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CHECK report for PrInCE on machv2

This page was generated on 2020-10-17 11:59:15 -0400 (Sat, 17 Oct 2020).

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 1349/1905HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
PrInCE 1.4.0
Michael Skinnider
Snapshot Date: 2020-10-16 14:40:19 -0400 (Fri, 16 Oct 2020)
URL: https://git.bioconductor.org/packages/PrInCE
Branch: RELEASE_3_11
Last Commit: 89b59e5
Last Changed Date: 2020-04-27 15:24:19 -0400 (Mon, 27 Apr 2020)
malbec2 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
machv2 macOS 10.14.6 Mojave / x86_64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: PrInCE
Version: 1.4.0
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_1.4.0.tar.gz
StartedAt: 2020-10-17 04:06:04 -0400 (Sat, 17 Oct 2020)
EndedAt: 2020-10-17 04:10:37 -0400 (Sat, 17 Oct 2020)
EllapsedTime: 273.5 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_1.4.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.11-bioc/meat/PrInCE.Rcheck’
* using R version 4.0.3 (2020-10-10)
* 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 ‘1.4.0’
* 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
calculate_precision  7.758  0.402   8.165
predict_ensemble     7.286  0.350   7.647
PrInCE               7.201  0.285   7.500
predict_interactions 7.108  0.182   7.309
threshold_precision  6.075  0.176   6.254
* 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
PrInCE7.2010.2857.500
adjacency_matrix_from_data_frame0.0020.0000.003
adjacency_matrix_from_list1.3310.0281.360
build_gaussians0.9080.0400.948
calculate_precision7.7580.4028.165
check_gaussians0.1770.0050.183
choose_gaussians0.3740.0070.380
clean_profile0.0640.0040.066
clean_profiles0.0630.0050.068
co_apex0.1600.0070.167
detect_complexes0.1600.0140.173
filter_profiles0.4540.0150.470
fit_curve0.300.020.32
fit_gaussians0.2610.0070.268
impute_neighbors0.0690.0040.073
is_unweighted1.4540.0211.476
is_weighted1.3780.0061.384
make_initial_conditions0.0650.0030.068
make_labels1.3730.0181.393
match_matrix_dimensions1.7460.0101.757
predict_ensemble7.2860.3507.647
predict_interactions7.1080.1827.309
threshold_precision6.0750.1766.254