ‘lute’ version ‘1.3.0’
* 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 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
  ‘/Users/biocbuild/bbs-3.21-bioc/meat/lute.Rcheck/00check.log’
for details.


Installation output

lute.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL lute
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/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-class1.1070.0531.169
bisqueParam0.4240.0210.446
cellProportionsPredictions-class0.0050.0000.006
cellProportionsPredictions0.0000.0000.001
deconvolution-bisqueParam-method0.9720.0351.017
deconvolution-deconvolutionParam-method0.0000.0010.000
deconvolution-independentbulkParam-method0.0010.0000.000
deconvolution-nnlsParam-method0.0040.0010.005
deconvolution-referencebasedParam-method0.0010.0000.001
deconvolution0.0010.0000.001
deconvolutionParam-class000
eset_to_sce0.1860.0030.188
eset_to_se0.1590.0050.164
findmarkersParam-class0.2120.0120.223
findmarkersParam0.1580.0040.163
getDeconvolutionExampleData000
getDeconvolutionExampleDataBisque0.1490.0010.152
getDeconvolutionExampleDataSCDC0.0310.0000.031
get_celltypes_from_sce000
get_csf_reference000
get_eset_from_matrix0.0000.0000.001
independentbulkParam-class0.0010.0000.000
independentbulkParam000
lute0.0320.0000.033
luteSupportedDeconvolutionAlgorithms0.0020.0000.003
new_workflow_table0.0000.0010.001
nnlsParam-class0.0020.0000.002
nnlsParam0.0010.0000.001
parseDeconvolutionPredictionsResults0.0000.0000.001
proportionsVectorsList0.0010.0000.000
randomMarkersVectorsList000
randomSingleCellExperiment0.0140.0000.014
referenceFromSingleCellExperiment000
referencebasedParam-class000
referencebasedParam0.0010.0000.000
rmse0.0000.0010.001
rmseTest000
sce_to_eset0.0290.0010.030
sce_to_se0.0190.0000.019
se_to_eset0.0260.0010.026
se_to_sce0.0230.0010.024
show-bisqueParam-method0.1760.0030.183
show-cellProportionsPredictions-method000
show-deconvolutionParam-method000
show-findmarkersParam-method0.1530.0020.155
show-independentbulkParam-method000
show-nnlsParam-method0.0010.0000.000
show-referencebasedParam-method0.0000.0000.001
show-typemarkersParam-method000
sub-sub-deconvolutionParam-ANY-ANY-method0.0000.0000.001
sub-sub-typemarkersParam-ANY-ANY-method000
typemarkers-findmarkersParam-method0.1470.0010.148
typemarkers-typemarkersParam-method0.0000.0000.001
typemarkers000
typemarkersParam-class000
typemarkersParam0.0000.0000.001
ypb_from_sce0.0210.0010.020
z_matrix_from_sce0.0180.0000.018