Alberto Valdeolivas Urbelz
| Snapshot Date: 2020-04-14 16:46:13 -0400 (Tue, 14 Apr 2020) |
| URL: https://git.bioconductor.org/packages/OmnipathR |
| Branch: RELEASE_3_10 |
| Last Commit: f0dd8eb |
| Last Changed Date: 2020-03-26 13:20:23 -0400 (Thu, 26 Mar 2020) |
| Back to Multiple platform build/check report for BioC 3.10 |
|
This page was generated on 2020-04-15 12:33:23 -0400 (Wed, 15 Apr 2020).
| Package 1184/1823 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| OmnipathR 1.0.1 Alberto Valdeolivas Urbelz
| malbec1 | Linux (Ubuntu 18.04.4 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | [ ERROR ] | OK | |||||||
| merida1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | |
| Package: OmnipathR |
| Version: 1.0.1 |
| Command: C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:OmnipathR.install-out.txt --library=C:\Users\biocbuild\bbs-3.10-bioc\R\library --no-vignettes --timings OmnipathR_1.0.1.tar.gz |
| StartedAt: 2020-04-15 05:12:56 -0400 (Wed, 15 Apr 2020) |
| EndedAt: 2020-04-15 05:39:45 -0400 (Wed, 15 Apr 2020) |
| EllapsedTime: 1609.6 seconds |
| RetCode: 1 |
| Status: ERROR |
| CheckDir: OmnipathR.Rcheck |
| Warnings: NA |
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### Running command:
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### C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:OmnipathR.install-out.txt --library=C:\Users\biocbuild\bbs-3.10-bioc\R\library --no-vignettes --timings OmnipathR_1.0.1.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.10-bioc/meat/OmnipathR.Rcheck'
* using R version 3.6.3 (2020-02-29)
* 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 '1.0.1'
* 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 files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
get_signed_ptms 62.67 14.50 78.16
OmnipathR 35.60 9.28 45.32
import_AllInteractions 36.30 8.34 45.27
printPath_vs 35.94 7.95 44.48
print_interactions 31.02 7.49 42.78
printPath_es 20.62 5.48 26.24
get_interaction_databases 20.18 4.56 24.85
interaction_graph 17.91 4.46 22.48
ptms_graph 17.64 4.51 22.25
import_Omnipath_PTMS 17.20 4.38 21.70
import_Omnipath_Interactions 17.36 4.16 21.62
get_intercell_categories 16.57 3.38 20.05
import_Omnipath_intercell 12.51 3.30 15.92
get_complex_genes 11.96 3.34 15.37
get_ptms_databases 11.93 2.75 14.82
get_complexes_databases 10.18 2.36 12.64
import_Omnipath_complexes 8.49 2.50 11.19
import_PathwayExtra_Interactions 8.10 2.08 10.36
import_KinaseExtra_Interactions 5.54 1.52 7.14
import_TFregulons_Interactions 4.57 0.78 5.47
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
import_Omnipath_intercell 46.46 16.43 63.00
get_signed_ptms 43.52 14.41 59.04
printPath_vs 31.45 10.19 41.83
OmnipathR 28.59 9.68 38.59
import_AllInteractions 26.81 9.27 36.16
print_interactions 22.36 6.36 28.92
printPath_es 19.54 5.73 25.38
import_Omnipath_Interactions 16.88 4.54 21.50
get_interaction_databases 14.63 5.78 24.55
ptms_graph 16.63 3.76 20.49
get_intercell_categories 13.47 4.66 18.90
import_Omnipath_PTMS 12.84 4.43 17.45
interaction_graph 13.11 3.11 16.34
get_complex_genes 8.80 2.98 12.03
get_complexes_databases 7.84 2.75 10.70
import_Omnipath_complexes 6.80 2.14 9.01
get_ptms_databases 6.81 1.87 8.97
import_PathwayExtra_Interactions 5.66 2.20 7.97
import_KinaseExtra_Interactions 5.69 1.45 7.27
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
Running 'testthat.R'
ERROR
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
-- 1. Failure: Check the databases/categories available in Omnipath (@test_fetch
get_interaction_databases() not equal to `interaction_databases`.
Lengths differ: 98 is not 63
-- 2. Failure: Check the databases/categories available in Omnipath (@test_fetch
get_intercell_categories() not equal to `intercell_categories`.
Lengths differ: 37 is not 79
== testthat results ===========================================================
[ OK: 7 | SKIPPED: 0 | WARNINGS: 1 | FAILED: 2 ]
1. Failure: Check the databases/categories available in Omnipath (@test_fetchingOmnipathWebserver.R#80)
2. Failure: Check the databases/categories available in Omnipath (@test_fetchingOmnipathWebserver.R#83)
Error: testthat unit tests failed
Execution halted
** running tests for arch 'x64' ...
Running 'testthat.R'
ERROR
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
union
>
> test_check("OmnipathR")
-- 1. Failure: Check the databases/categories available in Omnipath (@test_fetch
get_intercell_categories() not equal to `intercell_categories`.
Lengths differ: 79 is not 38
== testthat results ===========================================================
[ OK: 8 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 1 ]
1. Failure: Check the databases/categories available in Omnipath (@test_fetchingOmnipathWebserver.R#83)
Error: testthat unit tests failed
Execution halted
* 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: 2 ERRORs
See
'C:/Users/biocbuild/bbs-3.10-bioc/meat/OmnipathR.Rcheck/00check.log'
for details.
OmnipathR.Rcheck/00install.out
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###
### Running command:
###
### C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.10/bioc/src/contrib/OmnipathR_1.0.1.tar.gz && rm -rf OmnipathR.buildbin-libdir && mkdir OmnipathR.buildbin-libdir && C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=OmnipathR.buildbin-libdir OmnipathR_1.0.1.tar.gz && C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD INSTALL OmnipathR_1.0.1.zip && rm OmnipathR_1.0.1.tar.gz OmnipathR_1.0.1.zip
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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_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_1.0.1.zip
* DONE (OmnipathR)
* installing to library 'C:/Users/biocbuild/bbs-3.10-bioc/R/library'
package 'OmnipathR' successfully unpacked and MD5 sums checked
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OmnipathR.Rcheck/tests_i386/testthat.Rout.fail
R version 3.6.3 (2020-02-29) -- "Holding the Windsock"
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")
-- 1. Failure: Check the databases/categories available in Omnipath (@test_fetch
get_interaction_databases() not equal to `interaction_databases`.
Lengths differ: 98 is not 63
-- 2. Failure: Check the databases/categories available in Omnipath (@test_fetch
get_intercell_categories() not equal to `intercell_categories`.
Lengths differ: 37 is not 79
== testthat results ===========================================================
[ OK: 7 | SKIPPED: 0 | WARNINGS: 1 | FAILED: 2 ]
1. Failure: Check the databases/categories available in Omnipath (@test_fetchingOmnipathWebserver.R#80)
2. Failure: Check the databases/categories available in Omnipath (@test_fetchingOmnipathWebserver.R#83)
Error: testthat unit tests failed
Execution halted
|
OmnipathR.Rcheck/tests_x64/testthat.Rout.fail
R version 3.6.3 (2020-02-29) -- "Holding the Windsock"
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")
-- 1. Failure: Check the databases/categories available in Omnipath (@test_fetch
get_intercell_categories() not equal to `intercell_categories`.
Lengths differ: 79 is not 38
== testthat results ===========================================================
[ OK: 8 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 1 ]
1. Failure: Check the databases/categories available in Omnipath (@test_fetchingOmnipathWebserver.R#83)
Error: testthat unit tests failed
Execution halted
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OmnipathR.Rcheck/examples_i386/OmnipathR-Ex.timings
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OmnipathR.Rcheck/examples_x64/OmnipathR-Ex.timings
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