Back to Multiple platform build/check report for BioC 3.19: simplified long |
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This page was generated on 2024-10-11 20:43 -0400 (Fri, 11 Oct 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4763 |
palomino7 | Windows Server 2022 Datacenter | x64 | 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" | 4500 |
merida1 | macOS 12.7.5 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4529 |
kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4479 |
Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X |
Package 2033/2300 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
SpatialDecon 1.14.0 (landing page) Maddy Griswold
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | |||||||||
palomino7 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | |||||||||
merida1 | macOS 12.7.5 Monterey / x86_64 | OK | OK | OK | OK | |||||||||
kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | OK | OK | OK | |||||||||
To the developers/maintainers of the SpatialDecon package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/SpatialDecon.git to reflect on this report. See Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
Package: SpatialDecon |
Version: 1.14.0 |
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:SpatialDecon.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings SpatialDecon_1.14.0.tar.gz |
StartedAt: 2024-10-11 12:16:41 -0400 (Fri, 11 Oct 2024) |
EndedAt: 2024-10-11 12:28:11 -0400 (Fri, 11 Oct 2024) |
EllapsedTime: 690.0 seconds |
RetCode: 0 |
Status: OK |
CheckDir: SpatialDecon.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:SpatialDecon.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings SpatialDecon_1.14.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.19-bioc/meat/SpatialDecon.Rcheck’ * using R version 4.4.1 (2024-06-14) * using platform: aarch64-apple-darwin20 * R was compiled by Apple clang version 14.0.0 (clang-1400.0.29.202) GNU Fortran (GCC) 12.2.0 * running under: macOS Ventura 13.6.6 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘SpatialDecon/DESCRIPTION’ ... OK * this is package ‘SpatialDecon’ version ‘1.14.0’ * 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 for sufficient/correct file permissions ... OK * checking whether package ‘SpatialDecon’ can be installed ... OK * checking installed package size ... OK * checking package directory ... OK * checking ‘build’ directory ... OK * checking DESCRIPTION meta-information ... NOTE License stub is invalid DCF. * checking top-level files ... OK * checking for left-over files ... OK * checking index information ... OK * checking package subdirectories ... OK * checking code 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 download_profile_matrix: no visible binding for global variable ‘profile_matrix’ Undefined global functions or variables: profile_matrix * 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 ... OK * checking data for non-ASCII characters ... OK * checking LazyData ... OK * checking data for ASCII and uncompressed saves ... OK * checking files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed runReverseDecon 80.473 3.595 86.907 runCollapseCellTypes 79.751 4.077 88.167 runspatialdecon 58.401 2.139 64.565 runErrorModel 16.476 0.215 17.341 runMergeTumorIntoX 16.061 0.212 16.765 reverseDecon 6.948 0.300 7.438 SpatialDecon-package 5.578 0.126 5.826 spatialdecon 4.677 0.241 5.028 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘testthat.R’ OK * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... 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-3.19-bioc/meat/SpatialDecon.Rcheck/00check.log’ for details.
SpatialDecon.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL SpatialDecon ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library’ * installing *source* package ‘SpatialDecon’ ... ** using staged installation ** R ** data *** moving datasets to lazyload DB ** 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 (SpatialDecon)
SpatialDecon.Rcheck/tests/testthat.Rout
R version 4.4.1 (2024-06-14) -- "Race for Your Life" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: aarch64-apple-darwin20 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) > library(SpatialDecon) > > test_check("SpatialDecon") [1] "Creating Atlas" [1] "1 / 4 : B" [1] "2 / 4 : C" [1] "3 / 4 : A" [1] "4 / 4 : D" [ FAIL 0 | WARN 0 | SKIP 0 | PASS 96 ] > > proc.time() user system elapsed 174.882 8.756 191.482
SpatialDecon.Rcheck/SpatialDecon-Ex.timings
name | user | system | elapsed | |
SpatialDecon-package | 5.578 | 0.126 | 5.826 | |
TIL_barplot | 1.618 | 0.036 | 1.684 | |
collapseCellTypes | 1.626 | 0.020 | 1.738 | |
create_profile_matrix | 0.896 | 0.042 | 1.035 | |
derive_GeoMx_background | 0.004 | 0.002 | 0.006 | |
download_profile_matrix | 0.860 | 0.396 | 2.914 | |
florets | 1.566 | 0.081 | 1.704 | |
mergeTumorIntoX | 0.014 | 0.003 | 0.017 | |
reverseDecon | 6.948 | 0.300 | 7.438 | |
runCollapseCellTypes | 79.751 | 4.077 | 88.167 | |
runErrorModel | 16.476 | 0.215 | 17.341 | |
runMergeTumorIntoX | 16.061 | 0.212 | 16.765 | |
runReverseDecon | 80.473 | 3.595 | 86.907 | |
runspatialdecon | 58.401 | 2.139 | 64.565 | |
spatialdecon | 4.677 | 0.241 | 5.028 | |