Back to Multiple platform build/check report for BioC 3.22: simplified long |
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This page was generated on 2025-10-13 12:04 -0400 (Mon, 13 Oct 2025).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" | 4864 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4652 |
kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4597 |
taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4586 |
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 1642/2346 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
PRONE 1.3.2 (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. |
Package: PRONE |
Version: 1.3.2 |
Command: /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:PRONE.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings PRONE_1.3.2.tar.gz |
StartedAt: 2025-10-13 03:06:31 -0400 (Mon, 13 Oct 2025) |
EndedAt: 2025-10-13 03:14:35 -0400 (Mon, 13 Oct 2025) |
EllapsedTime: 484.4 seconds |
RetCode: 0 |
Status: OK |
CheckDir: PRONE.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:PRONE.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings PRONE_1.3.2.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/PRONE.Rcheck’ * using R version 4.5.1 Patched (2025-08-23 r88802) * using platform: x86_64-pc-linux-gnu * R was compiled by gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0 GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0 * running under: Ubuntu 24.04.3 LTS * using session charset: UTF-8 * checking for file ‘PRONE/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘PRONE’ version ‘1.3.2’ * 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 ... NOTE plot_upset_DE: no visible global function definition for ‘packageVersion’ Undefined global functions or variables: packageVersion Consider adding importFrom("utils", "packageVersion") 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 ... 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 * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking re-building of vignette outputs ... OK * checking PDF version of manual ... OK * DONE Status: 2 NOTEs See ‘/home/biocbuild/bbs-3.22-bioc/meat/PRONE.Rcheck/00check.log’ for details.
PRONE.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD INSTALL PRONE ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.22-bioc/R/site-library’ * installing *source* package ‘PRONE’ ... ** this is package ‘PRONE’ version ‘1.3.2’ ** 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 | 0.030 | 0.002 | 0.033 | |
detect_outliers_POMA | 1.758 | 0.076 | 1.834 | |
eigenMSNorm | 0.585 | 0.071 | 0.656 | |
export_data | 0.028 | 0.000 | 0.028 | |
extract_consensus_DE_candidates | 0.076 | 0.002 | 0.078 | |
filter_out_NA_proteins_by_threshold | 0.235 | 0.000 | 0.198 | |
filter_out_complete_NA_proteins | 0.051 | 0.000 | 0.052 | |
filter_out_proteins_by_ID | 0.150 | 0.002 | 0.152 | |
filter_out_proteins_by_value | 0.154 | 0.000 | 0.154 | |
get_NA_overview | 0.032 | 0.003 | 0.037 | |
get_normalization_methods | 0 | 0 | 0 | |
get_overview_DE | 0.040 | 0.001 | 0.042 | |
get_proteins_by_value | 0.161 | 0.002 | 0.161 | |
get_spiked_stats_DE | 0.084 | 0.004 | 0.087 | |
globalIntNorm | 0.127 | 0.001 | 0.128 | |
globalMeanNorm | 0.127 | 0.015 | 0.143 | |
globalMedianNorm | 0.130 | 0.000 | 0.131 | |
impute_se | 0.951 | 0.010 | 0.694 | |
irsNorm | 0.057 | 0.000 | 0.058 | |
limmaNorm | 0.068 | 0.000 | 0.068 | |
load_data | 0.048 | 0.000 | 0.049 | |
load_spike_data | 0.038 | 0.002 | 0.040 | |
loessCycNorm | 0.114 | 0.008 | 0.122 | |
loessFNorm | 0.085 | 0.001 | 0.086 | |
meanNorm | 0.043 | 0.002 | 0.045 | |
medianAbsDevNorm | 0.094 | 0.002 | 0.096 | |
medianNorm | 0.059 | 0.000 | 0.059 | |
normalize_se | 3.334 | 0.095 | 3.428 | |
normalize_se_combination | 3.964 | 0.209 | 4.173 | |
normalize_se_single | 3.131 | 0.079 | 3.209 | |
normicsNorm | 3.004 | 0.034 | 3.038 | |
plot_NA_density | 0.422 | 0.005 | 0.388 | |
plot_NA_frequency | 0.250 | 0.001 | 0.208 | |
plot_NA_heatmap | 1.275 | 0.027 | 1.303 | |
plot_PCA | 1.311 | 0.020 | 1.332 | |
plot_ROC_AUC_spiked | 1.229 | 0.019 | 1.181 | |
plot_TP_FP_spiked_bar | 0.320 | 0.001 | 0.321 | |
plot_TP_FP_spiked_box | 0.408 | 0.003 | 0.412 | |
plot_TP_FP_spiked_scatter | 0.421 | 0.005 | 0.426 | |
plot_boxplots | 4.845 | 0.028 | 4.515 | |
plot_condition_overview | 0.252 | 0.000 | 0.252 | |
plot_densities | 2.965 | 0.004 | 2.610 | |
plot_fold_changes_spiked | 0.619 | 0.002 | 0.547 | |
plot_heatmap | 3.606 | 0.002 | 3.608 | |
plot_heatmap_DE | 1.236 | 0.004 | 1.239 | |
plot_histogram_spiked | 0.497 | 0.003 | 0.416 | |
plot_identified_spiked_proteins | 0.441 | 0.004 | 0.445 | |
plot_intersection_enrichment | 0.863 | 0.011 | 2.600 | |
plot_intragroup_PCV | 0.555 | 0.001 | 0.556 | |
plot_intragroup_PEV | 0.504 | 0.001 | 0.505 | |
plot_intragroup_PMAD | 0.422 | 0.003 | 0.424 | |
plot_intragroup_correlation | 0.427 | 0.007 | 0.433 | |
plot_jaccard_heatmap | 0.312 | 0.008 | 0.308 | |
plot_logFC_thresholds_spiked | 0.720 | 0.010 | 0.731 | |
plot_markers_boxplots | 0.896 | 0.001 | 0.861 | |
plot_nr_prot_samples | 0.271 | 0.001 | 0.272 | |
plot_overview_DE_bar | 0.452 | 0.023 | 0.476 | |
plot_overview_DE_tile | 0.256 | 0.007 | 0.262 | |
plot_profiles_spiked | 0.988 | 0.112 | 0.980 | |
plot_pvalues_spiked | 0.529 | 0.035 | 0.564 | |
plot_stats_spiked_heatmap | 0.421 | 0.031 | 0.452 | |
plot_tot_int_samples | 0.263 | 0.033 | 0.295 | |
plot_upset | 0.898 | 0.091 | 0.989 | |
plot_upset_DE | 0.030 | 0.002 | 0.032 | |
plot_volcano_DE | 4.129 | 0.215 | 4.344 | |
quantileNorm | 0.046 | 0.001 | 0.048 | |
readPRONE_example | 0.001 | 0.000 | 0.001 | |
remove_POMA_outliers | 0.665 | 0.043 | 0.708 | |
remove_assays_from_SE | 0.044 | 0.004 | 0.048 | |
remove_reference_samples | 0.045 | 0.004 | 0.048 | |
remove_samples_manually | 0.038 | 0.003 | 0.041 | |
rlrMACycNorm | 0.640 | 0.057 | 0.697 | |
rlrMANorm | 0.101 | 0.006 | 0.107 | |
rlrNorm | 0.088 | 0.013 | 0.102 | |
robnormNorm | 0.075 | 0.011 | 0.086 | |
run_DE | 3.693 | 0.195 | 3.783 | |
specify_comparisons | 0.028 | 0.003 | 0.031 | |
subset_SE_by_norm | 0.079 | 0.000 | 0.080 | |
tmmNorm | 0.125 | 0.003 | 0.128 | |
vsnNorm | 0.072 | 0.002 | 0.073 | |