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This page was generated on 2024-11-20 12:07 -0500 (Wed, 20 Nov 2024).

HostnameOSArch (*)R versionInstalled pkgs
teran2Linux (Ubuntu 24.04.1 LTS)x86_644.4.2 (2024-10-31) -- "Pile of Leaves" 4481
nebbiolo2Linux (Ubuntu 24.04.1 LTS)x86_644.4.2 (2024-10-31) -- "Pile of Leaves" 4479
palomino8Windows Server 2022 Datacenterx644.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" 4359
lconwaymacOS 12.7.1 Montereyx86_644.4.1 (2024-06-14) -- "Race for Your Life" 4539
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch644.4.1 (2024-06-14) -- "Race for Your Life" 4493
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 1125/2289HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
lute 1.2.0  (landing page)
Sean K Maden
Snapshot Date: 2024-11-19 13:40 -0500 (Tue, 19 Nov 2024)
git_url: https://git.bioconductor.org/packages/lute
git_branch: RELEASE_3_20
git_last_commit: 566aeec
git_last_commit_date: 2024-10-29 11:25:42 -0500 (Tue, 29 Oct 2024)
teran2Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
nebbiolo2Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    OK  
palomino8Windows 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  


CHECK results for lute on kunpeng2

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: 1.2.0
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_1.2.0.tar.gz
StartedAt: 2024-11-20 09:22:42 -0000 (Wed, 20 Nov 2024)
EndedAt: 2024-11-20 09:27:06 -0000 (Wed, 20 Nov 2024)
EllapsedTime: 264.5 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_1.2.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/lute.Rcheck’
* using R version 4.4.1 (2024-06-14)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
    gcc (GCC) 12.2.1 20220819 (openEuler 12.2.1-14)
    GNU Fortran (GCC) 10.3.1
* running under: openEuler 22.03 (LTS-SP1)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘lute/DESCRIPTION’ ... OK
* this is package ‘lute’ version ‘1.2.0’
* 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’ ... 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: 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.20-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-4.4.1/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-class4.8940.0564.875
bisqueParam2.0720.0041.994
cellProportionsPredictions-class0.0150.0000.016
cellProportionsPredictions0.0000.0000.001
deconvolution-bisqueParam-method2.1350.0322.086
deconvolution-deconvolutionParam-method0.0010.0000.001
deconvolution-independentbulkParam-method0.0020.0000.002
deconvolution-nnlsParam-method0.0140.0000.014
deconvolution-referencebasedParam-method0.0030.0000.003
deconvolution0.0040.0000.004
deconvolutionParam-class000
eset_to_sce0.5210.0040.527
eset_to_se0.3820.0000.384
findmarkersParam-class0.8850.0120.899
findmarkersParam0.6930.0680.763
getDeconvolutionExampleData000
getDeconvolutionExampleDataBisque0.3860.0160.402
getDeconvolutionExampleDataSCDC0.1490.0120.161
get_celltypes_from_sce000
get_csf_reference000
get_eset_from_matrix000
independentbulkParam-class0.0010.0000.001
independentbulkParam0.0010.0000.001
lute0.150.000.15
luteSupportedDeconvolutionAlgorithms0.0060.0000.007
new_workflow_table0.0010.0000.001
nnlsParam-class0.0070.0000.007
nnlsParam0.0060.0000.006
parseDeconvolutionPredictionsResults000
proportionsVectorsList000
randomMarkersVectorsList0.0010.0000.001
randomSingleCellExperiment0.0740.0000.074
referenceFromSingleCellExperiment0.0000.0010.001
referencebasedParam-class0.0000.0020.002
referencebasedParam0.0020.0000.002
rmse0.0010.0000.001
rmseTest000
sce_to_eset0.1170.0080.126
sce_to_se0.1030.0000.103
se_to_eset0.1300.0040.135
se_to_sce0.1160.0000.116
show-bisqueParam-method1.3760.0361.414
show-cellProportionsPredictions-method0.0000.0000.001
show-deconvolutionParam-method000
show-findmarkersParam-method0.7200.0160.738
show-independentbulkParam-method0.0010.0000.001
show-nnlsParam-method0.0000.0020.002
show-referencebasedParam-method0.0010.0020.002
show-typemarkersParam-method0.0010.0000.001
sub-sub-deconvolutionParam-ANY-ANY-method000
sub-sub-typemarkersParam-ANY-ANY-method000
typemarkers-findmarkersParam-method0.7120.0000.714
typemarkers-typemarkersParam-method000
typemarkers000
typemarkersParam-class000
typemarkersParam000
ypb_from_sce0.1530.0000.155
z_matrix_from_sce0.0910.0000.092