Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-12-23 12:06 -0500 (Mon, 23 Dec 2024).
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" | 4744 |
palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" | 4487 |
merida1 | macOS 12.7.5 Monterey | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4515 |
kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4467 |
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 1.0.0 (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 | |||||||||
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: 1.0.0 |
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_1.0.0.tar.gz |
StartedAt: 2024-12-20 07:55:37 -0500 (Fri, 20 Dec 2024) |
EndedAt: 2024-12-20 08:06:34 -0500 (Fri, 20 Dec 2024) |
EllapsedTime: 657.9 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_1.0.0.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: x86_64-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 Monterey 12.7.6 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘PRONE/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘PRONE’ version ‘1.0.0’ * 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 normalize_se 11.342 0.120 11.529 normalize_se_single 10.946 0.071 11.133 normalize_se_combination 10.855 0.071 10.993 normicsNorm 10.599 0.056 10.725 plot_heatmap 10.389 0.065 10.511 plot_boxplots 10.350 0.089 10.000 plot_volcano_DE 6.810 0.050 6.938 plot_densities 5.932 0.117 5.999 run_DE 6.001 0.045 6.094 plot_intersection_enrichment 3.757 0.081 13.250 * 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-x86_64/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 | 0.051 | 0.004 | 0.056 | |
detect_outliers_POMA | 2.117 | 0.127 | 2.371 | |
eigenMSNorm | 2.512 | 0.040 | 2.707 | |
export_data | 0.042 | 0.005 | 0.049 | |
extract_consensus_DE_candidates | 0.160 | 0.012 | 0.175 | |
filter_out_NA_proteins_by_threshold | 0.497 | 0.057 | 0.649 | |
filter_out_complete_NA_proteins | 0.100 | 0.012 | 0.112 | |
filter_out_proteins_by_ID | 0.420 | 0.048 | 0.472 | |
filter_out_proteins_by_value | 0.413 | 0.050 | 0.472 | |
get_NA_overview | 0.061 | 0.008 | 0.069 | |
get_normalization_methods | 0.001 | 0.000 | 0.001 | |
get_overview_DE | 0.078 | 0.009 | 0.090 | |
get_proteins_by_value | 0.387 | 0.047 | 0.439 | |
get_spiked_stats_DE | 0.172 | 0.012 | 0.185 | |
globalIntNorm | 0.412 | 0.006 | 0.421 | |
globalMeanNorm | 0.409 | 0.005 | 0.420 | |
globalMedianNorm | 0.424 | 0.008 | 0.438 | |
impute_se | 1.799 | 0.054 | 1.782 | |
irsNorm | 0.119 | 0.011 | 0.131 | |
limmaNorm | 0.164 | 0.018 | 0.184 | |
load_data | 0.111 | 0.015 | 0.127 | |
load_spike_data | 0.110 | 0.007 | 0.119 | |
loessCycNorm | 0.274 | 0.023 | 0.298 | |
loessFNorm | 0.156 | 0.007 | 0.167 | |
meanNorm | 0.079 | 0.004 | 0.085 | |
medianAbsDevNorm | 0.209 | 0.008 | 0.224 | |
medianNorm | 0.113 | 0.006 | 0.122 | |
normalize_se | 11.342 | 0.120 | 11.529 | |
normalize_se_combination | 10.855 | 0.071 | 10.993 | |
normalize_se_single | 10.946 | 0.071 | 11.133 | |
normicsNorm | 10.599 | 0.056 | 10.725 | |
plot_NA_density | 0.687 | 0.017 | 0.701 | |
plot_NA_frequency | 0.413 | 0.009 | 0.425 | |
plot_NA_heatmap | 3.494 | 0.148 | 3.675 | |
plot_PCA | 2.553 | 0.032 | 2.639 | |
plot_ROC_AUC_spiked | 3.204 | 0.031 | 3.276 | |
plot_TP_FP_spiked_bar | 0.552 | 0.010 | 0.568 | |
plot_TP_FP_spiked_box | 0.756 | 0.011 | 0.770 | |
plot_TP_FP_spiked_scatter | 0.810 | 0.016 | 0.831 | |
plot_boxplots | 10.350 | 0.089 | 10.000 | |
plot_condition_overview | 0.440 | 0.007 | 0.467 | |
plot_densities | 5.932 | 0.117 | 5.999 | |
plot_fold_changes_spiked | 0.990 | 0.017 | 1.037 | |
plot_heatmap | 10.389 | 0.065 | 10.511 | |
plot_heatmap_DE | 2.773 | 0.030 | 2.865 | |
plot_histogram_spiked | 0.717 | 0.018 | 0.719 | |
plot_identified_spiked_proteins | 0.944 | 0.013 | 0.962 | |
plot_intersection_enrichment | 3.757 | 0.081 | 13.250 | |
plot_intragroup_PCV | 1.325 | 0.009 | 1.348 | |
plot_intragroup_PEV | 0.808 | 0.007 | 0.824 | |
plot_intragroup_PMAD | 0.802 | 0.008 | 0.813 | |
plot_intragroup_correlation | 0.813 | 0.007 | 0.824 | |
plot_jaccard_heatmap | 0.534 | 0.010 | 0.548 | |
plot_logFC_thresholds_spiked | 1.200 | 0.013 | 1.226 | |
plot_markers_boxplots | 1.696 | 0.016 | 1.727 | |
plot_nr_prot_samples | 0.511 | 0.007 | 0.521 | |
plot_overview_DE_bar | 0.672 | 0.007 | 0.684 | |
plot_overview_DE_tile | 0.395 | 0.007 | 0.404 | |
plot_profiles_spiked | 1.586 | 0.019 | 1.631 | |
plot_pvalues_spiked | 0.910 | 0.015 | 0.932 | |
plot_stats_spiked_heatmap | 0.667 | 0.011 | 0.685 | |
plot_tot_int_samples | 0.500 | 0.006 | 0.509 | |
plot_upset | 1.421 | 0.018 | 1.451 | |
plot_upset_DE | 1.883 | 0.052 | 1.956 | |
plot_volcano_DE | 6.810 | 0.050 | 6.938 | |
quantileNorm | 0.077 | 0.004 | 0.082 | |
readPRONE_example | 0.001 | 0.001 | 0.003 | |
remove_POMA_outliers | 1.226 | 0.009 | 1.249 | |
remove_assays_from_SE | 0.123 | 0.004 | 0.128 | |
remove_reference_samples | 0.079 | 0.005 | 0.084 | |
remove_samples_manually | 0.071 | 0.004 | 0.075 | |
rlrMACycNorm | 1.626 | 0.010 | 1.652 | |
rlrMANorm | 0.227 | 0.004 | 0.233 | |
rlrNorm | 0.185 | 0.004 | 0.190 | |
robnormNorm | 0.198 | 0.011 | 0.210 | |
run_DE | 6.001 | 0.045 | 6.094 | |
specify_comparisons | 0.047 | 0.005 | 0.050 | |
subset_SE_by_norm | 0.179 | 0.006 | 0.183 | |
tmmNorm | 0.300 | 0.013 | 0.317 | |
vsnNorm | 0.140 | 0.005 | 0.146 | |