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This page was generated on 2022-03-18 11:08:20 -0400 (Fri, 18 Mar 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 20.04.4 LTS)x86_64R Under development (unstable) (2022-02-17 r81757) -- "Unsuffered Consequences" 4334
riesling1Windows Server 2019 Standardx64R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences" 4097
palomino3Windows Server 2022 Datacenterx64R Under development (unstable) (2022-02-17 r81757 ucrt) -- "Unsuffered Consequences" 4083
merida1macOS 10.14.6 Mojavex86_64R Under development (unstable) (2022-03-02 r81842) -- "Unsuffered Consequences" 4134
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 riesling1


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? here 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 1463/2090HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
PrInCE 1.11.0  (landing page)
Michael Skinnider
Snapshot Date: 2022-03-17 13:55:23 -0400 (Thu, 17 Mar 2022)
git_url: https://git.bioconductor.org/packages/PrInCE
git_branch: master
git_last_commit: f854bc2
git_last_commit_date: 2021-10-26 12:49:58 -0400 (Tue, 26 Oct 2021)
nebbiolo1Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
riesling1Windows Server 2019 Standard / x64  OK    OK    WARNINGS    OK  
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: 1.11.0
Command: D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:PrInCE.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings PrInCE_1.11.0.tar.gz
StartedAt: 2022-03-17 19:55:09 -0400 (Thu, 17 Mar 2022)
EndedAt: 2022-03-17 19:57:59 -0400 (Thu, 17 Mar 2022)
EllapsedTime: 170.0 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: PrInCE.Rcheck
Warnings: 1

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:PrInCE.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings PrInCE_1.11.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'D:/biocbuild/bbs-3.15-bioc/meat/PrInCE.Rcheck'
* using R Under development (unstable) (2021-11-21 r81221)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'PrInCE/DESCRIPTION' ... OK
* this is package 'PrInCE' version '1.11.0'
* 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 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
  'D:/biocbuild/bbs-3.15-bioc/meat/PrInCE.Rcheck/00check.log'
for details.



Installation output

PrInCE.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL PrInCE
###
##############################################################################
##############################################################################


* installing to library 'D:/biocbuild/bbs-3.15-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
  converting help for package 'PrInCE'
    finding HTML links ... done
    PrInCE                                  html  
    finding level-2 HTML links ... done

    adjacency_matrix_from_data_frame        html  
    adjacency_matrix_from_list              html  
    aic                                     html  
    build_gaussians                         html  
    calculate_autocorrelation               html  
    calculate_features                      html  
    calculate_precision                     html  
    check_gaussians                         html  
    choose_gaussians                        html  
    clean_profile                           html  
    clean_profiles                          html  
    co_apex                                 html  
    concatenate_features                    html  
    detect_complexes                        html  
    filter_profiles                         html  
    fit_curve                               html  
    fit_gaussians                           html  
    gold_standard                           html  
    impute_neighbors                        html  
    is_unweighted                           html  
    is_weighted                             html  
    kristensen                              html  
    kristensen_gaussians                    html  
    make_feature_from_data_frame            html  
    make_feature_from_expression            html  
    make_initial_conditions                 html  
    make_labels                             html  
    match_matrix_dimensions                 html  
    predict_ensemble                        html  
    predict_interactions                    html  
    replace_missing_data                    html  
    scott                                   html  
    scott_gaussians                         html  
    threshold_precision                     html  
** 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)
Making 'packages.html' ...Warning in packageDescription(i, lib.loc = lib, fields = "Title", encoding = "UTF-8") :
  DESCRIPTION file of package 'lisaClust' is missing or broken
Warning in packageDescription(i, lib.loc = lib, fields = "Title", encoding = "UTF-8") :
  DESCRIPTION file of package 'SimBindProfiles' is missing or broken
Warning in packageDescription(i, lib.loc = lib, fields = "Title", encoding = "UTF-8") :
  DESCRIPTION file of package 'sva' is missing or broken
 done

Tests output


Example timings

PrInCE.Rcheck/PrInCE-Ex.timings

nameusersystemelapsed
PrInCE3.830.414.24
adjacency_matrix_from_data_frame000
adjacency_matrix_from_list0.340.060.41
build_gaussians0.390.080.47
calculate_precision3.030.253.28
check_gaussians0.080.110.19
choose_gaussians0.130.030.15
clean_profile0.030.010.05
clean_profiles0.010.020.03
co_apex0.140.050.19
detect_complexes0.050.040.09
filter_profiles0.170.030.21
fit_curve0.110.020.12
fit_gaussians0.140.000.14
impute_neighbors0.030.000.03
is_unweighted0.530.030.57
is_weighted0.470.030.50
make_initial_conditions0.050.000.04
make_labels0.390.030.42
match_matrix_dimensions0.670.030.72
predict_ensemble3.910.274.17
predict_interactions4.310.234.55
threshold_precision3.280.303.58