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CHECK report for OmnipathR on tokay1

This page was generated on 2021-05-06 12:32:37 -0400 (Thu, 06 May 2021).

To the developers/maintainers of the OmnipathR package:
Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 1260/1974HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
OmnipathR 2.0.0  (landing page)
Denes Turei
Snapshot Date: 2021-05-05 14:51:38 -0400 (Wed, 05 May 2021)
URL: https://git.bioconductor.org/packages/OmnipathR
Branch: RELEASE_3_12
Last Commit: 2c98139
Last Changed Date: 2020-10-27 11:50:30 -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: OmnipathR
Version: 2.0.0
Command: C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:OmnipathR.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings OmnipathR_2.0.0.tar.gz
StartedAt: 2021-05-06 05:13:46 -0400 (Thu, 06 May 2021)
EndedAt: 2021-05-06 05:20:03 -0400 (Thu, 06 May 2021)
EllapsedTime: 377.2 seconds
RetCode: 0
Status:   OK   
CheckDir: OmnipathR.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:OmnipathR.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings OmnipathR_2.0.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.12-bioc/meat/OmnipathR.Rcheck'
* using R version 4.0.5 (2021-03-31)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'OmnipathR/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'OmnipathR' version '2.0.0'
* 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 whether package 'OmnipathR' 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
pivot_annotations: no visible binding for global variable 'record_id'
Undefined global functions or variables:
  record_id
* 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 R/sysdata.rda ... 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
get_signed_ptms                 17.30   0.04   18.34
import_intercell_network        11.72   0.03   12.25
print_interactions              10.00   0.08   11.17
print_path_vs                    7.83   0.04    9.41
OmnipathR                        6.34   0.06    9.05
import_all_interactions          6.20   0.04    7.41
ptms_graph                       5.87   0.00    6.64
import_kinaseextra_interactions  4.25   0.03    5.08
import_omnipath_enzsub           4.25   0.01    5.03
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                          user system elapsed
get_signed_ptms          14.87   0.18   16.02
import_intercell_network 10.25   0.09   11.09
print_interactions        6.41   0.01    6.56
import_all_interactions   5.04   0.06    6.33
OmnipathR                 4.66   0.10    6.78
print_path_vs             4.64   0.00    6.59
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'testthat.R'
 OK
** running tests for arch 'x64' ...
  Running 'testthat.R'
 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 NOTE
See
  'C:/Users/biocbuild/bbs-3.12-bioc/meat/OmnipathR.Rcheck/00check.log'
for details.



Installation output

OmnipathR.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://172.29.0.3/BBS/3.12/bioc/src/contrib/OmnipathR_2.0.0.tar.gz && rm -rf OmnipathR.buildbin-libdir && mkdir OmnipathR.buildbin-libdir && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=OmnipathR.buildbin-libdir OmnipathR_2.0.0.tar.gz && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL OmnipathR_2.0.0.zip && rm OmnipathR_2.0.0.tar.gz OmnipathR_2.0.0.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
100 3050k  100 3050k    0     0  25.3M      0 --:--:-- --:--:-- --:--:-- 25.6M

install for i386

* installing *source* package 'OmnipathR' ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
Note: wrong number of arguments to '>' 
** help
*** installing help indices
  converting help for package 'OmnipathR'
    finding HTML links ... done
    OmnipathR                               html  
    dot-omnipath_options_defaults           html  
    get_annotation_resources                html  
    get_complex_genes                       html  
    get_complex_resources                   html  
    get_enzsub_resources                    html  
    get_interaction_resources               html  
    get_intercell_categories                html  
    get_intercell_generic_categories        html  
    get_intercell_resources                 html  
    get_resources                           html  
    get_signed_ptms                         html  
    import_all_interactions                 html  
    import_dorothea_interactions            html  
    import_intercell_network                html  
    import_kinaseextra_interactions         html  
    import_ligrecextra_interactions         html  
    import_lncrna_mrna_interactions         html  
    import_mirnatarget_interactions         html  
    import_omnipath_annotations             html  
    import_omnipath_complexes               html  
    import_omnipath_enzsub                  html  
    import_omnipath_interactions            html  
    import_omnipath_intercell               html  
    import_pathwayextra_interactions        html  
    import_post_translational_interactions
                                            html  
    import_tf_mirna_interactions            html  
    import_tf_target_interactions           html  
    import_transcriptional_interactions     html  
    interaction_graph                       html  
    pivot_annotations                       html  
    print_interactions                      html  
    print_path_es                           html  
    print_path_vs                           html  
    ptms_graph                              html  
*** copying figures
** 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 'OmnipathR' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'OmnipathR' as OmnipathR_2.0.0.zip
* DONE (OmnipathR)
* installing to library 'C:/Users/biocbuild/bbs-3.12-bioc/R/library'
package 'OmnipathR' successfully unpacked and MD5 sums checked

Tests output

OmnipathR.Rcheck/tests_i386/testthat.Rout


R version 4.0.5 (2021-03-31) -- "Shake and Throw"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> #!/usr/bin/env Rscript
> 
> #
> #  This file is part of the `OmnipathR` R package
> #
> #  Copyright
> #  2018-2020
> #  Saez Lab, Uniklinik RWTH Aachen, Heidelberg University
> #
> #  File author(s): Alberto Valdeolivas
> #                  Dénes Türei (turei.denes@gmail.com)
> #                  Attila Gábor
> #
> #  Distributed under the MIT (Expat) License.
> #  See accompanying file `LICENSE` or find a copy at
> #      https://directory.fsf.org/wiki/License:Expat
> #
> #  Website: https://saezlab.github.io/omnipathr
> #  Git repo: https://github.com/saezlab/OmnipathR
> #
> 
> 
> library(testthat)
> library(OmnipathR)
Loading required package: igraph

Attaching package: 'igraph'

The following object is masked from 'package:testthat':

    compare

The following objects are masked from 'package:stats':

    decompose, spectrum

The following object is masked from 'package:base':

    union

Loading required package: jsonlite
> 
> test_check("OmnipathR")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 24 ]
> 
> proc.time()
   user  system elapsed 
  33.09    0.20   50.26 

OmnipathR.Rcheck/tests_x64/testthat.Rout


R version 4.0.5 (2021-03-31) -- "Shake and Throw"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> #!/usr/bin/env Rscript
> 
> #
> #  This file is part of the `OmnipathR` R package
> #
> #  Copyright
> #  2018-2020
> #  Saez Lab, Uniklinik RWTH Aachen, Heidelberg University
> #
> #  File author(s): Alberto Valdeolivas
> #                  Dénes Türei (turei.denes@gmail.com)
> #                  Attila Gábor
> #
> #  Distributed under the MIT (Expat) License.
> #  See accompanying file `LICENSE` or find a copy at
> #      https://directory.fsf.org/wiki/License:Expat
> #
> #  Website: https://saezlab.github.io/omnipathr
> #  Git repo: https://github.com/saezlab/OmnipathR
> #
> 
> 
> library(testthat)
> library(OmnipathR)
Loading required package: igraph

Attaching package: 'igraph'

The following object is masked from 'package:testthat':

    compare

The following objects are masked from 'package:stats':

    decompose, spectrum

The following object is masked from 'package:base':

    union

Loading required package: jsonlite
> 
> test_check("OmnipathR")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 24 ]
> 
> proc.time()
   user  system elapsed 
  35.45    0.45   53.00 

Example timings

OmnipathR.Rcheck/examples_i386/OmnipathR-Ex.timings

nameusersystemelapsed
OmnipathR6.340.069.05
get_annotation_resources0.050.000.61
get_complex_genes4.320.024.56
get_complex_resources0.040.000.61
get_enzsub_resources0.090.000.66
get_interaction_resources0.030.000.61
get_intercell_categories0.060.000.26
get_intercell_generic_categories0.070.000.16
get_intercell_resources0.040.000.61
get_resources0.030.000.61
get_signed_ptms17.30 0.0418.34
import_all_interactions6.200.047.41
import_dorothea_interactions0.550.011.37
import_intercell_network11.72 0.0312.25
import_kinaseextra_interactions4.250.035.08
import_ligrecextra_interactions1.090.001.89
import_lncrna_mrna_interactions0.050.000.70
import_mirnatarget_interactions1.040.001.89
import_omnipath_annotations0.030.000.67
import_omnipath_complexes1.070.021.83
import_omnipath_enzsub4.250.015.03
import_omnipath_interactions1.090.001.85
import_omnipath_intercell0.580.000.67
import_pathwayextra_interactions1.560.022.26
import_post_translational_interactions2.560.023.38
import_tf_mirna_interactions0.710.001.44
import_tf_target_interactions0.090.001.15
import_transcriptional_interactions1.120.023.72
interaction_graph1.710.002.39
print_interactions10.00 0.0811.17
print_path_es1.420.002.53
print_path_vs7.830.049.41
ptms_graph5.870.006.64

OmnipathR.Rcheck/examples_x64/OmnipathR-Ex.timings

nameusersystemelapsed
OmnipathR4.660.106.78
get_annotation_resources0.030.010.61
get_complex_genes4.180.034.42
get_complex_resources0.070.000.64
get_enzsub_resources0.140.000.71
get_interaction_resources0.070.000.62
get_intercell_categories0.080.000.28
get_intercell_generic_categories0.070.000.16
get_intercell_resources0.080.000.65
get_resources0.080.000.61
get_signed_ptms14.87 0.1816.02
import_all_interactions5.040.066.33
import_dorothea_interactions0.310.001.17
import_intercell_network10.25 0.0911.09
import_kinaseextra_interactions3.440.024.28
import_ligrecextra_interactions0.900.011.93
import_lncrna_mrna_interactions0.060.000.68
import_mirnatarget_interactions0.860.001.85
import_omnipath_annotations0.100.030.72
import_omnipath_complexes1.330.022.14
import_omnipath_enzsub3.970.004.74
import_omnipath_interactions0.880.021.64
import_omnipath_intercell0.560.000.64
import_pathwayextra_interactions1.490.002.19
import_post_translational_interactions2.040.012.84
import_tf_mirna_interactions0.530.001.31
import_tf_target_interactions0.110.000.74
import_transcriptional_interactions0.980.002.53
interaction_graph1.060.021.74
print_interactions6.410.016.56
print_path_es0.910.001.72
print_path_vs4.640.006.59
ptms_graph3.700.004.53