Back to Multiple platform build/check report for BioC 3.13 |
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This page was generated on 2021-10-15 15:06:54 -0400 (Fri, 15 Oct 2021).
To the developers/maintainers of the spatialHeatmap package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/spatialHeatmap.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 1817/2041 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
spatialHeatmap 1.2.0 (landing page) Jianhai Zhang
| nebbiolo1 | Linux (Ubuntu 20.04.2 LTS) / x86_64 | OK | OK | OK | |||||||||
tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | |||||||||
machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | |||||||||
Package: spatialHeatmap |
Version: 1.2.0 |
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:spatialHeatmap.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings spatialHeatmap_1.2.0.tar.gz |
StartedAt: 2021-10-15 00:17:29 -0400 (Fri, 15 Oct 2021) |
EndedAt: 2021-10-15 00:23:59 -0400 (Fri, 15 Oct 2021) |
EllapsedTime: 390.9 seconds |
RetCode: 0 |
Status: OK |
CheckDir: spatialHeatmap.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:spatialHeatmap.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings spatialHeatmap_1.2.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.13-bioc/meat/spatialHeatmap.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 ‘spatialHeatmap/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘spatialHeatmap’ version ‘1.2.0’ * 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 ... NOTE Found the following hidden files and directories: .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 ‘spatialHeatmap’ can be installed ... OK * checking installed package size ... NOTE installed size is 11.2Mb sub-directories of 1Mb or more: extdata 10.7Mb * 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 ... OK * 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 write_hdf5 17.889 0.853 18.766 spatialHeatmap-package 13.919 0.907 14.901 spatial_hm 12.009 0.795 12.885 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘runTests.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: 2 NOTEs See ‘/Users/biocbuild/bbs-3.13-bioc/meat/spatialHeatmap.Rcheck/00check.log’ for details.
spatialHeatmap.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL spatialHeatmap ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.1/Resources/library’ * installing *source* package ‘spatialHeatmap’ ... ** using staged installation ** R ** inst ** 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 (spatialHeatmap)
spatialHeatmap.Rcheck/tests/runTests.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. > BiocGenerics:::testPackage("spatialHeatmap") Loading required package: Biobase 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 Welcome to Bioconductor Vignettes contain introductory material; view with 'browseVignettes()'. To cite Bioconductor, see 'citation("Biobase")', and for packages 'citation("pkgname")'. Loading required package: SummarizedExperiment Loading required package: MatrixGenerics Loading required package: matrixStats Attaching package: 'matrixStats' The following objects are masked from 'package:Biobase': anyMissing, rowMedians 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 The following object is masked from 'package:Biobase': rowMedians Loading required package: GenomicRanges Loading required package: stats4 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: limma Attaching package: 'limma' The following object is masked from 'package:BiocGenerics': plotMA Loading required package: xml2 Normalising: ESF type "ratio" Syntactically valid column names are made! Syntactically valid column names are made! All values before filtering: Min. 1st Qu. Median Mean 3rd Qu. Max. 0.000 0.000 0.287 2.442 4.268 19.991 All coefficient of variances (CVs) before filtering: Min. 1st Qu. Median Mean 3rd Qu. Max. 0.0007742 0.0767696 0.4019655 0.6217813 0.9956157 2.0000000 All values after filtering: Min. 1st Qu. Median Mean 3rd Qu. Max. 0.000 2.654 4.976 4.779 6.451 14.695 All coefficient of variances (CVs) after filtering: Min. 1st Qu. Median Mean 3rd Qu. Max. 0.3001 0.3648 0.4637 0.5651 0.7392 1.1548 Warning: variables of sample/condition are less than 5! ..connectivity.. ..matrix multiplication (system BLAS).. ..normalization.. ..done. ..done. ..done. Normalising: ESF type "ratio" Syntactically valid column names are made! Syntactically valid column names are made! All values before filtering: Min. 1st Qu. Median Mean 3rd Qu. Max. 0.000 0.000 0.287 2.442 4.268 19.991 All coefficient of variances (CVs) before filtering: Min. 1st Qu. Median Mean 3rd Qu. Max. 0.0007742 0.0767696 0.4019655 0.6217813 0.9956157 2.0000000 All values after filtering: Min. 1st Qu. Median Mean 3rd Qu. Max. 0.000 2.654 4.976 4.779 6.451 14.695 All coefficient of variances (CVs) after filtering: Min. 1st Qu. Median Mean 3rd Qu. Max. 0.3001 0.3648 0.4637 0.5651 0.7392 1.1548 RUNIT TEST PROTOCOL -- Fri Oct 15 00:23:50 2021 *********************************************** Number of test functions: 2 Number of errors: 0 Number of failures: 0 1 Test Suite : spatialHeatmap RUnit Tests - 2 test functions, 0 errors, 0 failures Number of test functions: 2 Number of errors: 0 Number of failures: 0 > > proc.time() user system elapsed 34.284 1.294 35.620
spatialHeatmap.Rcheck/spatialHeatmap-Ex.timings
name | user | system | elapsed | |
adj_mod | 2.640 | 0.068 | 2.712 | |
aggr_rep | 0.378 | 0.012 | 0.391 | |
com_factor | 0.018 | 0.001 | 0.020 | |
custom_shiny | 0.016 | 0.003 | 0.019 | |
edit_tar | 0.006 | 0.001 | 0.006 | |
filter_data | 0.922 | 0.037 | 0.960 | |
matrix_hm | 1.780 | 0.081 | 1.872 | |
network | 1.940 | 0.070 | 2.013 | |
norm_data | 0.712 | 0.030 | 0.743 | |
read_cache | 2.257 | 0.020 | 2.281 | |
read_fr | 0.004 | 0.000 | 0.005 | |
read_hdf5 | 0 | 0 | 0 | |
return_feature | 1.573 | 0.028 | 1.607 | |
save_cache | 1.960 | 0.031 | 1.993 | |
shiny_all | 0 | 0 | 0 | |
spatialHeatmap-package | 13.919 | 0.907 | 14.901 | |
spatial_hm | 12.009 | 0.795 | 12.885 | |
submatrix | 0.971 | 0.032 | 1.003 | |
update_feature | 0.000 | 0.001 | 0.000 | |
write_hdf5 | 17.889 | 0.853 | 18.766 | |