Back to Multiple platform build/check report for BioC 3.18: simplified long | |
This page was generated on 2023-07-08 11:37:01 -0400 (Sat, 08 Jul 2023).
Hostname | OS | Arch (*) | R version | Installed pkgs |
nebbiolo2 | Linux (Ubuntu 22.04.2 LTS) | x86_64 | 4.3.1 (2023-06-16) -- "Beagle Scouts"
| 4610 |
palomino4 | Windows Server 2022 Datacenter | x64 | 4.3.1 (2023-06-16 ucrt) -- "Beagle Scouts"
| 4344 |
lconway | macOS 12.6.5 Monterey | x86_64 | 4.3.1 Patched (2023-06-17 r84564) -- "Beagle Scouts"
| 4350 |
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | 4.3.1 (2023-06-16) -- "Beagle Scouts"
| 4347 |
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 |
| LineagePulse 1.21.0 (landing page) David S Fischer
Snapshot Date: 2023-07-07 14:05:07 -0400 (Fri, 07 Jul 2023) |
git_url: https://git.bioconductor.org/packages/LineagePulse |
git_branch: devel |
git_last_commit: c714473 |
git_last_commit_date: 2023-04-25 10:58:25 -0400 (Tue, 25 Apr 2023) |
| nebbiolo2 | Linux (Ubuntu 22.04.2 LTS) / x86_64 | OK | OK | WARNINGS | | | |
| palomino4 | Windows Server 2022 Datacenter / x64 | OK | OK | WARNINGS | OK | | |
| lconway | macOS 12.6.5 Monterey / x86_64 | OK | OK | WARNINGS | OK | | |
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | WARNINGS | | | |
CHECK results for LineagePulse on palomino4
The builds on kunpeng2 (Linux ARM64) are experimental! |
To the developers/maintainers of the LineagePulse package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/LineagePulse.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
Command output
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### Running command:
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### F:\biocbuild\bbs-3.18-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:LineagePulse.install-out.txt --library=F:\biocbuild\bbs-3.18-bioc\R\library --no-vignettes --timings LineagePulse_1.21.0.tar.gz
###
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* using log directory 'F:/biocbuild/bbs-3.18-bioc/meat/LineagePulse.Rcheck'
* using R version 4.3.1 (2023-06-16 ucrt)
* using platform: x86_64-w64-mingw32 (64-bit)
* R was compiled by
gcc.exe (GCC) 12.2.0
GNU Fortran (GCC) 12.2.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'LineagePulse/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'LineagePulse' version '1.21.0'
* 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 'LineagePulse' can be installed ... WARNING
Found the following significant warnings:
Note: possible error in 'evalLogLikGeneMM(vecCounts = vecCounts, ': unused arguments (matDispParam = matDispParam, matDropParam = matDropParam, matWeights = matWeights)
Note: possible error in 'evalLogLikGeneMM(vecCounts = vecCounts, ': unused arguments (matDispParam = do.call(cbind, lapply(seq_len(ncol(matWeights)), function(m) vecDispParam)), matDropParam = do.call(cbind, lapply(seq_len(ncol(matWeights)), function(m) vecPiParam)), matWeights = matWeights)
See 'F:/biocbuild/bbs-3.18-bioc/meat/LineagePulse.Rcheck/00install.out' for details.
Information on the location(s) of code generating the 'Note's can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to 'yes'.
* 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 ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
decompressDispByGeneMM: no visible binding for global variable
'lsDispModel'
evalLogLikMatrix : <anonymous>: possible error in
evalLogLikGeneMM(vecCounts = vecCounts, matMuParam = matMuParam,
vecNormConst = lsMuModel$lsMuModelGlobal$vecNormConst, matDispParam =
matDispParam, matDropParam = matDropParam, matWeights = matWeights,
vecidxNotZero = which(!is.na(vecCounts) & vecCounts > 0), vecidxZero
= which(!is.na(vecCounts) & vecCounts == 0), scaNCells =
length(vecCounts)): unused arguments (matDispParam = matDispParam,
matDropParam = matDropParam, matWeights = matWeights)
evalLogLikMatrix : <anonymous>: possible error in
evalLogLikGeneMM(vecCounts = vecCounts, matMuParam = do.call(cbind,
lapply(seq_len(ncol(matWeights)), function(m) vecMuParam)),
vecNormConst = lsMuModel$lsMuModelGlobal$vecNormConst, matDispParam =
do.call(cbind, lapply(seq_len(ncol(matWeights)), function(m)
vecDispParam)), matDropParam = do.call(cbind,
lapply(seq_len(ncol(matWeights)), function(m) vecPiParam)),
matWeights = matWeights, vecidxNotZero = which(!is.na(vecCounts) &
vecCounts > 0), vecidxZero = which(!is.na(vecCounts) & vecCounts ==
0), : unused arguments (matDispParam = do.call(cbind,
lapply(seq_len(ncol(matWeights)), function(m) vecDispParam)),
matDropParam = do.call(cbind, lapply(seq_len(ncol(matWeights)),
function(m) vecPiParam)), matWeights = matWeights)
evalLogLikMatrix : <anonymous>: possible error in scaNCells =
length(vecCounts)): unused arguments (matDispParam = do.call(cbind,
lapply(seq_len(ncol(matWeights)), function(m) vecDispParam)),
matDropParam = do.call(cbind, lapply(seq_len(ncol(matWeights)),
function(m) vecPiParam)), matWeights = matWeights)
plotCellDensity: no visible binding for global variable 'continuous'
plotGene: no visible binding for global variable 'x'
plotGene: no visible binding for global variable 'dropout_posterior'
plotGene: no visible binding for global variable 'groups'
plotGene: no visible binding for global variable 'dfAnnot'
plotGene: no visible binding for global variable 'mean_count'
plotGene: no visible binding for global variable 'quantile_25'
plotGene: no visible binding for global variable 'quantile_75'
plotGene: no visible binding for global variable 'model'
plotGene: no visible binding for global variable 'continuous'
plotGene: no visible binding for global variable 'trajectory_contour'
plotGene: no visible binding for global variable 'ncells'
Undefined global functions or variables:
continuous dfAnnot dropout_posterior groups lsDispModel mean_count
model ncells quantile_25 quantile_75 trajectory_contour x
* 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
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
plotCellDensity 37.25 0.12 37.37
accessors 19.30 0.05 19.34
writeReport 18.78 0.03 18.81
sub-sub-LineagePulseObject-character-missing-method 17.48 0.03 17.52
names-LineagePulseObject-method 16.96 0.05 17.02
cash-LineagePulseObject-method 16.84 0.03 16.88
getFitsDispersion 16.75 0.06 16.81
getFitsMean 16.76 0.01 16.79
getFitsDropout 16.57 0.05 16.61
getPostDrop 16.50 0.03 16.53
getNormData 16.32 0.02 16.33
testDropout 14.61 0.03 14.64
sortGeneTrajectories 14.36 0.05 14.47
runLineagePulse 14.17 0.06 14.24
plotGene 14.19 0.00 14.19
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in 'inst/doc' ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: 1 WARNING, 1 NOTE
See
'F:/biocbuild/bbs-3.18-bioc/meat/LineagePulse.Rcheck/00check.log'
for details.
Installation output
LineagePulse.Rcheck/00install.out
Tests output
Example timings
LineagePulse.Rcheck/LineagePulse-Ex.timings