Back to Multiple platform build/check report for BioC 3.13 |
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This page was generated on 2021-10-15 15:06:51 -0400 (Fri, 15 Oct 2021).
To the developers/maintainers of the scAlign package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/scAlign.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 1679/2041 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
scAlign 1.6.0 (landing page) Nelson Johansen
| 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: scAlign |
Version: 1.6.0 |
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:scAlign.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings scAlign_1.6.0.tar.gz |
StartedAt: 2021-10-14 23:34:29 -0400 (Thu, 14 Oct 2021) |
EndedAt: 2021-10-14 23:39:35 -0400 (Thu, 14 Oct 2021) |
EllapsedTime: 305.4 seconds |
RetCode: 0 |
Status: WARNINGS |
CheckDir: scAlign.Rcheck |
Warnings: 1 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:scAlign.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings scAlign_1.6.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.13-bioc/meat/scAlign.Rcheck’ * using R version 4.1.1 (2021-08-10) * using platform: x86_64-apple-darwin17.0 (64-bit) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘scAlign/DESCRIPTION’ ... OK * this is package ‘scAlign’ version ‘1.6.0’ * package encoding: UTF-8 * checking package namespace information ... OK * checking package dependencies ... NOTE Depends: includes the non-default packages: 'SingleCellExperiment', 'Seurat', 'tensorflow', 'purrr', 'irlba', 'Rtsne', 'ggplot2', 'FNN' Adding so many packages to the search path is excessive and importing selectively is preferable. * checking if this is a source package ... OK * checking if there is a namespace ... OK * checking for hidden files and directories ... NOTE Found the following hidden files and directories: .BBSoptions .git_fetch_output.txt .git_merge_output.txt These were most likely included in error. See section ‘Package structure’ in the ‘Writing R Extensions’ manual. * checking for portable file names ... OK * checking for sufficient/correct file permissions ... OK * checking whether package ‘scAlign’ can be installed ... OK * checking installed package size ... OK * checking package directory ... OK * checking ‘build’ directory ... OK * checking DESCRIPTION meta-information ... OK * checking top-level files ... NOTE File LICENSE is not mentioned in the DESCRIPTION file. * 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 .check_all_args: no visible global function definition for ‘metadata’ .check_all_args: no visible global function definition for ‘assays’ .data_setup: no visible global function definition for ‘assays’ .data_setup: no visible global function definition for ‘assay’ PlotTSNE: no visible global function definition for ‘assays’ PlotTSNE: no visible binding for global variable ‘scAlignHSC’ PlotTSNE: no visible global function definition for ‘assay’ scAlign: no visible global function definition for ‘metadata’ scAlign: no visible global function definition for ‘metadata<-’ scAlignCreateObject: no visible global function definition for ‘colData<-’ scAlignCreateObject: no visible global function definition for ‘metadata’ scAlignCreateObject: no visible global function definition for ‘metadata<-’ scAlignCreateObject: no visible global function definition for ‘assays’ scAlignCreateObject: no visible global function definition for ‘assay’ scAlignCreateObject: no visible global function definition for ‘GetCellEmbeddings’ scAlignCreateObject: no visible global function definition for ‘GetGeneLoadings’ scAlignCreateObject : <anonymous>: no visible global function definition for ‘assay’ scAlignMulti: no visible global function definition for ‘metadata’ scAlignMulti: no visible global function definition for ‘metadata<-’ scAlignMulti: no visible global function definition for ‘assays’ scAlignMulti: no visible global function definition for ‘assay’ Undefined global functions or variables: GetCellEmbeddings GetGeneLoadings assay assays colData<- metadata metadata<- scAlignHSC * 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 contents of ‘data’ directory ... WARNING Files not of a type allowed in a ‘data’ directory: ‘DESCRIPTION’ ‘LICENSE’ ‘NAMESPACE’ ‘NEWS’ ‘README.md’ Please use e.g. ‘inst/extdata’ for non-R data files * checking data for non-ASCII characters ... OK * checking data for ASCII and uncompressed saves ... OK * checking sizes of PDF files under ‘inst/doc’ ... OK * checking files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed PlotTSNE 41.763 14.370 20.842 scAlign 6.584 0.351 6.428 scAlignMulti 6.372 0.160 6.245 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘testthat.R’ OK * 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, 4 NOTEs See ‘/Users/biocbuild/bbs-3.13-bioc/meat/scAlign.Rcheck/00check.log’ for details.
scAlign.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL scAlign ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.1/Resources/library’ * installing *source* package ‘scAlign’ ... ** using staged installation ** R ** data ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** 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 (scAlign)
scAlign.Rcheck/tests/testthat.Rout
R version 4.1.1 (2021-08-10) -- "Kick Things" Copyright (C) 2021 The R Foundation for Statistical Computing Platform: x86_64-apple-darwin17.0 (64-bit) R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type 'license()' or 'licence()' for distribution details. R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R or R packages in publications. Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R. > library(testthat) > > test_check("scAlign") Loading required package: scAlign Loading required package: SingleCellExperiment Loading required package: SummarizedExperiment Loading required package: MatrixGenerics Loading required package: matrixStats Attaching package: 'MatrixGenerics' The following objects are masked from 'package:matrixStats': colAlls, colAnyNAs, colAnys, colAvgsPerRowSet, colCollapse, colCounts, colCummaxs, colCummins, colCumprods, colCumsums, colDiffs, colIQRDiffs, colIQRs, colLogSumExps, colMadDiffs, colMads, colMaxs, colMeans2, colMedians, colMins, colOrderStats, colProds, colQuantiles, colRanges, colRanks, colSdDiffs, colSds, colSums2, colTabulates, colVarDiffs, colVars, colWeightedMads, colWeightedMeans, colWeightedMedians, colWeightedSds, colWeightedVars, rowAlls, rowAnyNAs, rowAnys, rowAvgsPerColSet, rowCollapse, rowCounts, rowCummaxs, rowCummins, rowCumprods, rowCumsums, rowDiffs, rowIQRDiffs, rowIQRs, rowLogSumExps, rowMadDiffs, rowMads, rowMaxs, rowMeans2, rowMedians, rowMins, rowOrderStats, rowProds, rowQuantiles, rowRanges, rowRanks, rowSdDiffs, rowSds, rowSums2, rowTabulates, rowVarDiffs, rowVars, rowWeightedMads, rowWeightedMeans, rowWeightedMedians, rowWeightedSds, rowWeightedVars Loading required package: GenomicRanges Loading required package: stats4 Loading required package: BiocGenerics Loading required package: parallel Attaching package: 'BiocGenerics' The following objects are masked from 'package:parallel': clusterApply, clusterApplyLB, clusterCall, clusterEvalQ, clusterExport, clusterMap, parApply, parCapply, parLapply, parLapplyLB, parRapply, parSapply, parSapplyLB The following objects are masked from 'package:stats': IQR, mad, sd, var, xtabs The following objects are masked from 'package:base': Filter, Find, Map, Position, Reduce, anyDuplicated, append, as.data.frame, basename, cbind, colnames, dirname, do.call, duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted, lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table, tapply, union, unique, unsplit, which.max, which.min Loading required package: S4Vectors Attaching package: 'S4Vectors' The following objects are masked from 'package:base': I, expand.grid, unname Loading required package: IRanges Loading required package: GenomeInfoDb Loading required package: Biobase Welcome to Bioconductor Vignettes contain introductory material; view with 'browseVignettes()'. To cite Bioconductor, see 'citation("Biobase")', and for packages 'citation("pkgname")'. Attaching package: 'Biobase' The following object is masked from 'package:MatrixGenerics': rowMedians The following objects are masked from 'package:matrixStats': anyMissing, rowMedians Loading required package: Seurat Attaching SeuratObject Attaching package: 'Seurat' The following object is masked from 'package:SummarizedExperiment': Assays Loading required package: tensorflow Loading required package: purrr Attaching package: 'purrr' The following object is masked from 'package:GenomicRanges': reduce The following object is masked from 'package:IRanges': reduce The following object is masked from 'package:testthat': is_null Loading required package: irlba Loading required package: Matrix Attaching package: 'Matrix' The following object is masked from 'package:S4Vectors': expand Loading required package: Rtsne Loading required package: ggplot2 Loading required package: FNN 2021-10-14 23:39:27.440414: I tensorflow/compiler/xla/service/service.cc:168] XLA service 0x7fc31ee7f370 initialized for platform Host (this does not guarantee that XLA will be used). Devices: 2021-10-14 23:39:27.440468: I tensorflow/compiler/xla/service/service.cc:176] StreamExecutor device (0): Host, Default Version TensorFlow check: [Passed] [ FAIL 0 | WARN 0 | SKIP 0 | PASS 1 ] > > proc.time() user system elapsed 17.996 1.366 19.052
scAlign.Rcheck/scAlign-Ex.timings
name | user | system | elapsed | |
PlotTSNE | 41.763 | 14.370 | 20.842 | |
gaussianKernel | 0.611 | 0.039 | 0.580 | |
scAlign | 6.584 | 0.351 | 6.428 | |
scAlignCreateObject | 1.951 | 0.036 | 1.990 | |
scAlignMulti | 6.372 | 0.160 | 6.245 | |
scAlignOptions | 0.011 | 0.000 | 0.012 | |