CHECK report for LineagePulse on tokay1
This page was generated on 2021-05-06 12:31:57 -0400 (Thu, 06 May 2021).
To the developers/maintainers of the LineagePulse package:
Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
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| LineagePulse 1.10.0 (landing page)
David S Fischer
| Snapshot Date: 2021-05-05 14:51:38 -0400 (Wed, 05 May 2021) |
| URL: https://git.bioconductor.org/packages/LineagePulse |
| Branch: RELEASE_3_12 |
| Last Commit: 9ccb5a6 |
| Last Changed Date: 2020-10-27 11:30:28 -0400 (Tue, 27 Oct 2020) |
| malbec1 | Linux (Ubuntu 18.04.5 LTS) / x86_64 | OK | OK | WARNINGS | |  | |
| tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | WARNINGS | OK | | |
| merida1 | macOS 10.14.6 Mojave / x86_64 | OK | OK | WARNINGS | OK | | |
Summary
Command output
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### Running command:
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### C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:LineagePulse.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings LineagePulse_1.10.0.tar.gz
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* using log directory 'C:/Users/biocbuild/bbs-3.12-bioc/meat/LineagePulse.Rcheck'
* using R version 4.0.5 (2021-03-31)
* 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 '1.10.0'
* 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 'C:/Users/biocbuild/bbs-3.12-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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 ...
** running examples for arch 'i386' ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
plotCellDensity 46.95 0.00 46.95
runLineagePulse 20.49 0.00 20.49
sortGeneTrajectories 19.56 0.04 19.61
testDropout 19.52 0.00 19.53
sub-sub-LineagePulseObject-character-missing-method 19.50 0.00 19.50
plotGene 18.47 0.00 18.48
writeReport 17.08 0.00 17.08
getFitsMean 15.86 0.00 15.86
accessors 15.61 0.18 15.79
getFitsDispersion 15.60 0.11 15.70
getFitsDropout 15.64 0.02 15.66
getPostDrop 15.53 0.02 15.55
cash-LineagePulseObject-method 15.34 0.02 15.36
getNormData 15.30 0.01 15.31
names-LineagePulseObject-method 14.89 0.00 14.89
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
plotCellDensity 54.50 0.01 54.52
writeReport 26.16 0.00 26.20
getFitsMean 22.97 0.00 22.97
getNormData 22.20 0.05 22.25
testDropout 22.18 0.00 22.19
getFitsDropout 21.88 0.00 21.87
names-LineagePulseObject-method 20.89 0.00 20.89
runLineagePulse 20.82 0.00 20.81
sub-sub-LineagePulseObject-character-missing-method 20.66 0.00 20.66
plotGene 19.53 0.00 19.53
getFitsDispersion 19.47 0.00 19.47
sortGeneTrajectories 18.70 0.02 18.72
cash-LineagePulseObject-method 18.14 0.02 18.15
getPostDrop 18.06 0.00 18.06
accessors 17.77 0.03 17.80
* 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
'C:/Users/biocbuild/bbs-3.12-bioc/meat/LineagePulse.Rcheck/00check.log'
for details.
Installation output
LineagePulse.Rcheck/00install.out
Tests output
Example timings
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LineagePulse.Rcheck/examples_i386/LineagePulse-Ex.timings
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LineagePulse.Rcheck/examples_x64/LineagePulse-Ex.timings
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