CHECK report for LineagePulse on tokay1
This page was generated on 2019-04-13 11:28:39 -0400 (Sat, 13 Apr 2019).
LineagePulse 1.2.1
David S Fischer
| Snapshot Date: 2019-04-12 17:01:30 -0400 (Fri, 12 Apr 2019) |
| URL: https://git.bioconductor.org/packages/LineagePulse |
| Branch: RELEASE_3_8 |
| Last Commit: 1ec2a20 |
| Last Changed Date: 2019-01-04 13:15:17 -0400 (Fri, 04 Jan 2019) |
| malbec1 | Linux (Ubuntu 16.04.6 LTS) / x86_64 | OK | OK | WARNINGS | |  |
| tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | [ WARNINGS ] | OK | |
| merida1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | WARNINGS | OK | |
Summary
Command output
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### Running command:
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### C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:LineagePulse.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings LineagePulse_1.2.1.tar.gz
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* using log directory 'C:/Users/biocbuild/bbs-3.8-bioc/meat/LineagePulse.Rcheck'
* using R version 3.5.3 (2019-03-11)
* 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 '1.2.1'
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
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-3.8-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 or elapsed time > 5s
user system elapsed
plotCellDensity 38.32 0.03 38.34
getFitsDispersion 12.73 0.03 12.77
accessors 12.56 0.17 12.73
cash-LineagePulseObject-method 12.66 0.02 12.67
sub-sub-LineagePulseObject-character-missing-method 12.67 0.00 12.67
getPostDrop 12.61 0.00 12.61
writeReport 12.53 0.00 12.53
getFitsDropout 12.20 0.01 12.22
names-LineagePulseObject-method 12.14 0.00 12.14
getNormData 12.11 0.02 12.12
getFitsMean 11.77 0.02 11.78
testDropout 10.17 0.00 10.17
plotGene 9.79 0.00 9.80
sortGeneTrajectories 9.78 0.00 9.78
runLineagePulse 9.74 0.00 9.73
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
plotCellDensity 41.97 0.01 41.99
getFitsDropout 17.16 0.02 17.17
getFitsDispersion 16.28 0.05 16.33
getFitsMean 16.31 0.01 16.33
names-LineagePulseObject-method 15.38 0.02 15.39
cash-LineagePulseObject-method 15.36 0.02 15.37
getNormData 15.05 0.00 15.04
getPostDrop 14.54 0.00 14.55
accessors 14.46 0.06 14.51
writeReport 14.25 0.00 14.25
sub-sub-LineagePulseObject-character-missing-method 14.22 0.00 14.22
testDropout 11.25 0.00 11.25
plotGene 11.22 0.00 11.22
sortGeneTrajectories 11.14 0.02 11.15
runLineagePulse 10.89 0.01 10.91
* 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-3.8-bioc/meat/LineagePulse.Rcheck/00check.log'
for details.
Installation output
LineagePulse.Rcheck/00install.out
Tests output
Example timings
|
LineagePulse.Rcheck/examples_i386/LineagePulse-Ex.timings
|
LineagePulse.Rcheck/examples_x64/LineagePulse-Ex.timings
|