Back to Multiple platform build/check report for BioC 3.21: simplified long |
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This page was generated on 2024-12-24 11:42 -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 1581/2274 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
PrInCE 1.23.0 (landing page) Michael Skinnider
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | WARNINGS | |||||||||
palomino7 | Windows Server 2022 Datacenter / x64 | OK | OK | WARNINGS | OK | |||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | WARNINGS | OK | |||||||||
kjohnson3 | macOS 13.7.1 Ventura / arm64 | 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: 1.23.0 |
Command: E:\biocbuild\bbs-3.21-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:PrInCE.install-out.txt --library=E:\biocbuild\bbs-3.21-bioc\R\library --no-vignettes --timings PrInCE_1.23.0.tar.gz |
StartedAt: 2024-12-24 03:49:52 -0500 (Tue, 24 Dec 2024) |
EndedAt: 2024-12-24 03:55:37 -0500 (Tue, 24 Dec 2024) |
EllapsedTime: 345.3 seconds |
RetCode: 0 |
Status: WARNINGS |
CheckDir: PrInCE.Rcheck |
Warnings: 1 |
############################################################################## ############################################################################## ### ### Running command: ### ### E:\biocbuild\bbs-3.21-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:PrInCE.install-out.txt --library=E:\biocbuild\bbs-3.21-bioc\R\library --no-vignettes --timings PrInCE_1.23.0.tar.gz ### ############################################################################## ############################################################################## * using log directory 'E:/biocbuild/bbs-3.21-bioc/meat/PrInCE.Rcheck' * using R Under development (unstable) (2024-10-26 r87273 ucrt) * using platform: x86_64-w64-mingw32 * R was compiled by gcc.exe (GCC) 13.2.0 GNU Fortran (GCC) 13.2.0 * running under: Windows Server 2022 x64 (build 20348) * using session charset: UTF-8 * using option '--no-vignettes' * checking for file 'PrInCE/DESCRIPTION' ... OK * this is package 'PrInCE' version '1.23.0' * 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 ... 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 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 ... NOTE Found the following Rd file(s) with Rd \link{} targets missing package anchors: PrInCE.Rd: MSnSet-class build_gaussians.Rd: MSnSet-class calculate_autocorrelation.Rd: MSnSet-class calculate_features.Rd: MSnSet-class clean_profiles.Rd: MSnSet-class detect_complexes.Rd: MSnSet-class filter_profiles.Rd: MSnSet-class Please provide package anchors for all Rd \link{} targets not in the package itself and the base packages. * 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 7.36 0.28 7.67 calculate_precision 6.09 0.47 6.56 threshold_precision 6.02 0.47 6.47 predict_ensemble 6.17 0.30 6.47 predict_interactions 5.92 0.36 6.28 * 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, 3 NOTEs See 'E:/biocbuild/bbs-3.21-bioc/meat/PrInCE.Rcheck/00check.log' for details.
PrInCE.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### E:\biocbuild\bbs-3.21-bioc\R\bin\R.exe CMD INSTALL PrInCE ### ############################################################################## ############################################################################## * installing to library 'E:/biocbuild/bbs-3.21-bioc/R/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 | 7.36 | 0.28 | 7.67 | |
adjacency_matrix_from_data_frame | 0 | 0 | 0 | |
adjacency_matrix_from_list | 0.48 | 0.03 | 0.52 | |
build_gaussians | 0.41 | 0.14 | 0.54 | |
calculate_precision | 6.09 | 0.47 | 6.56 | |
check_gaussians | 0.20 | 0.09 | 0.29 | |
choose_gaussians | 0.20 | 0.00 | 0.21 | |
clean_profile | 0.03 | 0.02 | 0.04 | |
clean_profiles | 0.05 | 0.01 | 0.07 | |
co_apex | 0.23 | 0.13 | 0.36 | |
detect_complexes | 0.11 | 0.08 | 0.18 | |
filter_profiles | 0.32 | 0.03 | 0.36 | |
fit_curve | 0.20 | 0.01 | 0.22 | |
fit_gaussians | 0.20 | 0.04 | 0.24 | |
impute_neighbors | 0.05 | 0.01 | 0.06 | |
is_unweighted | 0.41 | 0.05 | 0.45 | |
is_weighted | 0.39 | 0.02 | 0.40 | |
make_initial_conditions | 0.04 | 0.02 | 0.07 | |
make_labels | 0.44 | 0.01 | 0.45 | |
match_matrix_dimensions | 0.55 | 0.06 | 0.61 | |
predict_ensemble | 6.17 | 0.30 | 6.47 | |
predict_interactions | 5.92 | 0.36 | 6.28 | |
threshold_precision | 6.02 | 0.47 | 6.47 | |