Back to Multiple platform build/check report for BioC 3.21: simplified long |
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This page was generated on 2025-02-03 12:37 -0500 (Mon, 03 Feb 2025).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | R Under development (unstable) (2025-01-20 r87609) -- "Unsuffered Consequences" | 4704 |
palomino7 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2025-01-21 r87610 ucrt) -- "Unsuffered Consequences" | 4467 |
lconway | macOS 12.7.1 Monterey | x86_64 | R Under development (unstable) (2025-01-22 r87618) -- "Unsuffered Consequences" | 4478 |
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 1601/2289 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
PRONE 1.1.2 (landing page) Lis Arend
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | |||||||||
palomino7 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | |||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | 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: 1.1.2 |
Command: /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:PRONE.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings PRONE_1.1.2.tar.gz |
StartedAt: 2025-02-03 01:20:59 -0500 (Mon, 03 Feb 2025) |
EndedAt: 2025-02-03 01:28:40 -0500 (Mon, 03 Feb 2025) |
EllapsedTime: 461.5 seconds |
RetCode: 0 |
Status: OK |
CheckDir: PRONE.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:PRONE.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings PRONE_1.1.2.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/PRONE.Rcheck’ * using R Under development (unstable) (2025-01-20 r87609) * 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 24.04.1 LTS * using session charset: UTF-8 * checking for file ‘PRONE/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘PRONE’ version ‘1.1.2’ * package encoding: UTF-8 * checking package namespace information ... OK * checking package dependencies ... INFO Imports includes 33 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 plot_intersection_enrichment 1.821 0.02 12.66 * 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-3.21-bioc/meat/PRONE.Rcheck/00check.log’ for details.
PRONE.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD INSTALL PRONE ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.21-bioc/R/site-library’ * installing *source* package ‘PRONE’ ... ** this is package ‘PRONE’ version ‘1.1.2’ ** 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 | 0.032 | 0.001 | 0.033 | |
detect_outliers_POMA | 1.797 | 0.038 | 1.835 | |
eigenMSNorm | 0.603 | 0.055 | 0.658 | |
export_data | 0.028 | 0.000 | 0.030 | |
extract_consensus_DE_candidates | 0.086 | 0.010 | 0.096 | |
filter_out_NA_proteins_by_threshold | 0.203 | 0.038 | 0.234 | |
filter_out_complete_NA_proteins | 0.054 | 0.005 | 0.059 | |
filter_out_proteins_by_ID | 0.152 | 0.027 | 0.179 | |
filter_out_proteins_by_value | 0.169 | 0.002 | 0.171 | |
get_NA_overview | 0.036 | 0.000 | 0.036 | |
get_normalization_methods | 0.001 | 0.001 | 0.000 | |
get_overview_DE | 0.041 | 0.000 | 0.042 | |
get_proteins_by_value | 0.139 | 0.001 | 0.140 | |
get_spiked_stats_DE | 0.080 | 0.006 | 0.085 | |
globalIntNorm | 0.125 | 0.003 | 0.127 | |
globalMeanNorm | 0.128 | 0.002 | 0.130 | |
globalMedianNorm | 0.134 | 0.001 | 0.136 | |
impute_se | 0.777 | 0.046 | 0.781 | |
irsNorm | 0.057 | 0.000 | 0.057 | |
limmaNorm | 0.065 | 0.004 | 0.068 | |
load_data | 0.052 | 0.002 | 0.056 | |
load_spike_data | 0.044 | 0.000 | 0.046 | |
loessCycNorm | 0.108 | 0.006 | 0.113 | |
loessFNorm | 0.101 | 0.003 | 0.103 | |
meanNorm | 0.042 | 0.002 | 0.044 | |
medianAbsDevNorm | 0.095 | 0.003 | 0.098 | |
medianNorm | 0.056 | 0.002 | 0.058 | |
normalize_se | 3.310 | 0.044 | 3.354 | |
normalize_se_combination | 3.299 | 0.039 | 3.338 | |
normalize_se_single | 3.207 | 0.101 | 3.309 | |
normicsNorm | 3.085 | 0.014 | 3.100 | |
plot_NA_density | 0.303 | 0.012 | 0.303 | |
plot_NA_frequency | 0.211 | 0.008 | 0.204 | |
plot_NA_heatmap | 1.306 | 0.033 | 1.339 | |
plot_PCA | 1.958 | 0.096 | 2.053 | |
plot_ROC_AUC_spiked | 0.941 | 0.017 | 0.949 | |
plot_TP_FP_spiked_bar | 0.258 | 0.004 | 0.261 | |
plot_TP_FP_spiked_box | 0.319 | 0.004 | 0.323 | |
plot_TP_FP_spiked_scatter | 0.341 | 0.002 | 0.343 | |
plot_boxplots | 3.830 | 0.063 | 3.846 | |
plot_condition_overview | 0.188 | 0.003 | 0.191 | |
plot_densities | 2.361 | 0.066 | 2.379 | |
plot_fold_changes_spiked | 0.417 | 0.004 | 0.414 | |
plot_heatmap | 3.663 | 0.042 | 3.706 | |
plot_heatmap_DE | 1.245 | 0.009 | 1.262 | |
plot_histogram_spiked | 0.299 | 0.002 | 0.294 | |
plot_identified_spiked_proteins | 0.387 | 0.005 | 0.392 | |
plot_intersection_enrichment | 1.821 | 0.020 | 12.660 | |
plot_intragroup_PCV | 0.445 | 0.007 | 0.452 | |
plot_intragroup_PEV | 0.327 | 0.000 | 0.327 | |
plot_intragroup_PMAD | 0.330 | 0.001 | 0.330 | |
plot_intragroup_correlation | 0.339 | 0.003 | 0.341 | |
plot_jaccard_heatmap | 0.232 | 0.003 | 0.224 | |
plot_logFC_thresholds_spiked | 0.601 | 0.003 | 0.604 | |
plot_markers_boxplots | 0.683 | 0.003 | 0.671 | |
plot_nr_prot_samples | 0.256 | 0.001 | 0.260 | |
plot_overview_DE_bar | 0.301 | 0.003 | 0.304 | |
plot_overview_DE_tile | 0.172 | 0.001 | 0.173 | |
plot_profiles_spiked | 0.716 | 0.026 | 0.720 | |
plot_pvalues_spiked | 0.439 | 0.034 | 0.473 | |
plot_stats_spiked_heatmap | 0.285 | 0.037 | 0.322 | |
plot_tot_int_samples | 0.207 | 0.031 | 0.237 | |
plot_upset | 0.593 | 0.067 | 0.659 | |
plot_upset_DE | 0.791 | 0.035 | 0.827 | |
plot_volcano_DE | 2.956 | 0.187 | 3.142 | |
quantileNorm | 0.046 | 0.005 | 0.052 | |
readPRONE_example | 0.001 | 0.001 | 0.002 | |
remove_POMA_outliers | 0.509 | 0.048 | 0.556 | |
remove_assays_from_SE | 0.049 | 0.003 | 0.052 | |
remove_reference_samples | 0.050 | 0.002 | 0.052 | |
remove_samples_manually | 0.040 | 0.002 | 0.042 | |
rlrMACycNorm | 0.642 | 0.061 | 0.702 | |
rlrMANorm | 0.104 | 0.005 | 0.110 | |
rlrNorm | 0.090 | 0.003 | 0.093 | |
robnormNorm | 0.105 | 0.012 | 0.117 | |
run_DE | 2.493 | 0.095 | 2.540 | |
specify_comparisons | 0.032 | 0.002 | 0.031 | |
subset_SE_by_norm | 0.076 | 0.013 | 0.090 | |
tmmNorm | 0.133 | 0.012 | 0.145 | |
vsnNorm | 0.073 | 0.002 | 0.074 | |