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This page was generated on 2025-09-27 12:06 -0400 (Sat, 27 Sep 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" 4832
lconwaymacOS 12.7.1 Montereyx86_644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4620
kjohnson3macOS 13.7.7 Venturaarm644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4565
taishanLinux (openEuler 24.03 LTS)aarch644.5.0 (2025-04-11) -- "How About a Twenty-Six" 4563
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 1619/2334HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
PrInCE 1.25.0  (landing page)
Michael Skinnider
Snapshot Date: 2025-09-26 13:45 -0400 (Fri, 26 Sep 2025)
git_url: https://git.bioconductor.org/packages/PrInCE
git_branch: devel
git_last_commit: 76730e5
git_last_commit_date: 2025-04-15 11:41:57 -0400 (Tue, 15 Apr 2025)
nebbiolo2Linux (Ubuntu 24.04.3 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
kjohnson3macOS 13.7.7 Ventura / arm64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
taishanLinux (openEuler 24.03 LTS) / aarch64  OK    OK    WARNINGS  


CHECK results for PrInCE on kjohnson3

To the developers/maintainers of the PrInCE package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/PrInCE.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: PrInCE
Version: 1.25.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:PrInCE.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings PrInCE_1.25.0.tar.gz
StartedAt: 2025-09-26 20:59:51 -0400 (Fri, 26 Sep 2025)
EndedAt: 2025-09-26 21:01:59 -0400 (Fri, 26 Sep 2025)
EllapsedTime: 127.6 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: PrInCE.Rcheck
Warnings: 1

Command output

##############################################################################
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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:PrInCE.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings PrInCE_1.25.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.22-bioc/meat/PrInCE.Rcheck’
* using R version 4.5.1 Patched (2025-09-10 r88807)
* using platform: aarch64-apple-darwin20
* R was compiled by
    Apple clang version 16.0.0 (clang-1600.0.26.6)
    GNU Fortran (GCC) 14.2.0
* running under: macOS Ventura 13.7.7
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘PrInCE/DESCRIPTION’ ... OK
* this is package ‘PrInCE’ version ‘1.25.0’
* 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 ... NOTE
Found the following hidden files and directories:
  .lintr
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘PrInCE’ 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
calculate_features: no visible global function definition for
  ‘quantile’
Undefined global functions or variables:
  quantile
Consider adding
  importFrom("stats", "quantile")
to your NAMESPACE file.
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... NOTE
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  PrInCE.Rd: MSnSet-class
  build_gaussians.Rd: MSnSet-class
  calculate_autocorrelation.Rd: MSnSet-class
  calculate_features.Rd: MSnSet-class
  clean_profiles.Rd: MSnSet-class
  detect_complexes.Rd: MSnSet-class
  filter_profiles.Rd: MSnSet-class
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... WARNING
Undocumented arguments in Rd file 'calculate_autocorrelation.Rd'
  ‘min_replicates’

Undocumented arguments in Rd file 'calculate_features.Rd'
  ‘n_pairs’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* 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 running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 1 WARNING, 3 NOTEs
See
  ‘/Users/biocbuild/bbs-3.22-bioc/meat/PrInCE.Rcheck/00check.log’
for details.


Installation output

PrInCE.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL PrInCE
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library’
* installing *source* package ‘PrInCE’ ...
** this is package ‘PrInCE’ version ‘1.25.0’
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
Loading required namespace: PrInCE
Registered S3 method overwritten by 'quantmod':
  method            from
  as.zoo.data.frame zoo 
*** installing help indices
** 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 (PrInCE)

Tests output


Example timings

PrInCE.Rcheck/PrInCE-Ex.timings

nameusersystemelapsed
PrInCE2.4130.1012.522
adjacency_matrix_from_data_frame0.0010.0000.000
adjacency_matrix_from_list0.0850.0040.088
build_gaussians0.1380.0130.152
calculate_precision2.0970.0842.181
check_gaussians0.0510.0020.052
choose_gaussians0.0560.0020.058
clean_profile0.0180.0020.018
clean_profiles0.0180.0010.019
co_apex0.0410.0020.043
detect_complexes0.0410.0020.044
filter_profiles0.0840.0040.089
fit_curve0.0440.0040.047
fit_gaussians0.0450.0040.050
impute_neighbors0.0190.0010.020
is_unweighted0.1040.0130.117
is_weighted0.0860.0020.089
make_initial_conditions0.0180.0010.019
make_labels0.0820.0020.083
match_matrix_dimensions0.1220.0050.127
predict_ensemble2.4500.1352.589
predict_interactions2.1330.1102.244
threshold_precision1.9750.1132.089