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This page was generated on 2022-04-13 12:07:07 -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 tokay2


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: C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:PrInCE.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings PrInCE_1.10.0.tar.gz
StartedAt: 2022-04-13 00:47:49 -0400 (Wed, 13 Apr 2022)
EndedAt: 2022-04-13 00:53:35 -0400 (Wed, 13 Apr 2022)
EllapsedTime: 346.2 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: PrInCE.Rcheck
Warnings: 1

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:PrInCE.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings PrInCE_1.10.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.14-bioc/meat/PrInCE.Rcheck'
* using R version 4.1.3 (2022-03-10)
* 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 '1.10.0'
* 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 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 ...
** running examples for arch 'i386' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                     user system elapsed
calculate_precision  6.15   0.22    6.38
PrInCE               5.45   0.17    5.63
predict_interactions 4.90   0.19    5.10
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
       user system elapsed
PrInCE 5.03   0.19    5.23
* 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
  'C:/Users/biocbuild/bbs-3.14-bioc/meat/PrInCE.Rcheck/00check.log'
for details.



Installation output

PrInCE.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.14/bioc/src/contrib/PrInCE_1.10.0.tar.gz && rm -rf PrInCE.buildbin-libdir && mkdir PrInCE.buildbin-libdir && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=PrInCE.buildbin-libdir PrInCE_1.10.0.tar.gz && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL PrInCE_1.10.0.zip && rm PrInCE_1.10.0.tar.gz PrInCE_1.10.0.zip
###
##############################################################################
##############################################################################


  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
 40 1811k   40  740k    0     0  1238k      0  0:00:01 --:--:--  0:00:01 1238k
100 1811k  100 1811k    0     0  1617k      0  0:00:01  0:00:01 --:--:-- 1618k

install for i386

* 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

install for x64

* installing *source* package 'PrInCE' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'PrInCE' as PrInCE_1.10.0.zip
* DONE (PrInCE)
* installing to library 'C:/Users/biocbuild/bbs-3.14-bioc/R/library'
package 'PrInCE' successfully unpacked and MD5 sums checked

Tests output


Example timings

PrInCE.Rcheck/examples_i386/PrInCE-Ex.timings

nameusersystemelapsed
PrInCE5.450.175.63
adjacency_matrix_from_data_frame000
adjacency_matrix_from_list0.580.050.62
build_gaussians0.710.210.92
calculate_precision6.150.226.38
check_gaussians0.220.030.25
choose_gaussians0.20.00.2
clean_profile0.070.020.08
clean_profiles0.060.000.06
co_apex0.160.090.25
detect_complexes0.110.040.14
filter_profiles0.310.010.33
fit_curve0.150.000.15
fit_gaussians0.180.000.18
impute_neighbors0.060.000.06
is_unweighted0.560.020.58
is_weighted0.560.010.58
make_initial_conditions0.050.000.04
make_labels0.500.050.55
match_matrix_dimensions1.190.031.22
predict_ensemble4.380.204.58
predict_interactions4.900.195.10
threshold_precision4.570.194.75

PrInCE.Rcheck/examples_x64/PrInCE-Ex.timings

nameusersystemelapsed
PrInCE5.030.195.23
adjacency_matrix_from_data_frame000
adjacency_matrix_from_list0.560.040.61
build_gaussians0.550.020.56
calculate_precision4.720.144.86
check_gaussians0.110.060.17
choose_gaussians0.190.020.20
clean_profile0.050.000.05
clean_profiles0.030.010.05
co_apex0.140.050.18
detect_complexes0.090.000.10
filter_profiles0.250.020.26
fit_curve0.160.000.16
fit_gaussians0.140.000.14
impute_neighbors0.050.000.05
is_unweighted0.560.000.56
is_weighted0.560.010.58
make_initial_conditions0.050.000.04
make_labels0.580.020.60
match_matrix_dimensions0.810.010.83
predict_ensemble4.470.084.54
predict_interactions4.000.144.14
threshold_precision4.110.084.19