Back to Multiple platform build/check report for BioC 3.13 |
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This page was generated on 2021-10-15 15:06:09 -0400 (Fri, 15 Oct 2021).
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 987/2041 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
LineagePulse 1.12.0 (landing page) David S Fischer
| nebbiolo1 | Linux (Ubuntu 20.04.2 LTS) / x86_64 | OK | OK | WARNINGS | |||||||||
tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | WARNINGS | OK | |||||||||
machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | WARNINGS | OK | |||||||||
Package: LineagePulse |
Version: 1.12.0 |
Command: C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:LineagePulse.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings LineagePulse_1.12.0.tar.gz |
StartedAt: 2021-10-15 01:08:21 -0400 (Fri, 15 Oct 2021) |
EndedAt: 2021-10-15 01:21:15 -0400 (Fri, 15 Oct 2021) |
EllapsedTime: 773.7 seconds |
RetCode: 0 |
Status: WARNINGS |
CheckDir: LineagePulse.Rcheck |
Warnings: 1 |
############################################################################## ############################################################################## ### ### Running command: ### ### C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:LineagePulse.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings LineagePulse_1.12.0.tar.gz ### ############################################################################## ############################################################################## * using log directory 'C:/Users/biocbuild/bbs-3.13-bioc/meat/LineagePulse.Rcheck' * using R version 4.1.1 (2021-08-10) * 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 '1.12.0' * 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-3.13-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 45.88 0.00 45.88 sortGeneTrajectories 16.49 0.04 16.52 getFitsDropout 16.33 0.00 16.33 cash-LineagePulseObject-method 16.24 0.00 16.23 accessors 15.89 0.22 16.11 names-LineagePulseObject-method 16.09 0.00 16.09 testDropout 15.94 0.00 15.94 getFitsDispersion 15.48 0.08 15.56 writeReport 15.20 0.02 15.22 sub-sub-LineagePulseObject-character-missing-method 15.14 0.01 15.15 getPostDrop 15.08 0.00 15.08 getNormData 14.86 0.01 14.87 runLineagePulse 14.75 0.00 14.75 getFitsMean 14.34 0.00 14.35 plotGene 13.81 0.00 13.81 ** running examples for arch 'x64' ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed plotCellDensity 48.43 0.11 48.53 plotGene 19.81 0.00 19.81 sortGeneTrajectories 19.30 0.04 19.34 accessors 18.66 0.00 18.65 sub-sub-LineagePulseObject-character-missing-method 18.50 0.02 18.52 getNormData 17.75 0.00 17.75 runLineagePulse 17.65 0.00 17.66 names-LineagePulseObject-method 17.56 0.00 17.56 cash-LineagePulseObject-method 17.44 0.01 17.45 writeReport 17.28 0.00 17.28 testDropout 17.04 0.00 17.04 getFitsMean 16.80 0.00 16.80 getFitsDropout 16.74 0.00 16.73 getFitsDispersion 16.68 0.00 16.69 getPostDrop 16.37 0.00 16.37 * 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-3.13-bioc/meat/LineagePulse.Rcheck/00check.log' for details.
LineagePulse.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### C:\cygwin\bin\curl.exe -O http://155.52.207.165/BBS/3.13/bioc/src/contrib/LineagePulse_1.12.0.tar.gz && rm -rf LineagePulse.buildbin-libdir && mkdir LineagePulse.buildbin-libdir && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=LineagePulse.buildbin-libdir LineagePulse_1.12.0.tar.gz && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL LineagePulse_1.12.0.zip && rm LineagePulse_1.12.0.tar.gz LineagePulse_1.12.0.zip ### ############################################################################## ############################################################################## % Total % Received % Xferd Average Speed Time Time Time Current Dload Upload Total Spent Left Speed 0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0 3 73196 3 2488 0 0 30193 0 0:00:02 --:--:-- 0:00:02 30341 100 73196 100 73196 0 0 350k 0 --:--:-- --:--:-- --:--:-- 350k install for i386 * 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 install for x64 * installing *source* package 'LineagePulse' ... ** testing if installed package can be loaded * MD5 sums packaged installation of 'LineagePulse' as LineagePulse_1.12.0.zip * DONE (LineagePulse) * installing to library 'C:/Users/biocbuild/bbs-3.13-bioc/R/library' package 'LineagePulse' successfully unpacked and MD5 sums checked
LineagePulse.Rcheck/examples_i386/LineagePulse-Ex.timings
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LineagePulse.Rcheck/examples_x64/LineagePulse-Ex.timings
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