Multiple platform build/check report for BioC 3.12 - CHECK report for OmnipathR on tokay1

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

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###
### 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
###
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* 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.

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###
### 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
###
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  % 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


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


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

name	user	system	elapsed
OmnipathR	6.34	0.06	9.05
get_annotation_resources	0.05	0.00	0.61
get_complex_genes	4.32	0.02	4.56
get_complex_resources	0.04	0.00	0.61
get_enzsub_resources	0.09	0.00	0.66
get_interaction_resources	0.03	0.00	0.61
get_intercell_categories	0.06	0.00	0.26
get_intercell_generic_categories	0.07	0.00	0.16
get_intercell_resources	0.04	0.00	0.61
get_resources	0.03	0.00	0.61
get_signed_ptms	17.30	0.04	18.34
import_all_interactions	6.20	0.04	7.41
import_dorothea_interactions	0.55	0.01	1.37
import_intercell_network	11.72	0.03	12.25
import_kinaseextra_interactions	4.25	0.03	5.08
import_ligrecextra_interactions	1.09	0.00	1.89
import_lncrna_mrna_interactions	0.05	0.00	0.70
import_mirnatarget_interactions	1.04	0.00	1.89
import_omnipath_annotations	0.03	0.00	0.67
import_omnipath_complexes	1.07	0.02	1.83
import_omnipath_enzsub	4.25	0.01	5.03
import_omnipath_interactions	1.09	0.00	1.85
import_omnipath_intercell	0.58	0.00	0.67
import_pathwayextra_interactions	1.56	0.02	2.26
import_post_translational_interactions	2.56	0.02	3.38
import_tf_mirna_interactions	0.71	0.00	1.44
import_tf_target_interactions	0.09	0.00	1.15
import_transcriptional_interactions	1.12	0.02	3.72
interaction_graph	1.71	0.00	2.39
print_interactions	10.00	0.08	11.17
print_path_es	1.42	0.00	2.53
print_path_vs	7.83	0.04	9.41
ptms_graph	5.87	0.00	6.64

name	user	system	elapsed
OmnipathR	4.66	0.10	6.78
get_annotation_resources	0.03	0.01	0.61
get_complex_genes	4.18	0.03	4.42
get_complex_resources	0.07	0.00	0.64
get_enzsub_resources	0.14	0.00	0.71
get_interaction_resources	0.07	0.00	0.62
get_intercell_categories	0.08	0.00	0.28
get_intercell_generic_categories	0.07	0.00	0.16
get_intercell_resources	0.08	0.00	0.65
get_resources	0.08	0.00	0.61
get_signed_ptms	14.87	0.18	16.02
import_all_interactions	5.04	0.06	6.33
import_dorothea_interactions	0.31	0.00	1.17
import_intercell_network	10.25	0.09	11.09
import_kinaseextra_interactions	3.44	0.02	4.28
import_ligrecextra_interactions	0.90	0.01	1.93
import_lncrna_mrna_interactions	0.06	0.00	0.68
import_mirnatarget_interactions	0.86	0.00	1.85
import_omnipath_annotations	0.10	0.03	0.72
import_omnipath_complexes	1.33	0.02	2.14
import_omnipath_enzsub	3.97	0.00	4.74
import_omnipath_interactions	0.88	0.02	1.64
import_omnipath_intercell	0.56	0.00	0.64
import_pathwayextra_interactions	1.49	0.00	2.19
import_post_translational_interactions	2.04	0.01	2.84
import_tf_mirna_interactions	0.53	0.00	1.31
import_tf_target_interactions	0.11	0.00	0.74
import_transcriptional_interactions	0.98	0.00	2.53
interaction_graph	1.06	0.02	1.74
print_interactions	6.41	0.01	6.56
print_path_es	0.91	0.00	1.72
print_path_vs	4.64	0.00	6.59
ptms_graph	3.70	0.00	4.53

CHECK report for OmnipathR on tokay1

Summary

Command output

Installation output

Tests output

Example timings