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 12:08 -0500 (Mon, 23 Dec 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.1 LTS)x86_644.4.2 (2024-10-31) -- "Pile of Leaves" 4744
palomino8Windows Server 2022 Datacenterx644.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" 4487
merida1macOS 12.7.5 Montereyx86_644.4.2 (2024-10-31) -- "Pile of Leaves" 4515
kjohnson1macOS 13.6.6 Venturaarm644.4.2 (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 1604/2289HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
PRONE 1.0.0  (landing page)
Lis Arend
Snapshot Date: 2024-12-19 13:00 -0500 (Thu, 19 Dec 2024)
git_url: https://git.bioconductor.org/packages/PRONE
git_branch: RELEASE_3_20
git_last_commit: 0833b5f
git_last_commit_date: 2024-10-29 11:34:43 -0500 (Tue, 29 Oct 2024)
nebbiolo2Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino8Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 12.7.5 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.6 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published


CHECK results for PRONE on kjohnson1

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.

raw results


Summary

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: 2024-12-21 05:23:30 -0500 (Sat, 21 Dec 2024)
EndedAt: 2024-12-21 05:29:07 -0500 (Sat, 21 Dec 2024)
EllapsedTime: 337.3 seconds
RetCode: 0
Status:   OK  
CheckDir: PRONE.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### 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: 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 ‘1.0.0’
* 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
plot_intersection_enrichment 1.61  0.062   7.133
* 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.


Installation output

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)

Tests output


Example timings

PRONE.Rcheck/PRONE-Ex.timings

nameusersystemelapsed
apply_thresholds0.0430.0040.047
detect_outliers_POMA1.0640.0521.117
eigenMSNorm1.5480.0161.565
export_data0.0420.0040.046
extract_consensus_DE_candidates0.1000.0070.107
filter_out_NA_proteins_by_threshold0.3760.0370.250
filter_out_complete_NA_proteins0.0840.0070.077
filter_out_proteins_by_ID0.1610.0140.174
filter_out_proteins_by_value0.1600.0150.174
get_NA_overview0.0520.0040.056
get_normalization_methods000
get_overview_DE0.0530.0040.057
get_proteins_by_value0.1510.0140.165
get_spiked_stats_DE0.1460.0110.159
globalIntNorm0.1470.0030.150
globalMeanNorm0.1470.0040.153
globalMedianNorm0.1480.0040.152
impute_se1.3740.1000.805
irsNorm0.1410.0140.081
limmaNorm0.1050.0100.095
load_data0.0680.0050.073
load_spike_data0.0750.0050.079
loessCycNorm0.1240.0100.133
loessFNorm0.1120.0050.115
meanNorm0.0600.0040.063
medianAbsDevNorm0.1180.0050.123
medianNorm0.0820.0030.086
normalize_se3.3500.0593.411
normalize_se_combination3.2910.0463.339
normalize_se_single3.2820.0583.340
normicsNorm3.1240.0563.181
plot_NA_density0.5190.0220.346
plot_NA_frequency0.3180.0220.207
plot_NA_heatmap1.5660.0841.618
plot_PCA0.6220.0220.659
plot_ROC_AUC_spiked2.1080.0272.103
plot_TP_FP_spiked_bar0.2880.0070.295
plot_TP_FP_spiked_box0.3410.0070.349
plot_TP_FP_spiked_scatter0.4050.0100.416
plot_boxplots4.0810.1073.795
plot_condition_overview0.2050.0040.209
plot_densities3.2840.1862.509
plot_fold_changes_spiked0.6390.0320.484
plot_heatmap3.9140.0423.958
plot_heatmap_DE1.2780.0231.302
plot_histogram_spiked0.5420.0310.383
plot_identified_spiked_proteins0.4250.0080.433
plot_intersection_enrichment1.6100.0627.133
plot_intragroup_PCV0.5000.0060.507
plot_intragroup_PEV0.3370.0050.342
plot_intragroup_PMAD0.3360.0060.342
plot_intragroup_correlation0.3780.0060.385
plot_jaccard_heatmap0.4040.0290.249
plot_logFC_thresholds_spiked0.5580.0110.559
plot_markers_boxplots0.8680.0330.706
plot_nr_prot_samples0.2380.0050.244
plot_overview_DE_bar0.2870.0060.293
plot_overview_DE_tile0.1860.0040.192
plot_profiles_spiked0.8930.0320.731
plot_pvalues_spiked0.4690.0090.481
plot_stats_spiked_heatmap0.3280.0080.337
plot_tot_int_samples0.2360.0060.243
plot_upset0.6950.0150.711
plot_upset_DE0.8660.0300.898
plot_volcano_DE2.8110.0302.844
quantileNorm0.0600.0030.063
readPRONE_example0.0010.0000.002
remove_POMA_outliers0.4870.0080.495
remove_assays_from_SE0.1010.0030.104
remove_reference_samples0.0690.0030.072
remove_samples_manually0.0550.0030.058
rlrMACycNorm0.5580.0080.568
rlrMANorm0.1140.0030.117
rlrNorm0.1020.0040.105
robnormNorm0.1290.0060.134
run_DE2.8120.1102.209
specify_comparisons0.0840.0080.048
subset_SE_by_norm0.1720.0160.096
tmmNorm0.1950.0150.163
vsnNorm0.0800.0030.083