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This page was generated on 2022-04-13 12:05:46 -0400 (Wed, 13 Apr 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.1.3 (2022-03-10) -- "One Push-Up" 4324
tokay2Windows Server 2012 R2 Standardx644.1.3 (2022-03-10) -- "One Push-Up" 4077
machv2macOS 10.14.6 Mojavex86_644.1.3 (2022-03-10) -- "One Push-Up" 4137
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 nebbiolo2


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 1456/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
PrInCE 1.10.0  (landing page)
Michael Skinnider
Snapshot Date: 2022-04-12 01:55:07 -0400 (Tue, 12 Apr 2022)
git_url: https://git.bioconductor.org/packages/PrInCE
git_branch: RELEASE_3_14
git_last_commit: d2e07dc
git_last_commit_date: 2021-10-26 12:49:58 -0400 (Tue, 26 Oct 2021)
nebbiolo2Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published

Summary

Package: PrInCE
Version: 1.10.0
Command: /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD check --install=check:PrInCE.install-out.txt --library=/home/biocbuild/bbs-3.14-bioc/R/library --no-vignettes --timings PrInCE_1.10.0.tar.gz
StartedAt: 2022-04-12 08:47:55 -0400 (Tue, 12 Apr 2022)
EndedAt: 2022-04-12 08:50:51 -0400 (Tue, 12 Apr 2022)
EllapsedTime: 175.9 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: PrInCE.Rcheck
Warnings: 1

Command output

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###
### Running command:
###
###   /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD check --install=check:PrInCE.install-out.txt --library=/home/biocbuild/bbs-3.14-bioc/R/library --no-vignettes --timings PrInCE_1.10.0.tar.gz
###
##############################################################################
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* using log directory ‘/home/biocbuild/bbs-3.14-bioc/meat/PrInCE.Rcheck’
* using R version 4.1.3 (2022-03-10)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘PrInCE/DESCRIPTION’ ... OK
* this is package ‘PrInCE’ version ‘1.10.0’
* 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
* 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
  ‘/home/biocbuild/bbs-3.14-bioc/meat/PrInCE.Rcheck/00check.log’
for details.



Installation output

PrInCE.Rcheck/00install.out

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD INSTALL PrInCE
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.14-bioc/R/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
PrInCE4.4730.2204.694
adjacency_matrix_from_data_frame0.0010.0000.001
adjacency_matrix_from_list0.4520.0080.460
build_gaussians0.4090.0320.440
calculate_precision4.7140.0924.806
check_gaussians0.1240.0000.124
choose_gaussians0.1610.0000.161
clean_profile0.0430.0000.043
clean_profiles0.0410.0000.041
co_apex0.0950.0000.095
detect_complexes0.0910.0000.091
filter_profiles0.2300.0080.238
fit_curve0.1440.0000.144
fit_gaussians0.1190.0000.119
impute_neighbors0.0410.0000.041
is_unweighted0.4680.0000.468
is_weighted0.5210.0080.529
make_initial_conditions0.0430.0000.043
make_labels0.4890.0080.497
match_matrix_dimensions0.6810.0030.685
predict_ensemble4.7690.1044.874
predict_interactions4.5220.0564.578
threshold_precision3.7090.0563.765