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CHECK report for PrInCE on merida1

This page was generated on 2021-05-06 12:36:11 -0400 (Thu, 06 May 2021).

To the developers/maintainers of the PrInCE package:
Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 1384/1974HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
PrInCE 1.6.0  (landing page)
Michael Skinnider
Snapshot Date: 2021-05-05 14:51:38 -0400 (Wed, 05 May 2021)
URL: https://git.bioconductor.org/packages/PrInCE
Branch: RELEASE_3_12
Last Commit: 82a1b68
Last Changed Date: 2020-10-27 11:43:34 -0400 (Tue, 27 Oct 2020)
malbec1Linux (Ubuntu 18.04.5 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version exists in internal repository
tokay1Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version exists in internal repository
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version exists in internal repository

Summary

Package: PrInCE
Version: 1.6.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:PrInCE.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings PrInCE_1.6.0.tar.gz
StartedAt: 2021-05-06 04:53:05 -0400 (Thu, 06 May 2021)
EndedAt: 2021-05-06 04:57:12 -0400 (Thu, 06 May 2021)
EllapsedTime: 247.1 seconds
RetCode: 0
Status:   OK  
CheckDir: PrInCE.Rcheck
Warnings: 0

Command output

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:PrInCE.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings PrInCE_1.6.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.12-bioc/meat/PrInCE.Rcheck’
* using R version 4.0.5 (2021-03-31)
* 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 ‘1.6.0’
* 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 ‘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 ... 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
predict_ensemble     6.093  0.215   6.319
calculate_precision  5.803  0.311   6.120
PrInCE               5.589  0.188   5.782
predict_interactions 5.448  0.196   5.648
threshold_precision  5.021  0.212   5.239
* 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: OK


Installation output

PrInCE.Rcheck/00install.out

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL PrInCE
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.0/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
PrInCE5.5890.1885.782
adjacency_matrix_from_data_frame0.0010.0000.001
adjacency_matrix_from_list1.1180.0341.153
build_gaussians0.7370.0490.786
calculate_precision5.8030.3116.120
check_gaussians0.1590.0050.164
choose_gaussians0.2660.0090.275
clean_profile0.0440.0070.051
clean_profiles0.0410.0070.049
co_apex0.1190.0100.128
detect_complexes0.1220.0080.131
filter_profiles0.3750.0120.386
fit_curve0.2230.0090.232
fit_gaussians0.2180.0050.225
impute_neighbors0.0480.0030.051
is_unweighted0.9760.0080.984
is_weighted1.1000.0131.114
make_initial_conditions0.0510.0030.054
make_labels1.1310.0081.142
match_matrix_dimensions1.4860.0061.493
predict_ensemble6.0930.2156.319
predict_interactions5.4480.1965.648
threshold_precision5.0210.2125.239