Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-12-23 12:08 -0500 (Mon, 23 Dec 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4744 |
palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" | 4487 |
merida1 | macOS 12.7.5 Monterey | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4515 |
kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4467 |
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 1909/2289 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
scTGIF 1.20.0 (landing page) Koki Tsuyuzaki
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | |||||||||
palomino8 | 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 scTGIF package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/scTGIF.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: scTGIF |
Version: 1.20.0 |
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:scTGIF.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings scTGIF_1.20.0.tar.gz |
StartedAt: 2024-12-21 08:53:24 -0500 (Sat, 21 Dec 2024) |
EndedAt: 2024-12-21 08:58:16 -0500 (Sat, 21 Dec 2024) |
EllapsedTime: 291.4 seconds |
RetCode: 0 |
Status: OK |
CheckDir: scTGIF.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:scTGIF.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings scTGIF_1.20.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/scTGIF.Rcheck’ * using R version 4.4.2 (2024-10-31) * 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 13.7.1 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘scTGIF/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘scTGIF’ version ‘1.20.0’ * 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 ‘scTGIF’ 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 ... 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 ... NOTE Unexported object imported by a ':::' call: ‘schex:::.make_hexbin_function’ See the note in ?`:::` about the use of this operator. * 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 contents of ‘data’ directory ... OK * checking data for non-ASCII characters ... OK * checking data for ASCII and uncompressed saves ... OK * checking files in ‘vignettes’ ... OK * checking examples ... OK * 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: 1 NOTE See ‘/Users/biocbuild/bbs-3.20-bioc/meat/scTGIF.Rcheck/00check.log’ for details.
scTGIF.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL scTGIF ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library’ * installing *source* package ‘scTGIF’ ... ** using staged installation ** R ** data ** 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 (scTGIF)
scTGIF.Rcheck/tests/testthat.Rout
R version 4.4.2 (2024-10-31) -- "Pile of Leaves" 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("scTGIF") > > options(testthat.use_colours = FALSE) > > test_file("testthat/test_DistalLungEpithelium.R") ══ Testing test_DistalLungEpithelium.R ═════════════════════════════════════════ [ FAIL 0 | WARN 0 | SKIP 0 | PASS 0 ] [ FAIL 0 | WARN 0 | SKIP 0 | PASS 0 ] [ FAIL 0 | WARN 0 | SKIP 0 | PASS 1 ] [ FAIL 0 | WARN 0 | SKIP 0 | PASS 2 ] [ FAIL 0 | WARN 0 | SKIP 0 | PASS 3 ] [ FAIL 0 | WARN 0 | SKIP 0 | PASS 4 ] [ FAIL 0 | WARN 0 | SKIP 0 | PASS 5 ] Done! > test_file("testthat/test_TGIFFunctions.R") ══ Testing test_TGIFFunctions.R ════════════════════════════════════════════════ [ FAIL 0 | WARN 0 | SKIP 0 | PASS 0 ] [ FAIL 0 | WARN 0 | SKIP 0 | PASS 0 ] [ FAIL 0 | WARN 0 | SKIP 0 | PASS 1 ] [ FAIL 0 | WARN 0 | SKIP 0 | PASS 2 ] [ FAIL 0 | WARN 0 | SKIP 0 | PASS 3 ] Done! > test_file("testthat/test_convertRowID.R") ══ Testing test_convertRowID.R ═════════════════════════════════════════════════ [ FAIL 0 | WARN 0 | SKIP 0 | PASS 0 ] [ FAIL 0 | WARN 0 | SKIP 0 | PASS 0 ] | | | 0% | |================== | 25% | |=================================== | 50% | |==================================================== | 75% | |======================================================================| 100% [ FAIL 0 | WARN 0 | SKIP 0 | PASS 1 ] | | | 0% | |================== | 25% | |=================================== | 50% | |==================================================== | 75% | |======================================================================| 100% [ FAIL 0 | WARN 0 | SKIP 0 | PASS 2 ] [ FAIL 0 | WARN 0 | SKIP 0 | PASS 3 ] [ FAIL 0 | WARN 0 | SKIP 0 | PASS 4 ] [ FAIL 0 | WARN 0 | SKIP 0 | PASS 5 ] | | | 0% | |============== | 20% | |============================ | 40% | |========================================== | 60% | |======================================================== | 80% | |======================================================================| 100% [ FAIL 1 | WARN 0 | SKIP 0 | PASS 5 ] | | | 0% | |============== | 20% | |============================ | 40% | |========================================== | 60% | |======================================================== | 80% | |======================================================================| 100% [ FAIL 2 | WARN 0 | SKIP 0 | PASS 5 ] [ FAIL 3 | WARN 0 | SKIP 0 | PASS 5 ] ── Failure ('test_convertRowID.R:48:1'): (code run outside of `test_that()`) ─── identical(rownames(out$output), c("3", "2", "4", "7")) is not TRUE `actual`: FALSE `expected`: TRUE ── Failure ('test_convertRowID.R:51:1'): (code run outside of `test_that()`) ─── identical(rownames(out$output), c("3", "2", "4", "7")) is not TRUE `actual`: FALSE `expected`: TRUE ── Error ('test_convertRowID.R:53:1'): (code run outside of `test_that()`) ───── Error in `i_set_edge_attr(x, attr(value, "name"), index = value, value = attr(value, "value"), check = FALSE)`: Length of new attribute value must be 1 or 5, the number of target edges, not 4 Backtrace: ▆ 1. └─scTGIF::convertRowID(input, rowID, LtoR, "large.mean") at test_convertRowID.R:53:1 2. └─scTGIF (local) f(input, rowID, LtoR, score, unique.right) 3. └─igraph::`E<-`(`*tmp*`, value = `*vtmp*`) 4. └─igraph:::i_set_edge_attr(...) [ FAIL 3 | WARN 0 | SKIP 0 | PASS 5 ] > test_file("testthat/test_cellMarkerToGmt.R") ══ Testing test_cellMarkerToGmt.R ══════════════════════════════════════════════ [ FAIL 0 | WARN 0 | SKIP 0 | PASS 0 ] [ FAIL 0 | WARN 0 | SKIP 0 | PASS 0 ] [ FAIL 0 | WARN 1 | SKIP 0 | PASS 0 ] [ FAIL 0 | WARN 2 | SKIP 0 | PASS 0 ] [ FAIL 0 | WARN 3 | SKIP 0 | PASS 0 ] [ FAIL 0 | WARN 4 | SKIP 0 | PASS 0 ] [ FAIL 0 | WARN 4 | SKIP 0 | PASS 1 ] [ FAIL 0 | WARN 4 | SKIP 0 | PASS 2 ] [ FAIL 0 | WARN 4 | SKIP 0 | PASS 3 ] [ FAIL 0 | WARN 4 | SKIP 0 | PASS 4 ] [ FAIL 0 | WARN 4 | SKIP 0 | PASS 5 ] [ FAIL 0 | WARN 4 | SKIP 0 | PASS 6 ] [ FAIL 0 | WARN 4 | SKIP 0 | PASS 7 ] [ FAIL 0 | WARN 4 | SKIP 0 | PASS 8 ] [ FAIL 0 | WARN 4 | SKIP 0 | PASS 9 ] [ FAIL 0 | WARN 4 | SKIP 0 | PASS 10 ] [ FAIL 0 | WARN 4 | SKIP 0 | PASS 11 ] [ FAIL 0 | WARN 4 | SKIP 0 | PASS 12 ] [ FAIL 0 | WARN 4 | SKIP 0 | PASS 13 ] [ FAIL 0 | WARN 4 | SKIP 0 | PASS 14 ] [ FAIL 0 | WARN 4 | SKIP 0 | PASS 15 ] [ FAIL 0 | WARN 4 | SKIP 0 | PASS 16 ] ── Warning ('test_cellMarkerToGmt.R:134:1'): (code run outside of `test_that()`) ── 1 record(s) contain duplicate ids: Meniscus Backtrace: ▆ 1. └─GSEABase::getGmt(outfile2_1) at test_cellMarkerToGmt.R:134:1 2. └─GSEABase:::.warningf(...) ── Warning ('test_cellMarkerToGmt.R:135:1'): (code run outside of `test_that()`) ── 1 record(s) contain duplicate ids: Meniscus Backtrace: ▆ 1. └─GSEABase::getGmt(outfile2_2) at test_cellMarkerToGmt.R:135:1 2. └─GSEABase:::.warningf(...) ── Warning ('test_cellMarkerToGmt.R:140:1'): (code run outside of `test_that()`) ── 1 record(s) contain duplicate ids: Pancreas Backtrace: ▆ 1. └─GSEABase::getGmt(outfile3_1) at test_cellMarkerToGmt.R:140:1 2. └─GSEABase:::.warningf(...) ── Warning ('test_cellMarkerToGmt.R:141:1'): (code run outside of `test_that()`) ── 1 record(s) contain duplicate ids: Pancreas Backtrace: ▆ 1. └─GSEABase::getGmt(outfile3_2) at test_cellMarkerToGmt.R:141:1 2. └─GSEABase:::.warningf(...) [ FAIL 0 | WARN 4 | SKIP 0 | PASS 16 ] > > proc.time() user system elapsed 16.628 1.088 17.890
scTGIF.Rcheck/scTGIF-Ex.timings
name | user | system | elapsed | |
DistalLungEpithelium | 0.026 | 0.004 | 0.029 | |
calcTGIF | 0.004 | 0.001 | 0.004 | |
cellMarkerToGmt | 0.279 | 0.034 | 0.324 | |
convertRowID | 0.041 | 0.009 | 0.055 | |
label.DistalLungEpithelium | 0.001 | 0.002 | 0.004 | |
pca.DistalLungEpithelium | 0.001 | 0.002 | 0.003 | |
reportTGIF | 0.008 | 0.001 | 0.010 | |
settingTGIF | 0.002 | 0.000 | 0.003 | |