Back to Multiple platform build/check report for BioC 3.15
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This page was generated on 2022-10-19 13:23:29 -0400 (Wed, 19 Oct 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 20.04.5 LTS)x86_644.2.1 (2022-06-23) -- "Funny-Looking Kid" 4386
palomino3Windows Server 2022 Datacenterx644.2.1 (2022-06-23 ucrt) -- "Funny-Looking Kid" 4138
merida1macOS 10.14.6 Mojavex86_644.2.1 (2022-06-23) -- "Funny-Looking Kid" 4205
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

CHECK results for PrInCE on merida1


To the developers/maintainers of the PrInCE package:
- Please 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 How and When does the builder pull? When will my changes propagate? for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 1493/2140HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
PrInCE 1.12.0  (landing page)
Michael Skinnider
Snapshot Date: 2022-10-18 13:55:19 -0400 (Tue, 18 Oct 2022)
git_url: https://git.bioconductor.org/packages/PrInCE
git_branch: RELEASE_3_15
git_last_commit: 308cf69
git_last_commit_date: 2022-04-26 11:53:38 -0400 (Tue, 26 Apr 2022)
nebbiolo1Linux (Ubuntu 20.04.5 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
palomino3Windows Server 2022 Datacenter / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published

Summary

Package: PrInCE
Version: 1.12.0
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_1.12.0.tar.gz
StartedAt: 2022-10-19 06:22:11 -0400 (Wed, 19 Oct 2022)
EndedAt: 2022-10-19 06:27:43 -0400 (Wed, 19 Oct 2022)
EllapsedTime: 332.2 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_1.12.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.15-bioc/meat/PrInCE.Rcheck’
* using R version 4.2.1 (2022-06-23)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘PrInCE/DESCRIPTION’ ... OK
* this is package ‘PrInCE’ version ‘1.12.0’
* 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 R 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 ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... WARNING
Undocumented arguments in documentation object 'calculate_autocorrelation'
  ‘min_replicates’

Undocumented arguments in documentation object 'calculate_features'
  ‘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
Examples with CPU (user + system) or elapsed time > 5s
                      user system elapsed
calculate_precision  7.441  0.172   7.624
PrInCE               7.074  0.330   7.412
predict_interactions 7.274  0.111   7.400
predict_ensemble     6.853  0.234   7.095
threshold_precision  6.424  0.119   6.550
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... 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, 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.15-bioc/meat/PrInCE.Rcheck/00check.log’
for details.



Installation output

PrInCE.Rcheck/00install.out

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


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.2/Resources/library’
* installing *source* package ‘PrInCE’ ...
** 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
PrInCE7.0740.3307.412
adjacency_matrix_from_data_frame0.0020.0000.003
adjacency_matrix_from_list0.7300.0040.734
build_gaussians1.1450.0471.193
calculate_precision7.4410.1727.624
check_gaussians0.2190.0050.223
choose_gaussians0.4060.0060.412
clean_profile0.0920.0030.095
clean_profiles0.0930.0030.097
co_apex0.2070.0050.213
detect_complexes0.1910.0070.199
filter_profiles0.6570.0230.682
fit_curve0.3140.0030.318
fit_gaussians0.3100.0070.318
impute_neighbors0.0800.0040.084
is_unweighted0.7540.0100.764
is_weighted0.7660.0070.774
make_initial_conditions0.0710.0040.074
make_labels1.2540.0161.271
match_matrix_dimensions1.0420.0171.061
predict_ensemble6.8530.2347.095
predict_interactions7.2740.1117.400
threshold_precision6.4240.1196.550