Multiple platform build/check report for BioC 3.11 - CHECK report for OmnipathR on tokay2

Package: OmnipathR

Version: 1.2.1

Command: C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:OmnipathR.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings OmnipathR_1.2.1.tar.gz

StartedAt: 2020-10-17 06:36:09 -0400 (Sat, 17 Oct 2020)

EndedAt: 2020-10-17 06:45:28 -0400 (Sat, 17 Oct 2020)

EllapsedTime: 559.2 seconds

RetCode: 0

Status: OK

CheckDir: OmnipathR.Rcheck

Warnings: 0

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### Running command:
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###   C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:OmnipathR.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings OmnipathR_1.2.1.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.11-bioc/meat/OmnipathR.Rcheck'
* using R version 4.0.3 (2020-10-10)
* 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 '1.2.1'
* 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 ... OK
* 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
import_Omnipath_intercell        63.33   0.56   65.56
get_signed_ptms                  34.16   0.23   35.07
printPath_vs                     21.23   0.12   21.81
OmnipathR                        20.68   0.19   22.89
import_AllInteractions           18.22   0.22   18.68
print_interactions               14.21   0.03   14.69
printPath_es                     12.92   0.05   14.35
interaction_graph                10.47   0.08   10.78
import_Omnipath_Interactions      9.65   0.03    9.85
get_interaction_databases         9.56   0.03    9.83
import_Omnipath_PTMS              9.16   0.08    9.45
ptms_graph                        8.98   0.05    9.26
import_PathwayExtra_Interactions  6.25   0.02    6.50
get_ptms_databases                6.11   0.02    6.28
import_Omnipath_complexes         6.11   0.01    6.59
get_complex_genes                 6.01   0.03    6.28
get_complexes_databases           5.85   0.03    6.11
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                              user system elapsed
get_signed_ptms              28.80   0.38   29.90
printPath_vs                 17.48   0.24   18.17
import_AllInteractions       17.06   0.34   17.65
import_Omnipath_intercell    15.00   0.28   16.59
OmnipathR                    14.74   0.31   15.91
print_interactions           13.84   0.15   14.55
interaction_graph             9.44   0.19    9.84
get_interaction_databases     9.41   0.19    9.83
ptms_graph                    9.50   0.10    9.85
import_Omnipath_Interactions  9.08   0.10    9.34
printPath_es                  8.72   0.12    9.08
import_Omnipath_PTMS          6.77   0.12    7.14
get_ptms_databases            6.44   0.07    6.69
get_complex_genes             5.14   0.06    5.44
* 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: OK

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.11/bioc/src/contrib/OmnipathR_1.2.1.tar.gz && rm -rf OmnipathR.buildbin-libdir && mkdir OmnipathR.buildbin-libdir && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=OmnipathR.buildbin-libdir OmnipathR_1.2.1.tar.gz && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL OmnipathR_1.2.1.zip && rm OmnipathR_1.2.1.tar.gz OmnipathR_1.2.1.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  122k  100  122k    0     0  3593k      0 --:--:-- --:--:-- --:--:-- 4238k

install for i386

* installing *source* package 'OmnipathR' ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'OmnipathR'
    finding HTML links ... done
    OmnipathR                               html  
    get_annotation_databases                html  
    get_complex_genes                       html  
    get_complexes_databases                 html  
    get_interaction_databases               html  
    get_intercell_categories                html  
    get_intercell_classes                   html  
    get_ptms_databases                      html  
    get_signed_ptms                         html  
    import_AllInteractions                  html  
    import_KinaseExtra_Interactions         html  
    import_LigrecExtra_Interactions         html  
    import_Omnipath_Interactions            html  
    import_Omnipath_PTMS                    html  
    import_Omnipath_annotations             html  
    import_Omnipath_complexes               html  
    import_Omnipath_intercell               html  
    import_PathwayExtra_Interactions        html  
    import_TFregulons_Interactions          html  
    import_miRNAtarget_Interactions         html  
    interaction_graph                       html  
    printPath_es                            html  
    printPath_vs                            html  
    print_interactions                      html  
    ptms_graph                              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 'OmnipathR' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'OmnipathR' as OmnipathR_1.2.1.zip
* DONE (OmnipathR)
* installing to library 'C:/Users/biocbuild/bbs-3.11-bioc/R/library'
package 'OmnipathR' successfully unpacked and MD5 sums checked


R version 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out"
Copyright (C) 2020 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.

> 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

> 
> test_check("OmnipathR")
== testthat results  ===========================================================
[ OK: 0 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
    2.1     0.1     2.2


R version 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out"
Copyright (C) 2020 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.

> 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

> 
> test_check("OmnipathR")
== testthat results  ===========================================================
[ OK: 0 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
   1.84    0.07    1.90

name	user	system	elapsed
OmnipathR	20.68	0.19	22.89
get_annotation_databases	2.46	0.00	2.68
get_complex_genes	6.01	0.03	6.28
get_complexes_databases	5.85	0.03	6.11
get_interaction_databases	9.56	0.03	9.83
get_intercell_categories	0.12	0.00	0.42
get_intercell_classes	0.11	0.00	0.27
get_ptms_databases	6.11	0.02	6.28
get_signed_ptms	34.16	0.23	35.07
import_AllInteractions	18.22	0.22	18.68
import_KinaseExtra_Interactions	4.14	0.02	4.39
import_LigrecExtra_Interactions	0.93	0.00	1.14
import_Omnipath_Interactions	9.65	0.03	9.85
import_Omnipath_PTMS	9.16	0.08	9.45
import_Omnipath_annotations	2.62	0.00	3.38
import_Omnipath_complexes	6.11	0.01	6.59
import_Omnipath_intercell	63.33	0.56	65.56
import_PathwayExtra_Interactions	6.25	0.02	6.50
import_TFregulons_Interactions	2.74	0.01	3.13
import_miRNAtarget_Interactions	2.20	0.02	2.90
interaction_graph	10.47	0.08	10.78
printPath_es	12.92	0.05	14.35
printPath_vs	21.23	0.12	21.81
print_interactions	14.21	0.03	14.69
ptms_graph	8.98	0.05	9.26

name	user	system	elapsed
OmnipathR	14.74	0.31	15.91
get_annotation_databases	1.84	0.02	2.09
get_complex_genes	5.14	0.06	5.44
get_complexes_databases	4.53	0.11	4.87
get_interaction_databases	9.41	0.19	9.83
get_intercell_categories	0.13	0.00	0.35
get_intercell_classes	0.10	0.00	0.26
get_ptms_databases	6.44	0.07	6.69
get_signed_ptms	28.80	0.38	29.90
import_AllInteractions	17.06	0.34	17.65
import_KinaseExtra_Interactions	3.39	0.00	3.62
import_LigrecExtra_Interactions	0.86	0.00	1.11
import_Omnipath_Interactions	9.08	0.10	9.34
import_Omnipath_PTMS	6.77	0.12	7.14
import_Omnipath_annotations	1.79	0.03	2.21
import_Omnipath_complexes	3.66	0.03	3.92
import_Omnipath_intercell	15.00	0.28	16.59
import_PathwayExtra_Interactions	3.47	0.04	3.67
import_TFregulons_Interactions	2.09	0.00	2.33
import_miRNAtarget_Interactions	1.33	0.01	1.58
interaction_graph	9.44	0.19	9.84
printPath_es	8.72	0.12	9.08
printPath_vs	17.48	0.24	18.17
print_interactions	13.84	0.15	14.55
ptms_graph	9.50	0.10	9.85

CHECK report for OmnipathR on tokay2

Summary

Command output

Installation output

Tests output

Example timings