Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2025-02-06 12:10 -0500 (Thu, 06 Feb 2025).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4753 |
palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" | 4501 |
merida1 | macOS 12.7.5 Monterey | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4524 |
kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4476 |
taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4407 |
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 1604/2289 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
PRONE 1.0.2 (landing page) Lis Arend
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | ![]() | ||||||||
palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | ![]() | ||||||||
merida1 | macOS 12.7.5 Monterey / x86_64 | OK | OK | OK | OK | ![]() | ||||||||
kjohnson1 | macOS 13.6.6 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. |
Package: PRONE |
Version: 1.0.2 |
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:PRONE.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings PRONE_1.0.2.tar.gz |
StartedAt: 2025-02-05 06:05:19 -0500 (Wed, 05 Feb 2025) |
EndedAt: 2025-02-05 06:11:02 -0500 (Wed, 05 Feb 2025) |
EllapsedTime: 343.4 seconds |
RetCode: 0 |
Status: OK |
CheckDir: PRONE.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:PRONE.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings PRONE_1.0.2.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/PRONE.Rcheck’ * using R version 4.4.2 (2024-10-31) * using platform: aarch64-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 Ventura 13.7.1 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘PRONE/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘PRONE’ version ‘1.0.2’ * 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 ... 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 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 plot_intersection_enrichment 1.621 0.059 9.154 * 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 ‘/Users/biocbuild/bbs-3.20-bioc/meat/PRONE.Rcheck/00check.log’ for details.
PRONE.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL PRONE ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library’ * installing *source* package ‘PRONE’ ... ** 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 | 0.043 | 0.004 | 0.048 | |
detect_outliers_POMA | 0.950 | 0.074 | 1.048 | |
eigenMSNorm | 0.689 | 0.029 | 0.719 | |
export_data | 0.042 | 0.004 | 0.044 | |
extract_consensus_DE_candidates | 0.103 | 0.005 | 0.108 | |
filter_out_NA_proteins_by_threshold | 1.374 | 0.029 | 1.253 | |
filter_out_complete_NA_proteins | 0.103 | 0.007 | 0.073 | |
filter_out_proteins_by_ID | 0.152 | 0.003 | 0.155 | |
filter_out_proteins_by_value | 0.153 | 0.004 | 0.156 | |
get_NA_overview | 0.052 | 0.003 | 0.055 | |
get_normalization_methods | 0.001 | 0.000 | 0.000 | |
get_overview_DE | 0.053 | 0.004 | 0.056 | |
get_proteins_by_value | 0.145 | 0.004 | 0.149 | |
get_spiked_stats_DE | 0.119 | 0.006 | 0.125 | |
globalIntNorm | 0.154 | 0.016 | 0.170 | |
globalMeanNorm | 0.153 | 0.018 | 0.172 | |
globalMedianNorm | 0.153 | 0.018 | 0.172 | |
impute_se | 1.426 | 0.112 | 0.840 | |
irsNorm | 0.141 | 0.012 | 0.079 | |
limmaNorm | 0.105 | 0.006 | 0.087 | |
load_data | 0.064 | 0.004 | 0.069 | |
load_spike_data | 0.055 | 0.003 | 0.059 | |
loessCycNorm | 0.147 | 0.014 | 0.162 | |
loessFNorm | 0.111 | 0.003 | 0.115 | |
meanNorm | 0.060 | 0.003 | 0.062 | |
medianAbsDevNorm | 0.120 | 0.005 | 0.124 | |
medianNorm | 0.078 | 0.003 | 0.082 | |
normalize_se | 3.377 | 0.100 | 3.480 | |
normalize_se_combination | 3.281 | 0.060 | 3.345 | |
normalize_se_single | 3.232 | 0.047 | 3.281 | |
normicsNorm | 3.163 | 0.045 | 3.210 | |
plot_NA_density | 0.502 | 0.033 | 0.345 | |
plot_NA_frequency | 0.320 | 0.022 | 0.206 | |
plot_NA_heatmap | 1.582 | 0.078 | 1.610 | |
plot_PCA | 0.992 | 0.015 | 1.008 | |
plot_ROC_AUC_spiked | 1.191 | 0.041 | 1.045 | |
plot_TP_FP_spiked_bar | 0.280 | 0.008 | 0.289 | |
plot_TP_FP_spiked_box | 0.360 | 0.021 | 0.382 | |
plot_TP_FP_spiked_scatter | 1.537 | 0.027 | 1.565 | |
plot_boxplots | 4.399 | 0.138 | 3.610 | |
plot_condition_overview | 0.213 | 0.005 | 0.218 | |
plot_densities | 3.150 | 0.152 | 2.446 | |
plot_fold_changes_spiked | 0.635 | 0.032 | 0.478 | |
plot_heatmap | 3.906 | 0.065 | 3.972 | |
plot_heatmap_DE | 1.266 | 0.023 | 1.292 | |
plot_histogram_spiked | 0.499 | 0.028 | 0.338 | |
plot_identified_spiked_proteins | 0.428 | 0.009 | 0.438 | |
plot_intersection_enrichment | 1.621 | 0.059 | 9.154 | |
plot_intragroup_PCV | 0.494 | 0.007 | 0.501 | |
plot_intragroup_PEV | 0.339 | 0.006 | 0.345 | |
plot_intragroup_PMAD | 0.325 | 0.006 | 0.330 | |
plot_intragroup_correlation | 0.358 | 0.006 | 0.364 | |
plot_jaccard_heatmap | 0.391 | 0.028 | 0.248 | |
plot_logFC_thresholds_spiked | 0.564 | 0.012 | 0.564 | |
plot_markers_boxplots | 0.840 | 0.031 | 0.681 | |
plot_nr_prot_samples | 0.235 | 0.005 | 0.240 | |
plot_overview_DE_bar | 0.283 | 0.005 | 0.287 | |
plot_overview_DE_tile | 0.183 | 0.004 | 0.187 | |
plot_profiles_spiked | 0.905 | 0.037 | 0.738 | |
plot_pvalues_spiked | 0.466 | 0.011 | 0.477 | |
plot_stats_spiked_heatmap | 0.328 | 0.008 | 0.337 | |
plot_tot_int_samples | 0.257 | 0.006 | 0.263 | |
plot_upset | 0.567 | 0.010 | 0.584 | |
plot_upset_DE | 0.808 | 0.019 | 0.868 | |
plot_volcano_DE | 2.036 | 0.025 | 2.081 | |
quantileNorm | 0.061 | 0.004 | 0.064 | |
readPRONE_example | 0.002 | 0.001 | 0.003 | |
remove_POMA_outliers | 0.535 | 0.006 | 0.541 | |
remove_assays_from_SE | 0.065 | 0.003 | 0.069 | |
remove_reference_samples | 0.067 | 0.003 | 0.070 | |
remove_samples_manually | 0.055 | 0.003 | 0.057 | |
rlrMACycNorm | 0.759 | 0.009 | 0.769 | |
rlrMANorm | 0.111 | 0.003 | 0.114 | |
rlrNorm | 0.105 | 0.003 | 0.108 | |
robnormNorm | 0.090 | 0.006 | 0.097 | |
run_DE | 2.841 | 0.103 | 2.239 | |
specify_comparisons | 0.084 | 0.008 | 0.048 | |
subset_SE_by_norm | 0.181 | 0.013 | 0.103 | |
tmmNorm | 0.190 | 0.014 | 0.167 | |
vsnNorm | 0.082 | 0.003 | 0.086 | |