David S Fischer
| Snapshot Date: 2022-03-17 13:55:23 -0400 (Thu, 17 Mar 2022) |
| git_url: https://git.bioconductor.org/packages/LineagePulse |
| git_branch: master |
| git_last_commit: f1d6a55 |
| git_last_commit_date: 2021-10-26 12:40:27 -0400 (Tue, 26 Oct 2021) |
| Back to Multiple platform build/check report for BioC 3.15 |
|
This page was generated on 2022-03-18 11:07:52 -0400 (Fri, 18 Mar 2022).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 20.04.4 LTS) | x86_64 | R Under development (unstable) (2022-02-17 r81757) -- "Unsuffered Consequences" | 4334 |
| riesling1 | Windows Server 2019 Standard | x64 | R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences" | 4097 |
| palomino3 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2022-02-17 r81757 ucrt) -- "Unsuffered Consequences" | 4083 |
| merida1 | macOS 10.14.6 Mojave | x86_64 | R Under development (unstable) (2022-03-02 r81842) -- "Unsuffered Consequences" | 4134 |
| 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 | ||||
|
To the developers/maintainers of the LineagePulse package: - Please 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 How and When does the builder pull? When will my changes propagate? here for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 1001/2090 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| LineagePulse 1.15.0 (landing page) David S Fischer
| nebbiolo1 | Linux (Ubuntu 20.04.4 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||||
| riesling1 | Windows Server 2019 Standard / x64 | OK | OK | WARNINGS | OK | |||||||||
| palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | WARNINGS | OK | | ||||||||
| merida1 | macOS 10.14.6 Mojave / x86_64 | OK | OK | WARNINGS | OK | | ||||||||
| Package: LineagePulse |
| Version: 1.15.0 |
| Command: D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:LineagePulse.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings LineagePulse_1.15.0.tar.gz |
| StartedAt: 2022-03-17 19:26:35 -0400 (Thu, 17 Mar 2022) |
| EndedAt: 2022-03-17 19:32:15 -0400 (Thu, 17 Mar 2022) |
| EllapsedTime: 340.4 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: LineagePulse.Rcheck |
| Warnings: 1 |
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###
### Running command:
###
### D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:LineagePulse.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings LineagePulse_1.15.0.tar.gz
###
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* using log directory 'D:/biocbuild/bbs-3.15-bioc/meat/LineagePulse.Rcheck'
* using R Under development (unstable) (2021-11-21 r81221)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'LineagePulse/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'LineagePulse' version '1.15.0'
* 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 'D:/biocbuild/bbs-3.15-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 28.06 0.19 28.25
sub-sub-LineagePulseObject-character-missing-method 15.00 0.00 15.00
writeReport 13.44 0.00 13.44
accessors 12.32 0.03 12.35
cash-LineagePulseObject-method 12.04 0.00 12.04
names-LineagePulseObject-method 11.78 0.00 11.78
getNormData 11.64 0.00 11.64
getFitsMean 11.48 0.00 11.49
getFitsDispersion 11.44 0.00 11.44
getPostDrop 11.41 0.00 11.41
getFitsDropout 11.33 0.00 11.32
runLineagePulse 10.78 0.00 10.78
testDropout 10.39 0.00 10.39
sortGeneTrajectories 10.33 0.00 10.33
plotGene 9.88 0.00 9.87
* 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
'D:/biocbuild/bbs-3.15-bioc/meat/LineagePulse.Rcheck/00check.log'
for details.
LineagePulse.Rcheck/00install.out
##############################################################################
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###
### Running command:
###
### D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL LineagePulse
###
##############################################################################
##############################################################################
* installing to library 'D:/biocbuild/bbs-3.15-bioc/R/library'
* installing *source* package 'LineagePulse' ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
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)
** help
*** installing help indices
converting help for package 'LineagePulse'
finding HTML links ... done
LPsetters html
LineagePulseObject-class html
accessors html
calcNormConst html
calcPostDrop_Matrix html
calcPostDrop_Vector html
cash-LineagePulseObject-method html
decompressDispByGene html
decompressDispByGeneMM html
decompressDropoutRateByCell html
decompressDropoutRateByGene html
decompressMeansByGene html
decompressMuByGeneMM html
evalDropoutModel html
evalDropoutModel_comp html
evalImpulseModel html
evalImpulseModel_comp html
evalLogLikGene html
evalLogLikGeneMM html
evalLogLikMatrix html
evalLogLikMuDispGeneFit html
evalLogLikMuDispGeneFit_comp html
evalLogLikNB html
evalLogLikNB_comp html
evalLogLikPiZINB_ManyCells html
evalLogLikPiZINB_ManyCells_comp html
evalLogLikPiZINB_SingleCell html
evalLogLikPiZINB_SingleCell_comp html
evalLogLikZINB html
evalLogLikZINB_comp html
fitLPModels html
fitModel html
fitMuDisp html
fitMuDispGene html
fitMuDispGeneImpulse html
fitMuDispGeneMM html
fitPi html
fitPi_ManyCells html
fitPi_SingleCell html
getFitsDispersion html
getFitsDropout html
getFitsMean html
getNormData html
getPostDrop html
initDispModel html
initDropModel html
initMuModel html
initialiseImpulseParameters html
names-LineagePulseObject-method html
plotCellDensity html
plotGene html
processSCData html
runDEAnalysis html
runLineagePulse html
simulateContinuousDataSet html
sortGeneTrajectories html
sub-sub-LineagePulseObject-character-missing-method
html
testDropout html
writeReport html
** 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 (LineagePulse)
Making 'packages.html' ...Warning in packageDescription(i, lib.loc = lib, fields = "Title", encoding = "UTF-8") :
DESCRIPTION file of package 'LRcell' is missing or broken
done
LineagePulse.Rcheck/LineagePulse-Ex.timings
| name | user | system | elapsed | |
| accessors | 12.32 | 0.03 | 12.35 | |
| cash-LineagePulseObject-method | 12.04 | 0.00 | 12.04 | |
| getFitsDispersion | 11.44 | 0.00 | 11.44 | |
| getFitsDropout | 11.33 | 0.00 | 11.32 | |
| getFitsMean | 11.48 | 0.00 | 11.49 | |
| getNormData | 11.64 | 0.00 | 11.64 | |
| getPostDrop | 11.41 | 0.00 | 11.41 | |
| names-LineagePulseObject-method | 11.78 | 0.00 | 11.78 | |
| plotCellDensity | 28.06 | 0.19 | 28.25 | |
| plotGene | 9.88 | 0.00 | 9.87 | |
| runLineagePulse | 10.78 | 0.00 | 10.78 | |
| simulateContinuousDataSet | 0.01 | 0.00 | 0.02 | |
| sortGeneTrajectories | 10.33 | 0.00 | 10.33 | |
| sub-sub-LineagePulseObject-character-missing-method | 15 | 0 | 15 | |
| testDropout | 10.39 | 0.00 | 10.39 | |
| writeReport | 13.44 | 0.00 | 13.44 | |