Back to Multiple platform build/check report for BioC 3.21: simplified long |
|
This page was generated on 2024-12-24 11:47 -0500 (Tue, 24 Dec 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | R Under development (unstable) (2024-10-21 r87258) -- "Unsuffered Consequences" | 4754 |
palomino7 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2024-10-26 r87273 ucrt) -- "Unsuffered Consequences" | 4472 |
lconway | macOS 12.7.1 Monterey | x86_64 | R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" | 4426 |
kjohnson3 | macOS 13.7.1 Ventura | arm64 | R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" | 4381 |
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | R Under development (unstable) (2024-11-24 r87369) -- "Unsuffered Consequences" | 4373 |
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 1701/2274 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
RegionalST 1.5.8 (landing page) Ziyi Li
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | |||||||||
palomino7 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | |||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | ERROR | ERROR | skipped | skipped | |||||||||
kjohnson3 | macOS 13.7.1 Ventura / arm64 | OK | OK | OK | OK | |||||||||
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | OK | ||||||||||
To the developers/maintainers of the RegionalST package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/RegionalST.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. - See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host. |
Package: RegionalST |
Version: 1.5.8 |
Command: /home/biocbuild/R/R/bin/R CMD check --install=check:RegionalST.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings RegionalST_1.5.8.tar.gz |
StartedAt: 2024-12-24 10:20:21 -0000 (Tue, 24 Dec 2024) |
EndedAt: 2024-12-24 10:26:25 -0000 (Tue, 24 Dec 2024) |
EllapsedTime: 363.5 seconds |
RetCode: 0 |
Status: OK |
CheckDir: RegionalST.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R/bin/R CMD check --install=check:RegionalST.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings RegionalST_1.5.8.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/RegionalST.Rcheck’ * using R Under development (unstable) (2024-11-24 r87369) * using platform: aarch64-unknown-linux-gnu * R was compiled by aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0 GNU Fortran (GCC) 14.2.0 * running under: openEuler 24.03 (LTS) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘RegionalST/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘RegionalST’ version ‘1.5.8’ * 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 ‘RegionalST’ 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 loading without being on the library search path ... OK * checking dependencies in R code ... NOTE Namespace in Imports field not imported from: ‘BiocStyle’ All declared Imports should be used. * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... NOTE GetCellTypeSpecificDE_withProp: no visible binding for global variable ‘OneRegOut1’ GetCellTypeSpecificDE_withProp: no visible binding for global variable ‘twoCenter’ GetCellTypeSpecificDE_withProp: no visible binding for global variable ‘OneRegOut2’ Undefined global functions or variables: OneRegOut1 OneRegOut2 twoCenter * 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 Examples with CPU (user + system) or elapsed time > 5s user system elapsed GetCrossRegionalDE_raw 10.854 0.539 11.421 RankCenterByEntropy 7.716 0.100 7.832 RankCenterByEntropy_withProp 7.292 0.024 7.332 GetOneRadiusEntropy 6.949 0.044 7.010 DoGSEA 5.431 0.586 5.906 GetCrossRegionalDE_withProp 5.410 0.211 5.636 GetOneRadiusEntropy_withProp 5.484 0.128 5.627 * 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 ‘/home/biocbuild/bbs-3.21-bioc/meat/RegionalST.Rcheck/00check.log’ for details.
RegionalST.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R/bin/R CMD INSTALL RegionalST ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library’ * installing *source* package ‘RegionalST’ ... ** 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 (RegionalST)
RegionalST.Rcheck/tests/testthat.Rout
R Under development (unstable) (2024-11-24 r87369) -- "Unsuffered Consequences" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: aarch64-unknown-linux-gnu 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. > # This file is part of the standard setup for testthat. > # It is recommended that you do not modify it. > # > # Where should you do additional test configuration? > # Learn more about the roles of various files in: > # * https://r-pkgs.org/testing-design.html#sec-tests-files-overview > # * https://testthat.r-lib.org/articles/special-files.html > > library(testthat) > library(RegionalST) > > test_check("RegionalST") Normalizing layer: counts Performing log-normalization 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| Centering and scaling data matrix | | | 0% | |======================================================================| 100% Finding variable features for layer counts Calculating gene variances 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| Calculating feature variances of standardized and clipped values 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| PC_ 1 Positive: PADI2, MIIP, YARS, CLSTN1, VWA1, CITED4, STK40, PSMB2, SDHB, ARHGEF16 MACO1, TMEM54, MRTO4, NOC2L, MTOR, SERINC2, SRRM1, NADK, FBLIM1, TMEM35B NECAP2, CSF3R, CPTP, TPRG1L, MEAF6, COL9A2, RCC2, HNRNPR, PRXL2B, AKIRIN1 Negative: IFI6, MXRA8, RBP7, RAB42, PADI3, FAM131C, C1orf127, C1QC, PDPN, NBL1 C1QB, RSPO1, SAMD11, TRIM63, MMP23B, TAS1R1, LAPTM5, SLC2A5, OXCT2, HPCA CNR2, TP73, HSPB7, PRAMEF4, ANKRD65, SRARP, PADI4, HTR1D, A3GALT2, PERM1 PC_ 2 Positive: CNKSR1, CASZ1, CITED4, PADI2, ARHGEF16, SMIM1, EDN2, CD164L2, KDF1, CAMK2N1 NCMAP, GRHL3, IFI6, GRIK3, SMPDL3B, KCNQ4, FOXO6, VPS13D, CTPS1, SH3D21 TRIM62, KAZN, PHF13, TMEM234, EXO5, PADI3, MFSD2A, KIAA1522, RIMS3, PLOD1 Negative: CD52, C1QB, LAPTM5, KCNAB2, C1QC, LCK, HSPG2, TNFRSF4, TNFRSF1B, RUNX3 MXRA8, ID3, PIK3CD, TNFRSF18, NBL1, THEMIS2, SH3BGRL3, FGR, ZNF683, H6PD RSRP1, HEYL, COL8A2, TNFRSF8, WASF2, PSMB2, SDF4, ECE1, SFPQ, PLA2G2D PC_ 3 Positive: TTLL10, DISP3, SCNN1D, ADGRB2, AUNIP, CROCC, EXTL1, TRNP1, FAM167B, SPOCD1 CDCA8, STMN1, MYOM3, FAM110D, EMC1, TMEM35B, SLC45A1, CRYBG2, TEKT2, ALDH4A1 PEX10, DNAJC11, GJB5, BMP8A, KDF1, ZNF683, STPG1, PINK1, ERRFI1, LYPLA2 Negative: FOXO6, PLOD1, C1orf174, SLC30A2, NPHP4, CORT, SLC25A34, FBXO6, DHDDS, CCNL2 HP1BP3, NFYC, KIAA1522, PANK4, KLHL17, COL8A2, MYCBP, TNFRSF14, PLA2G2C, PITHD1 NDUFS5, CITED4, UBIAD1, ADPRHL2, GPN2, PLEKHM2, C1orf109, ZFP69, SF3A3, KPNA6 PC_ 4 Positive: NBL1, MXRA8, ZNF436, ID3, ZCCHC17, NCDN, NOL9, PINK1, COL8A2, HSPG2 PEX14, SLC25A33, CASP9, EPHB2, ASAP3, SYNC, CCNL2, KLHL21, SNIP1, ZBTB8A ANKRD65, UTP11, FNDC5, MACF1, IGSF21, MECR, COL16A1, TENT5B, MAP3K6, TMEM200B Negative: TNFRSF18, IFI6, FGR, C1QTNF12, ZMYM6, ALDH4A1, RCC1, TNFRSF4, KLHL17, SLC25A34 GNL2, ADGRB2, MAD2L2, PIK3CD, ZNF684, DISP3, UQCRHL, PLA2G2D, SMAP2, SPEN ZMYM4, MEAF6, TTLL10, PNRC2, CTNNBIP1, ZNF683, THEMIS2, PITHD1, STK40, NADK PC_ 5 Positive: ADGRB2, SLC25A34, AUNIP, TTLL10, CROCC, DISP3, C1orf216, NMNAT1, ATP13A2, SLC30A2 NCMAP, MFAP2, SLC45A1, CD164L2, KLHL17, RHBDL2, UBE4B, FHAD1, SCMH1, SYNC GABRD, SCNN1D, TMEM51, PRXL2B, PLA2G2C, ZNF362, SYF2, C1QB, DFFB, PLA2G2F Negative: CLSPN, BMP8A, IFNLR1, CRYBG2, ZNF683, ZBTB8A, KDF1, LDLRAD2, TMEM234, EMC1 INTS11, IFI6, GPR157, MTF1, KIAA0319L, MIB2, ZNF593, C1orf159, SLC35E2A, HEYL EIF4G3, PLEKHN1, MIIP, CLCN6, IL22RA1, DNAJC16, AHDC1, MYCL, PHACTR4, MORN1 Computing nearest neighbor graph Computing SNN Modularity Optimizer version 1.3.0 by Ludo Waltman and Nees Jan van Eck Number of nodes: 246 Number of edges: 9889 Running Louvain algorithm... 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| Maximum modularity in 10 random starts: 0.6836 Number of communities: 3 Elapsed time: 0 seconds Processing to cell type:CAFs For a (much!) faster implementation of the Wilcoxon Rank Sum Test, (default method for FindMarkers) please install the presto package -------------------------------------------- install.packages('devtools') devtools::install_github('immunogenomics/presto') -------------------------------------------- After installation of presto, Seurat will automatically use the more efficient implementation (no further action necessary). This message will be shown once per session Processing to cell type:Myeloid Processing to cell type:T-cells Processing to cell type:Cancer Epithelial Processing to cell type:Normal Epithelial Processing to cell type:Endothelial Processing to Radius = 5 | | | 0% | | | 1% | |= | 1% | |= | 2% | |== | 3% | |== | 4% | |=== | 5% | |==== | 6% | |==== | 7% | |===== | 8% | |===== | 9% | |====== | 9% | |====== | 10% | |====== | 11% | |======= | 11% | |======= | 12% | |======== | 13% | |======== | 14% | |========= | 15% | |========== | 16% | |========== | 17% | |=========== | 18% | |=========== | 19% | |============ | 19% | |============ | 20% | |============ | 21% | |============= | 21% | |============= | 22% | |============== | 23% | |============== | 24% | |=============== | 25% | |================ | 26% | |================ | 27% | |================= | 28% | |================= | 29% | |================== | 29% | |================== | 30% | |================== | 31% | |=================== | 31% | |=================== | 32% | |==================== | 33% | |==================== | 34% | |===================== | 35% | |====================== | 36% | |====================== | 37% | |======================= | 38% | |======================= | 39% | |======================== | 39% | |======================== | 40% | |======================== | 41% | |========================= | 41% | |========================= | 42% | |========================== | 43% | |========================== | 44% | |=========================== | 45% | |============================ | 46% | |============================ | 47% | |============================= | 48% | |============================= | 49% | |============================== | 49% | |============================== | 50% | |============================== | 51% | |=============================== | 51% | |=============================== | 52% | |================================ | 53% | |================================ | 54% | |================================= | 55% | |================================== | 56% | |================================== | 57% | |=================================== | 58% | |=================================== | 59% | |==================================== | 59% | |==================================== | 60% | |==================================== | 61% | |===================================== | 61% | |===================================== | 62% | |====================================== | 63% | |====================================== | 64% | |======================================= | 65% | |======================================== | 66% | |======================================== | 67% | |========================================= | 68% | |========================================= | 69% | |========================================== | 69% | |========================================== | 70% | |========================================== | 71% | |=========================================== | 71% | |=========================================== | 72% | |============================================ | 73% | |============================================ | 74% | |============================================= | 75% | |============================================== | 76% | |============================================== | 77% | |=============================================== | 78% | |=============================================== | 79% | |================================================ | 79% | |================================================ | 80% | |================================================ | 81% | |================================================= | 81% | |================================================= | 82% | |================================================== | 83% | |================================================== | 84% | |=================================================== | 85% | |==================================================== | 86% | |==================================================== | 87% | |===================================================== | 88% | |===================================================== | 89% | |====================================================== | 89% | |====================================================== | 90% | |====================================================== | 91% | |======================================================= | 91% | |======================================================= | 92% | |======================================================== | 93% | |======================================================== | 94% | |========================================================= | 95% | |========================================================== | 96% | |========================================================== | 97% | |=========================================================== | 98% | |=========================================================== | 99% | |============================================================| 99% | |============================================================| 100% [ FAIL 0 | WARN 3 | SKIP 0 | PASS 4 ] [ FAIL 0 | WARN 3 | SKIP 0 | PASS 4 ] > > proc.time() user system elapsed 36.372 1.124 37.563
RegionalST.Rcheck/RegionalST-Ex.timings
name | user | system | elapsed | |
DoGSEA | 5.431 | 0.586 | 5.906 | |
DrawDotplot | 2.724 | 0.735 | 3.310 | |
DrawRegionProportion | 0.609 | 0.071 | 0.683 | |
DrawRegionProportion_withProp | 0.455 | 0.020 | 0.477 | |
FindRegionalCells | 0 | 0 | 0 | |
GetCellTypeSpecificDE_withProp | 3.574 | 0.120 | 3.713 | |
GetCrossRegionalDE_raw | 10.854 | 0.539 | 11.421 | |
GetCrossRegionalDE_withProp | 5.410 | 0.211 | 5.636 | |
GetOneRadiusEntropy | 6.949 | 0.044 | 7.010 | |
GetOneRadiusEntropy_withProp | 5.484 | 0.128 | 5.627 | |
ManualSelectCenter | 2.775 | 0.004 | 2.784 | |
PlotOneSelectedCenter | 2.763 | 0.024 | 2.791 | |
RankCenterByEntropy | 7.716 | 0.100 | 7.832 | |
RankCenterByEntropy_withProp | 7.292 | 0.024 | 7.332 | |
exampleRes | 0.002 | 0.000 | 0.003 | |
example_sce | 0.006 | 0.000 | 0.006 | |
getProportion | 0 | 0 | 0 | |
mySpatialPreprocess | 2.653 | 0.012 | 2.670 | |
pathways_hallmark | 0.012 | 0.000 | 0.011 | |
pathways_kegg | 0.013 | 0.004 | 0.018 | |
pathways_reactome | 0.150 | 0.000 | 0.151 | |