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 |
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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 1591/2289 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
PrInCE 1.22.0 (landing page) Michael Skinnider
| teran2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | WARNINGS | |||||||||
nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | WARNINGS | ||||||||||
palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | WARNINGS | OK | |||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | WARNINGS | OK | |||||||||
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | WARNINGS | ||||||||||
To the developers/maintainers of the PrInCE package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/PrInCE.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: PrInCE |
Version: 1.22.0 |
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:PrInCE.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings PrInCE_1.22.0.tar.gz |
StartedAt: 2024-11-20 01:19:12 -0500 (Wed, 20 Nov 2024) |
EndedAt: 2024-11-20 01:27:03 -0500 (Wed, 20 Nov 2024) |
EllapsedTime: 470.6 seconds |
RetCode: 0 |
Status: WARNINGS |
CheckDir: PrInCE.Rcheck |
Warnings: 1 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:PrInCE.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings PrInCE_1.22.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/PrInCE.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 ‘PrInCE/DESCRIPTION’ ... OK * this is package ‘PrInCE’ version ‘1.22.0’ * 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 ... NOTE Found the following hidden files and directories: .lintr 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 ‘PrInCE’ 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 ... NOTE calculate_features: no visible global function definition for ‘quantile’ Undefined global functions or variables: quantile Consider adding importFrom("stats", "quantile") to your NAMESPACE file. * 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 ... WARNING Undocumented arguments in Rd file 'calculate_autocorrelation.Rd' ‘min_replicates’ Undocumented arguments in Rd file 'calculate_features.Rd' ‘n_pairs’ Functions with \usage entries need to have the appropriate \alias entries, and all their arguments documented. The \usage entries must correspond to syntactically valid R code. See chapter ‘Writing R documentation files’ in the ‘Writing R Extensions’ manual. * 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 PrInCE 5.013 0.259 5.344 * 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 WARNING, 2 NOTEs See ‘/Users/biocbuild/bbs-3.20-bioc/meat/PrInCE.Rcheck/00check.log’ for details.
PrInCE.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL PrInCE ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library’ * installing *source* package ‘PrInCE’ ... ** using staged installation ** R ** data ** inst ** byte-compile and prepare package for lazy loading ** help Loading required namespace: PrInCE Registered S3 method overwritten by 'quantmod': method from as.zoo.data.frame zoo *** 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 (PrInCE)
PrInCE.Rcheck/PrInCE-Ex.timings
name | user | system | elapsed | |
PrInCE | 5.013 | 0.259 | 5.344 | |
adjacency_matrix_from_data_frame | 0.001 | 0.000 | 0.002 | |
adjacency_matrix_from_list | 0.273 | 0.004 | 0.277 | |
build_gaussians | 0.385 | 0.040 | 0.427 | |
calculate_precision | 3.938 | 0.237 | 4.185 | |
check_gaussians | 0.088 | 0.003 | 0.091 | |
choose_gaussians | 0.139 | 0.003 | 0.142 | |
clean_profile | 0.034 | 0.005 | 0.040 | |
clean_profiles | 0.034 | 0.002 | 0.036 | |
co_apex | 0.083 | 0.003 | 0.085 | |
detect_complexes | 0.086 | 0.010 | 0.096 | |
filter_profiles | 0.198 | 0.008 | 0.207 | |
fit_curve | 0.111 | 0.007 | 0.119 | |
fit_gaussians | 0.111 | 0.004 | 0.115 | |
impute_neighbors | 0.037 | 0.003 | 0.040 | |
is_unweighted | 0.322 | 0.029 | 0.351 | |
is_weighted | 0.284 | 0.005 | 0.289 | |
make_initial_conditions | 0.035 | 0.004 | 0.039 | |
make_labels | 0.274 | 0.004 | 0.278 | |
match_matrix_dimensions | 0.395 | 0.018 | 0.413 | |
predict_ensemble | 3.840 | 0.217 | 4.060 | |
predict_interactions | 3.798 | 0.158 | 3.962 | |
threshold_precision | 3.563 | 0.175 | 3.741 | |