Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-11-20 12:06 -0500 (Wed, 20 Nov 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
teran2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4481 |
nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4479 |
palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" | 4359 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4539 |
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4493 |
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 521/2289 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
deconvR 1.12.0 (landing page) Irem B. Gündüz
| teran2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | |||||||||
nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | ||||||||||
palomino8 | Windows Server 2022 Datacenter / x64 | ERROR | ERROR | skipped | skipped | |||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | |||||||||
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | OK | ||||||||||
To the developers/maintainers of the deconvR package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/deconvR.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: deconvR |
Version: 1.12.0 |
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:deconvR.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings deconvR_1.12.0.tar.gz |
StartedAt: 2024-11-19 21:16:26 -0500 (Tue, 19 Nov 2024) |
EndedAt: 2024-11-19 21:31:47 -0500 (Tue, 19 Nov 2024) |
EllapsedTime: 921.6 seconds |
RetCode: 0 |
Status: OK |
CheckDir: deconvR.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:deconvR.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings deconvR_1.12.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/deconvR.Rcheck’ * using R version 4.4.1 (2024-06-14) * using platform: x86_64-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 Monterey 12.7.6 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘deconvR/DESCRIPTION’ ... OK * this is package ‘deconvR’ version ‘1.12.0’ * package encoding: UTF-8 * checking package namespace information ... OK * checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib: cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES' 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 ‘deconvR’ 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 ... 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 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: OK
deconvR.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL deconvR ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library’ * installing *source* package ‘deconvR’ ... ** 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 (deconvR)
deconvR.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: x86_64-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(deconvR) Loading required package: data.table Setting options('download.file.method.GEOquery'='auto') Setting options('GEOquery.inmemory.gpl'=FALSE) > > test_check("deconvR") Received list of locations. Reading file. Reading file. uniting... BSmeth2Probe couldn't find any match between the probe IDs and WGBS data you have provided. Please make sure that you're using an appropriate probe ID locations with your WGBS data. Received list of locations. Reading file. Reading file. Received list of locations. Reading file. Reading file. uniting... BSmeth2Probe couldn't find any match between the probe IDs and WGBS data you have provided. Please make sure that you're using an appropriate probe ID locations with your WGBS data. Received list of locations. Reading file. Reading file. uniting... BSmeth2Probe couldn't find any match between the probe IDs and WGBS data you have provided. Please make sure that you're using an appropriate probe ID locations with your WGBS data. DECONVOLUTION WITH NNLS SUMMARY OF PARTIAL R-SQUARED VALUES FOR NNLS: Min. 1st Qu. Median Mean 3rd Qu. Max. 1 1 1 1 1 1 DECONVOLUTION WITH NNLS SUMMARY OF PARTIAL R-SQUARED VALUES FOR NNLS: DECONVOLUTION WITH NNLS DECONVOLUTION WITH NNLS SUMMARY OF PARTIAL R-SQUARED VALUES FOR NNLS: SUMMARY OF PARTIAL R-SQUARED VALUES FOR NNLS : DECONVOLUTION WITH NNLS SUMMARY OF PARTIAL R-SQUARED VALUES FOR NNLS: Min. 1st Qu. Median Mean 3rd Qu. Max. 1 1 1 1 1 1 [1] "double" DECONVOLUTION WITH NNLS DECONVOLUTION WITH NNLS SUMMARY OF PARTIAL R-SQUARED VALUES FOR NNLS: Min. 1st Qu. Median Mean 3rd Qu. Max. 1 1 1 1 1 1 DECONVOLUTION WITH NNLS DECONVOLUTION WITH NNLS DECONVOLUTION WITH NNLS DECONVOLUTION WITH SVR SUMMARY OF PARTIAL R-SQUARED VALUES FOR SVR: Min. 1st Qu. Median Mean 3rd Qu. Max. 1 1 1 1 1 1 DECONVOLUTION WITH SVR SUMMARY OF PARTIAL R-SQUARED VALUES FOR SVR: DECONVOLUTION WITH SVR DECONVOLUTION WITH SVR SUMMARY OF PARTIAL R-SQUARED VALUES FOR SVR: SUMMARY OF PARTIAL R-SQUARED VALUES FOR SVR : DECONVOLUTION WITH SVR SUMMARY OF PARTIAL R-SQUARED VALUES FOR SVR: Min. 1st Qu. Median Mean 3rd Qu. Max. 1 1 1 1 1 1 [1] "double" DECONVOLUTION WITH SVR DECONVOLUTION WITH SVR SUMMARY OF PARTIAL R-SQUARED VALUES FOR SVR: Min. 1st Qu. Median Mean 3rd Qu. Max. 1 1 1 1 1 1 DECONVOLUTION WITH SVR DECONVOLUTION WITH SVR DECONVOLUTION WITH QP SUMMARY OF PARTIAL R-SQUARED VALUES FOR QP: Min. 1st Qu. Median Mean 3rd Qu. Max. 1 1 1 1 1 1 DECONVOLUTION WITH QP SUMMARY OF PARTIAL R-SQUARED VALUES FOR QP: DECONVOLUTION WITH QP DECONVOLUTION WITH QP SUMMARY OF PARTIAL R-SQUARED VALUES FOR QP: SUMMARY OF PARTIAL R-SQUARED VALUES FOR QP : DECONVOLUTION WITH QP SUMMARY OF PARTIAL R-SQUARED VALUES FOR QP: Min. 1st Qu. Median Mean 3rd Qu. Max. 1 1 1 1 1 1 [1] "double" DECONVOLUTION WITH QP DECONVOLUTION WITH QP SUMMARY OF PARTIAL R-SQUARED VALUES FOR QP: Min. 1st Qu. Median Mean 3rd Qu. Max. 1 1 1 1 1 1 DECONVOLUTION WITH QP DECONVOLUTION WITH QP DECONVOLUTION WITH RLM SUMMARY OF PARTIAL R-SQUARED VALUES FOR RLM: Min. 1st Qu. Median Mean 3rd Qu. Max. 1 1 1 1 1 1 DECONVOLUTION WITH RLM SUMMARY OF PARTIAL R-SQUARED VALUES FOR RLM: DECONVOLUTION WITH RLM DECONVOLUTION WITH RLM SUMMARY OF PARTIAL R-SQUARED VALUES FOR RLM: SUMMARY OF PARTIAL R-SQUARED VALUES FOR RLM : DECONVOLUTION WITH RLM SUMMARY OF PARTIAL R-SQUARED VALUES FOR RLM: Min. 1st Qu. Median Mean 3rd Qu. Max. 1 1 1 1 1 1 [1] "double" DECONVOLUTION WITH RLM DECONVOLUTION WITH RLM SUMMARY OF PARTIAL R-SQUARED VALUES FOR RLM: Min. 1st Qu. Median Mean 3rd Qu. Max. 1 1 1 1 1 1 DECONVOLUTION WITH RLM DECONVOLUTION WITH RLM CELL TYPES IN EXTENDED ATLAS: example_cell_type CELL TYPES IN EXTENDED ATLAS: else that this CELL TYPES IN EXTENDED ATLAS: else that this CELL TYPES IN EXTENDED ATLAS: this_v2 that else else_v2 that_v2 Monocytes_EPIC this CELL TYPES IN EXTENDED ATLAS: example_cell_type Monocytes_EPIC B.cells_EPIC CD4T.cells_EPIC NK.cells_EPIC CD8T.cells_EPIC Neutrophils_EPIC Erythrocyte_progenitors Adipocytes Cortical_neurons Hepatocytes Lung_cells Pancreatic_beta_cells Pancreatic_acinar_cells Pancreatic_duct_cells Vascular_endothelial_cells Colon_epithelial_cells Left_atrium Bladder Breast Head_and_neck_larynx Kidney Prostate Thyroid Upper_GI Uterus_cervix Unique used IDs: 0 example_cell_type Unique used IDs: 200 Monocytes_EPIC Unique used IDs: 400 B.cells_EPIC Unique used IDs: 600 CD4T.cells_EPIC Unique used IDs: 800 NK.cells_EPIC Unique used IDs: 1000 CD8T.cells_EPIC Unique used IDs: 1200 Neutrophils_EPIC Unique used IDs: 1400 Erythrocyte_progenitors Unique used IDs: 1600 Adipocytes Unique used IDs: 1800 Cortical_neurons Unique used IDs: 2000 Hepatocytes Unique used IDs: 2200 Lung_cells Unique used IDs: 2400 Pancreatic_beta_cells Unique used IDs: 2600 Pancreatic_acinar_cells Unique used IDs: 2800 Pancreatic_duct_cells Unique used IDs: 3000 Vascular_endothelial_cells Unique used IDs: 3200 Colon_epithelial_cells Unique used IDs: 3400 Left_atrium Unique used IDs: 3600 Bladder Unique used IDs: 3800 Breast Unique used IDs: 4000 Head_and_neck_larynx Unique used IDs: 4200 Kidney Unique used IDs: 4400 Prostate Unique used IDs: 4600 Thyroid Unique used IDs: 4800 Upper_GI Unique used IDs: 5000 Uterus_cervix CELL TYPES IN EXTENDED ATLAS: example_cell_type Monocytes_EPIC B.cells_EPIC CD4T.cells_EPIC NK.cells_EPIC CD8T.cells_EPIC Neutrophils_EPIC Erythrocyte_progenitors Adipocytes Cortical_neurons Hepatocytes Lung_cells Pancreatic_beta_cells Pancreatic_acinar_cells Pancreatic_duct_cells Vascular_endothelial_cells Colon_epithelial_cells Left_atrium Bladder Breast Head_and_neck_larynx Kidney Prostate Thyroid Upper_GI Uterus_cervix Extracting DMPs for example_sample DMPs hyper: 0 Extracting DMPs for Monocytes_EPIC DMPs hyper: 79 Extracting DMPs for B.cells_EPIC DMPs hyper: 152 Extracting DMPs for CD4T.cells_EPIC DMPs hyper: 89 Extracting DMPs for NK.cells_EPIC DMPs hyper: 155 Extracting DMPs for CD8T.cells_EPIC DMPs hyper: 62 Extracting DMPs for Neutrophils_EPIC DMPs hyper: 147 Extracting DMPs for Erythrocyte_progenitors DMPs hyper: 134 Extracting DMPs for Adipocytes DMPs hyper: 48 Extracting DMPs for Cortical_neurons DMPs hyper: 371 Extracting DMPs for Hepatocytes DMPs hyper: 284 Extracting DMPs for Lung_cells DMPs hyper: 139 Extracting DMPs for Pancreatic_beta_cells DMPs hyper: 158 Extracting DMPs for Pancreatic_acinar_cells DMPs hyper: 249 Extracting DMPs for Pancreatic_duct_cells DMPs hyper: 116 Extracting DMPs for Vascular_endothelial_cells DMPs hyper: 43 Extracting DMPs for Colon_epithelial_cells DMPs hyper: 365 Extracting DMPs for Left_atrium DMPs hyper: 38 Extracting DMPs for Bladder DMPs hyper: 81 Extracting DMPs for Breast DMPs hyper: 72 Extracting DMPs for Head_and_neck_larynx DMPs hyper: 63 Extracting DMPs for Kidney DMPs hyper: 141 Extracting DMPs for Prostate DMPs hyper: 53 Extracting DMPs for Thyroid DMPs hyper: 145 Extracting DMPs for Upper_GI DMPs hyper: 54 Extracting DMPs for Uterus_cervix DMPs hyper: 24 [ FAIL 0 | WARN 195 | SKIP 0 | PASS 154 ] [ FAIL 0 | WARN 195 | SKIP 0 | PASS 154 ] > > proc.time() user system elapsed 372.186 8.658 386.185
deconvR.Rcheck/deconvR-Ex.timings
name | user | system | elapsed | |
BSmeth2Probe | 2.365 | 0.084 | 2.454 | |
deconvolute | 0.981 | 0.105 | 1.091 | |
findSignatures | 1.215 | 0.043 | 1.261 | |
simulateCellMix | 0.184 | 0.028 | 0.212 | |