Back to Multiple platform build/check report for BioC 3.22: simplified long |
|
This page was generated on 2025-08-21 12:08 -0400 (Thu, 21 Aug 2025).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4819 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4597 |
kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" | 4539 |
taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4536 |
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 1620/2318 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
PRONE 1.3.1 (landing page) Lis Arend
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | OK | ![]() | ||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | ![]() | ||||||||
kjohnson3 | macOS 13.7.7 Ventura / arm64 | OK | OK | OK | OK | ![]() | ||||||||
taishan | Linux (openEuler 24.03 LTS) / aarch64 | OK | OK | OK | ||||||||||
To the developers/maintainers of the PRONE package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/PRONE.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: PRONE |
Version: 1.3.1 |
Command: /home/biocbuild/R/R/bin/R CMD check --install=check:PRONE.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings PRONE_1.3.1.tar.gz |
StartedAt: 2025-08-19 11:14:02 -0000 (Tue, 19 Aug 2025) |
EndedAt: 2025-08-19 11:20:57 -0000 (Tue, 19 Aug 2025) |
EllapsedTime: 415.3 seconds |
RetCode: 0 |
Status: OK |
CheckDir: PRONE.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R/bin/R CMD check --install=check:PRONE.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings PRONE_1.3.1.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/PRONE.Rcheck’ * using R version 4.5.0 (2025-04-11) * 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 ‘PRONE/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘PRONE’ version ‘1.3.1’ * package encoding: UTF-8 * checking package namespace information ... OK * checking package dependencies ... INFO Imports includes 34 non-default packages. Importing from so many packages makes the package vulnerable to any of them becoming unavailable. Move as many as possible to Suggests and use conditionally. * 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 ‘PRONE’ 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 Unexported objects imported by ':::' calls: ‘NormalyzerDE:::calculateAvgMadMem’ ‘NormalyzerDE:::calculateAvgReplicateVariation’ ‘NormalyzerDE:::calculatePercentageAvgDiffInMat’ ‘NormalyzerDE:::calculateReplicateCV’ ‘NormalyzerDE:::calculateSummarizedCorrelationVector’ 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 Examples with CPU (user + system) or elapsed time > 5s user system elapsed normalize_se 5.970 0.123 6.107 plot_boxplots 5.819 0.056 5.880 plot_heatmap 5.753 0.064 5.830 normalize_se_single 5.705 0.068 5.783 normalize_se_combination 5.642 0.076 5.730 normicsNorm 5.487 0.028 5.525 * 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 ‘/home/biocbuild/bbs-3.22-bioc/meat/PRONE.Rcheck/00check.log’ for details.
PRONE.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R/bin/R CMD INSTALL PRONE ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/R/R-4.5.0/site-library’ * installing *source* package ‘PRONE’ ... ** this is package ‘PRONE’ version ‘1.3.1’ ** using staged installation ** R ** data ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices *** copying figures ** 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 (PRONE)
PRONE.Rcheck/PRONE-Ex.timings
name | user | system | elapsed | |
apply_thresholds | 0.033 | 0.000 | 0.033 | |
detect_outliers_POMA | 1.849 | 0.080 | 1.932 | |
eigenMSNorm | 0.872 | 0.132 | 1.006 | |
export_data | 0.023 | 0.000 | 0.023 | |
extract_consensus_DE_candidates | 0.099 | 0.000 | 0.100 | |
filter_out_NA_proteins_by_threshold | 0.271 | 0.008 | 0.278 | |
filter_out_complete_NA_proteins | 0.056 | 0.000 | 0.056 | |
filter_out_proteins_by_ID | 0.217 | 0.000 | 0.217 | |
filter_out_proteins_by_value | 0.215 | 0.000 | 0.215 | |
get_NA_overview | 0.035 | 0.000 | 0.034 | |
get_normalization_methods | 0 | 0 | 0 | |
get_overview_DE | 0.046 | 0.000 | 0.045 | |
get_proteins_by_value | 0.194 | 0.004 | 0.198 | |
get_spiked_stats_DE | 0.085 | 0.000 | 0.085 | |
globalIntNorm | 0.189 | 0.004 | 0.194 | |
globalMeanNorm | 0.203 | 0.008 | 0.211 | |
globalMedianNorm | 0.201 | 0.020 | 0.222 | |
impute_se | 1.066 | 0.028 | 1.091 | |
irsNorm | 0.075 | 0.000 | 0.076 | |
limmaNorm | 0.086 | 0.004 | 0.091 | |
load_data | 0.067 | 0.004 | 0.074 | |
load_spike_data | 0.055 | 0.000 | 0.058 | |
loessCycNorm | 0.179 | 0.000 | 0.180 | |
loessFNorm | 0.122 | 0.004 | 0.126 | |
meanNorm | 0.046 | 0.000 | 0.046 | |
medianAbsDevNorm | 0.126 | 0.008 | 0.134 | |
medianNorm | 0.068 | 0.004 | 0.072 | |
normalize_se | 5.970 | 0.123 | 6.107 | |
normalize_se_combination | 5.642 | 0.076 | 5.730 | |
normalize_se_single | 5.705 | 0.068 | 5.783 | |
normicsNorm | 5.487 | 0.028 | 5.525 | |
plot_NA_density | 0.479 | 0.008 | 0.487 | |
plot_NA_frequency | 0.236 | 0.003 | 0.239 | |
plot_NA_heatmap | 2.799 | 0.072 | 2.877 | |
plot_PCA | 1.469 | 0.020 | 1.493 | |
plot_ROC_AUC_spiked | 1.326 | 0.012 | 1.343 | |
plot_TP_FP_spiked_bar | 0.314 | 0.004 | 0.319 | |
plot_TP_FP_spiked_box | 0.446 | 0.000 | 0.447 | |
plot_TP_FP_spiked_scatter | 0.477 | 0.000 | 0.478 | |
plot_boxplots | 5.819 | 0.056 | 5.880 | |
plot_condition_overview | 0.292 | 0.000 | 0.292 | |
plot_densities | 3.539 | 0.044 | 3.585 | |
plot_fold_changes_spiked | 0.636 | 0.016 | 0.653 | |
plot_heatmap | 5.753 | 0.064 | 5.830 | |
plot_heatmap_DE | 1.764 | 0.012 | 1.779 | |
plot_histogram_spiked | 0.414 | 0.012 | 0.427 | |
plot_identified_spiked_proteins | 0.580 | 0.011 | 0.594 | |
plot_intersection_enrichment | 0.857 | 0.051 | 3.077 | |
plot_intragroup_PCV | 0.720 | 0.004 | 0.726 | |
plot_intragroup_PEV | 0.554 | 0.000 | 0.557 | |
plot_intragroup_PMAD | 0.469 | 0.000 | 0.471 | |
plot_intragroup_correlation | 0.514 | 0.004 | 0.520 | |
plot_jaccard_heatmap | 0.310 | 0.004 | 0.314 | |
plot_logFC_thresholds_spiked | 0.765 | 0.012 | 0.779 | |
plot_markers_boxplots | 0.970 | 0.004 | 0.976 | |
plot_nr_prot_samples | 0.334 | 0.000 | 0.335 | |
plot_overview_DE_bar | 0.39 | 0.00 | 0.39 | |
plot_overview_DE_tile | 0.233 | 0.000 | 0.234 | |
plot_profiles_spiked | 0.954 | 0.004 | 0.957 | |
plot_pvalues_spiked | 0.577 | 0.004 | 0.583 | |
plot_stats_spiked_heatmap | 0.381 | 0.000 | 0.382 | |
plot_tot_int_samples | 0.297 | 0.000 | 0.298 | |
plot_upset | 0.839 | 0.008 | 0.849 | |
plot_upset_DE | 1.132 | 0.020 | 1.161 | |
plot_volcano_DE | 4.309 | 0.036 | 4.357 | |
quantileNorm | 0.046 | 0.000 | 0.048 | |
readPRONE_example | 0.001 | 0.000 | 0.002 | |
remove_POMA_outliers | 0.778 | 0.016 | 0.796 | |
remove_assays_from_SE | 0.056 | 0.000 | 0.055 | |
remove_reference_samples | 0.036 | 0.000 | 0.036 | |
remove_samples_manually | 0.040 | 0.000 | 0.041 | |
rlrMACycNorm | 0.936 | 0.008 | 0.947 | |
rlrMANorm | 0.125 | 0.004 | 0.130 | |
rlrNorm | 0.108 | 0.000 | 0.108 | |
robnormNorm | 0.222 | 0.000 | 0.223 | |
run_DE | 3.442 | 0.056 | 3.502 | |
specify_comparisons | 0.024 | 0.002 | 0.026 | |
subset_SE_by_norm | 0.101 | 0.001 | 0.102 | |
tmmNorm | 0.166 | 0.008 | 0.175 | |
vsnNorm | 0.082 | 0.000 | 0.082 | |