Back to Multiple platform build/check report for BioC 3.22: simplified long |
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This page was generated on 2025-09-11 12:04 -0400 (Thu, 11 Sep 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" | 4539 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4474 |
kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4519 |
taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4544 |
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 1623/2322 | 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. |
Package: PRONE |
Version: 1.3.1 |
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_1.3.1.tar.gz |
StartedAt: 2025-09-11 03:56:31 -0400 (Thu, 11 Sep 2025) |
EndedAt: 2025-09-11 04:04:25 -0400 (Thu, 11 Sep 2025) |
EllapsedTime: 473.5 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_1.3.1.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 ‘1.3.1’ * 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 * 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: 1 NOTE 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 ‘1.3.1’ ** 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 | 0.031 | 0.001 | 0.033 | |
detect_outliers_POMA | 1.639 | 0.055 | 1.692 | |
eigenMSNorm | 0.611 | 0.081 | 0.693 | |
export_data | 0.027 | 0.000 | 0.028 | |
extract_consensus_DE_candidates | 0.080 | 0.001 | 0.080 | |
filter_out_NA_proteins_by_threshold | 0.243 | 0.000 | 0.208 | |
filter_out_complete_NA_proteins | 0.054 | 0.001 | 0.055 | |
filter_out_proteins_by_ID | 0.157 | 0.001 | 0.158 | |
filter_out_proteins_by_value | 0.157 | 0.002 | 0.159 | |
get_NA_overview | 0.037 | 0.000 | 0.038 | |
get_normalization_methods | 0 | 0 | 0 | |
get_overview_DE | 0.043 | 0.001 | 0.045 | |
get_proteins_by_value | 0.142 | 0.002 | 0.144 | |
get_spiked_stats_DE | 0.084 | 0.003 | 0.087 | |
globalIntNorm | 0.131 | 0.002 | 0.133 | |
globalMeanNorm | 0.133 | 0.024 | 0.159 | |
globalMedianNorm | 0.150 | 0.003 | 0.154 | |
impute_se | 1.008 | 0.017 | 0.727 | |
irsNorm | 0.059 | 0.001 | 0.060 | |
limmaNorm | 0.068 | 0.001 | 0.070 | |
load_data | 0.046 | 0.004 | 0.049 | |
load_spike_data | 0.059 | 0.004 | 0.063 | |
loessCycNorm | 0.102 | 0.000 | 0.102 | |
loessFNorm | 0.086 | 0.001 | 0.087 | |
meanNorm | 0.044 | 0.000 | 0.044 | |
medianAbsDevNorm | 0.095 | 0.005 | 0.099 | |
medianNorm | 0.059 | 0.002 | 0.061 | |
normalize_se | 3.452 | 0.066 | 3.517 | |
normalize_se_combination | 3.301 | 0.041 | 3.342 | |
normalize_se_single | 3.238 | 0.074 | 3.312 | |
normicsNorm | 3.163 | 0.043 | 3.206 | |
plot_NA_density | 0.381 | 0.011 | 0.350 | |
plot_NA_frequency | 0.214 | 0.003 | 0.174 | |
plot_NA_heatmap | 2.253 | 0.102 | 2.355 | |
plot_PCA | 1.014 | 0.000 | 1.014 | |
plot_ROC_AUC_spiked | 1.014 | 0.011 | 0.959 | |
plot_TP_FP_spiked_bar | 0.255 | 0.005 | 0.260 | |
plot_TP_FP_spiked_box | 0.330 | 0.001 | 0.330 | |
plot_TP_FP_spiked_scatter | 0.351 | 0.002 | 0.354 | |
plot_boxplots | 4.144 | 0.021 | 3.847 | |
plot_condition_overview | 0.195 | 0.001 | 0.196 | |
plot_densities | 2.682 | 0.006 | 2.365 | |
plot_fold_changes_spiked | 0.490 | 0.005 | 0.447 | |
plot_heatmap | 3.604 | 0.003 | 3.609 | |
plot_heatmap_DE | 1.204 | 0.004 | 1.209 | |
plot_histogram_spiked | 0.384 | 0.003 | 0.295 | |
plot_identified_spiked_proteins | 0.392 | 0.000 | 0.392 | |
plot_intersection_enrichment | 0.694 | 0.006 | 2.999 | |
plot_intragroup_PCV | 0.474 | 0.001 | 0.475 | |
plot_intragroup_PEV | 0.384 | 0.002 | 0.386 | |
plot_intragroup_PMAD | 0.319 | 0.001 | 0.320 | |
plot_intragroup_correlation | 0.332 | 0.002 | 0.334 | |
plot_jaccard_heatmap | 0.229 | 0.001 | 0.217 | |
plot_logFC_thresholds_spiked | 0.552 | 0.001 | 0.553 | |
plot_markers_boxplots | 0.740 | 0.001 | 0.706 | |
plot_nr_prot_samples | 0.259 | 0.002 | 0.261 | |
plot_overview_DE_bar | 0.305 | 0.002 | 0.308 | |
plot_overview_DE_tile | 0.177 | 0.012 | 0.190 | |
plot_profiles_spiked | 0.847 | 0.029 | 0.765 | |
plot_pvalues_spiked | 0.425 | 0.027 | 0.452 | |
plot_stats_spiked_heatmap | 0.309 | 0.031 | 0.341 | |
plot_tot_int_samples | 0.229 | 0.014 | 0.243 | |
plot_upset | 0.620 | 0.049 | 0.669 | |
plot_upset_DE | 0.791 | 0.030 | 0.822 | |
plot_volcano_DE | 2.906 | 0.191 | 3.099 | |
quantileNorm | 0.041 | 0.008 | 0.051 | |
readPRONE_example | 0.001 | 0.000 | 0.001 | |
remove_POMA_outliers | 0.483 | 0.026 | 0.509 | |
remove_assays_from_SE | 0.048 | 0.003 | 0.050 | |
remove_reference_samples | 0.047 | 0.004 | 0.051 | |
remove_samples_manually | 0.042 | 0.002 | 0.043 | |
rlrMACycNorm | 0.632 | 0.062 | 0.694 | |
rlrMANorm | 0.102 | 0.005 | 0.108 | |
rlrNorm | 0.089 | 0.005 | 0.093 | |
robnormNorm | 0.246 | 0.027 | 0.273 | |
run_DE | 2.421 | 0.021 | 2.381 | |
specify_comparisons | 0.039 | 0.000 | 0.031 | |
subset_SE_by_norm | 0.083 | 0.000 | 0.083 | |
tmmNorm | 0.138 | 0.006 | 0.144 | |
vsnNorm | 0.075 | 0.003 | 0.078 | |