Back to Multiple platform build/check report for BioC 3.22: simplified long |
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This page was generated on 2025-08-23 12:07 -0400 (Sat, 23 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" | 4821 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4599 |
kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" | 4553 |
taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4539 |
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 1621/2319 | 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: 2025-08-22 11:12:15 -0000 (Fri, 22 Aug 2025) |
EndedAt: 2025-08-22 11:19:08 -0000 (Fri, 22 Aug 2025) |
EllapsedTime: 412.5 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_single 5.856 0.586 6.463 plot_boxplots 6.269 0.136 6.424 normalize_se 5.939 0.140 6.097 plot_heatmap 5.877 0.083 5.983 normalize_se_combination 5.735 0.223 5.976 normicsNorm 5.489 0.232 5.743 * 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 | 0.034 | 0.000 | 0.034 | |
detect_outliers_POMA | 2.063 | 0.055 | 2.125 | |
eigenMSNorm | 1.002 | 0.068 | 1.073 | |
export_data | 0.024 | 0.000 | 0.024 | |
extract_consensus_DE_candidates | 0.111 | 0.000 | 0.112 | |
filter_out_NA_proteins_by_threshold | 0.316 | 0.008 | 0.324 | |
filter_out_complete_NA_proteins | 0.059 | 0.000 | 0.059 | |
filter_out_proteins_by_ID | 0.24 | 0.00 | 0.24 | |
filter_out_proteins_by_value | 0.235 | 0.004 | 0.240 | |
get_NA_overview | 0.034 | 0.003 | 0.037 | |
get_normalization_methods | 0 | 0 | 0 | |
get_overview_DE | 0.048 | 0.000 | 0.047 | |
get_proteins_by_value | 0.214 | 0.000 | 0.214 | |
get_spiked_stats_DE | 0.082 | 0.004 | 0.087 | |
globalIntNorm | 0.184 | 0.000 | 0.185 | |
globalMeanNorm | 0.193 | 0.016 | 0.209 | |
globalMedianNorm | 0.223 | 0.004 | 0.228 | |
impute_se | 1.093 | 0.036 | 1.129 | |
irsNorm | 0.07 | 0.00 | 0.07 | |
limmaNorm | 0.091 | 0.000 | 0.091 | |
load_data | 0.070 | 0.004 | 0.078 | |
load_spike_data | 0.056 | 0.000 | 0.059 | |
loessCycNorm | 0.183 | 0.000 | 0.183 | |
loessFNorm | 0.129 | 0.000 | 0.128 | |
meanNorm | 0.046 | 0.004 | 0.049 | |
medianAbsDevNorm | 0.129 | 0.004 | 0.140 | |
medianNorm | 0.069 | 0.004 | 0.073 | |
normalize_se | 5.939 | 0.140 | 6.097 | |
normalize_se_combination | 5.735 | 0.223 | 5.976 | |
normalize_se_single | 5.856 | 0.586 | 6.463 | |
normicsNorm | 5.489 | 0.232 | 5.743 | |
plot_NA_density | 0.467 | 0.028 | 0.496 | |
plot_NA_frequency | 0.242 | 0.000 | 0.242 | |
plot_NA_heatmap | 2.818 | 0.075 | 2.902 | |
plot_PCA | 1.504 | 0.016 | 1.524 | |
plot_ROC_AUC_spiked | 1.395 | 0.032 | 1.437 | |
plot_TP_FP_spiked_bar | 0.337 | 0.008 | 0.345 | |
plot_TP_FP_spiked_box | 0.482 | 0.012 | 0.494 | |
plot_TP_FP_spiked_scatter | 0.515 | 0.000 | 0.518 | |
plot_boxplots | 6.269 | 0.136 | 6.424 | |
plot_condition_overview | 0.284 | 0.000 | 0.286 | |
plot_densities | 3.742 | 0.092 | 3.843 | |
plot_fold_changes_spiked | 0.639 | 0.016 | 0.657 | |
plot_heatmap | 5.877 | 0.083 | 5.983 | |
plot_heatmap_DE | 2.004 | 0.032 | 2.042 | |
plot_histogram_spiked | 0.481 | 0.016 | 0.498 | |
plot_identified_spiked_proteins | 0.627 | 0.020 | 0.649 | |
plot_intersection_enrichment | 0.946 | 0.040 | 2.762 | |
plot_intragroup_PCV | 0.784 | 0.012 | 0.799 | |
plot_intragroup_PEV | 0.598 | 0.016 | 0.615 | |
plot_intragroup_PMAD | 0.528 | 0.008 | 0.537 | |
plot_intragroup_correlation | 0.540 | 0.016 | 0.558 | |
plot_jaccard_heatmap | 0.348 | 0.000 | 0.348 | |
plot_logFC_thresholds_spiked | 0.786 | 0.016 | 0.805 | |
plot_markers_boxplots | 1.070 | 0.012 | 1.084 | |
plot_nr_prot_samples | 0.369 | 0.008 | 0.378 | |
plot_overview_DE_bar | 0.421 | 0.000 | 0.422 | |
plot_overview_DE_tile | 0.255 | 0.000 | 0.254 | |
plot_profiles_spiked | 1.041 | 0.008 | 1.052 | |
plot_pvalues_spiked | 0.620 | 0.008 | 0.630 | |
plot_stats_spiked_heatmap | 0.422 | 0.012 | 0.436 | |
plot_tot_int_samples | 0.318 | 0.004 | 0.322 | |
plot_upset | 0.883 | 0.000 | 0.889 | |
plot_upset_DE | 1.210 | 0.048 | 1.267 | |
plot_volcano_DE | 4.497 | 0.091 | 4.600 | |
quantileNorm | 0.044 | 0.004 | 0.049 | |
readPRONE_example | 0.001 | 0.000 | 0.001 | |
remove_POMA_outliers | 0.815 | 0.008 | 0.824 | |
remove_assays_from_SE | 0.051 | 0.004 | 0.056 | |
remove_reference_samples | 0.034 | 0.004 | 0.038 | |
remove_samples_manually | 0.043 | 0.000 | 0.044 | |
rlrMACycNorm | 1.063 | 0.020 | 1.087 | |
rlrMANorm | 0.140 | 0.000 | 0.141 | |
rlrNorm | 0.115 | 0.008 | 0.122 | |
robnormNorm | 0.226 | 0.016 | 0.242 | |
run_DE | 3.613 | 0.016 | 3.638 | |
specify_comparisons | 0.026 | 0.000 | 0.027 | |
subset_SE_by_norm | 0.101 | 0.008 | 0.110 | |
tmmNorm | 0.175 | 0.004 | 0.179 | |
vsnNorm | 0.085 | 0.000 | 0.085 | |