| Back to Multiple platform build/check report for BioC 3.9 |
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This page was generated on 2019-10-16 12:11:14 -0400 (Wed, 16 Oct 2019).
| Package 1090/1741 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| ndexr 1.6.1 Florian Auer
| malbec2 | Linux (Ubuntu 18.04.2 LTS) / x86_64 | OK | OK | [ ERROR ] | |||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | ERROR | OK | |||||||
| celaya2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | ERROR | OK |
| Package: ndexr |
| Version: 1.6.1 |
| Command: /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:ndexr.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings ndexr_1.6.1.tar.gz |
| StartedAt: 2019-10-16 03:31:51 -0400 (Wed, 16 Oct 2019) |
| EndedAt: 2019-10-16 03:32:50 -0400 (Wed, 16 Oct 2019) |
| EllapsedTime: 59.0 seconds |
| RetCode: 1 |
| Status: ERROR |
| CheckDir: ndexr.Rcheck |
| Warnings: NA |
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###
### Running command:
###
### /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:ndexr.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings ndexr_1.6.1.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.9-bioc/meat/ndexr.Rcheck’
* using R version 3.6.1 (2019-07-05)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘ndexr/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘ndexr’ version ‘1.6.1’
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘ndexr’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Deprecated license: BSD
* 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
* 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 ... NOTE
Package in Depends field not imported from: ‘igraph’
These packages need to be imported from (in the NAMESPACE file)
for when this namespace is loaded but not attached.
Unexported object imported by a ':::' call: ‘httr:::default_ua’
See the note in ?`:::` about the use of this operator.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
ndex_create_network: no visible global function definition for ‘tail’
ndex_rest_DELETE: no visible global function definition for
‘packageVersion’
ndex_rest_GET: no visible global function definition for
‘packageVersion’
ndex_rest_POST: no visible global function definition for
‘packageVersion’
ndex_rest_PUT: no visible global function definition for
‘packageVersion’
rcx_fromRCXgraph: no visible binding for global variable ‘po’
rcx_toRCXgraph: no visible global function definition for ‘V’
rcx_toRCXgraph: no visible global function definition for ‘V<-’
rcx_toRCXgraph: no visible global function definition for ‘E’
rcx_toRCXgraph: no visible global function definition for ‘E<-’
rcxgraph_fromRCX: no visible global function definition for ‘V’
rcxgraph_fromRCX: no visible global function definition for ‘V<-’
rcxgraph_fromRCX: no visible global function definition for ‘E’
rcxgraph_fromRCX: no visible global function definition for ‘E<-’
rcxgraph_toRCX: no visible binding for global variable ‘po’
Undefined global functions or variables:
E E<- V V<- packageVersion po tail
Consider adding
importFrom("utils", "packageVersion", "tail")
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 ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’
ERROR
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
Checking column names of found network list (start=1, size=5) using api Version_2.0
── 3. Failure: Get list of networks from a server (ndex_find_networks) (@test_02
Checking column names of found network list (start=1, size=5) using api Version_1.3
══ testthat results ═══════════════════════════════════════════════════════════
[ OK: 137 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 3 ]
1. Failure: Get list of networks from a server (ndex_find_networks) (@test_02_finding_networks.r#90)
2. Failure: Get list of networks from a server (ndex_find_networks) (@test_02_finding_networks.r#90)
3. Failure: Get list of networks from a server (ndex_find_networks) (@test_02_finding_networks.r#90)
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: 1 ERROR, 3 NOTEs
See
‘/home/biocbuild/bbs-3.9-bioc/meat/ndexr.Rcheck/00check.log’
for details.
ndexr.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD INSTALL ndexr ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.9-bioc/R/library’ * installing *source* package ‘ndexr’ ... ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** 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 * DONE (ndexr)
ndexr.Rcheck/tests/testthat.Rout.fail
R version 3.6.1 (2019-07-05) -- "Action of the Toes"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (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(ndexr)
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("ndexr")
── 1. Failure: Get list of networks from a server (ndex_find_networks) (@test_02
Checking column names of found network list (start=1, size=5) using api Version_2.1
── 2. Failure: Get list of networks from a server (ndex_find_networks) (@test_02
Checking column names of found network list (start=1, size=5) using api Version_2.0
── 3. Failure: Get list of networks from a server (ndex_find_networks) (@test_02
Checking column names of found network list (start=1, size=5) using api Version_1.3
══ testthat results ═══════════════════════════════════════════════════════════
[ OK: 137 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 3 ]
1. Failure: Get list of networks from a server (ndex_find_networks) (@test_02_finding_networks.r#90)
2. Failure: Get list of networks from a server (ndex_find_networks) (@test_02_finding_networks.r#90)
3. Failure: Get list of networks from a server (ndex_find_networks) (@test_02_finding_networks.r#90)
Error: testthat unit tests failed
Execution halted
ndexr.Rcheck/ndexr-Ex.timings
| name | user | system | elapsed | |
| listToRCode | 0.000 | 0.000 | 0.001 | |
| ndex_conf_header | 0 | 0 | 0 | |
| ndex_config | 0.001 | 0.000 | 0.001 | |
| ndex_connect | 0.075 | 0.004 | 0.361 | |
| ndex_create_group | 0.000 | 0.000 | 0.001 | |
| ndex_create_network | 0.000 | 0.000 | 0.001 | |
| ndex_create_user | 0 | 0 | 0 | |
| ndex_delete_group | 0 | 0 | 0 | |
| ndex_delete_network | 0 | 0 | 0 | |
| ndex_delete_user | 0 | 0 | 0 | |
| ndex_find_groups | 0.054 | 0.000 | 0.252 | |
| ndex_find_networks | 0.081 | 0.000 | 0.501 | |
| ndex_find_user_byId | 0.030 | 0.000 | 0.313 | |
| ndex_find_user_byName | 0.024 | 0.003 | 0.216 | |
| ndex_find_users | 0.026 | 0.000 | 0.217 | |
| ndex_get_group | 0.037 | 0.001 | 0.326 | |
| ndex_get_network | 0.316 | 0.004 | 0.644 | |
| ndex_group_delete_membership | 0.000 | 0.000 | 0.001 | |
| ndex_group_list_networks | 0.050 | 0.000 | 0.434 | |
| ndex_group_list_users | 0.025 | 0.000 | 0.221 | |
| ndex_group_network_get_permission | 0.038 | 0.000 | 0.326 | |
| ndex_group_set_membership | 0.001 | 0.000 | 0.001 | |
| ndex_helper_encodeParams | 0.003 | 0.000 | 0.002 | |
| ndex_helper_getApi | 0.005 | 0.000 | 0.103 | |
| ndex_helper_httpResponseHandler | 0.020 | 0.000 | 0.142 | |
| ndex_internal_addAspects | 0.001 | 0.000 | 0.001 | |
| ndex_network_aspect_get_metadata | 0.091 | 0.003 | 0.438 | |
| ndex_network_delete_permission | 0.000 | 0.000 | 0.001 | |
| ndex_network_get_aspect | 0.09 | 0.00 | 0.49 | |
| ndex_network_get_metadata | 0.103 | 0.001 | 0.536 | |
| ndex_network_get_permission | 0.000 | 0.000 | 0.001 | |
| ndex_network_get_provenance | 0.184 | 0.000 | 0.578 | |
| ndex_network_get_summary | 0.089 | 0.004 | 0.419 | |
| ndex_network_set_systemProperties | 0 | 0 | 0 | |
| ndex_network_update_aspect | 0 | 0 | 0 | |
| ndex_network_update_permission | 0.001 | 0.000 | 0.000 | |
| ndex_network_update_profile | 0 | 0 | 0 | |
| ndex_rest_DELETE | 0.006 | 0.000 | 0.100 | |
| ndex_rest_GET | 0.003 | 0.003 | 0.100 | |
| ndex_rest_POST | 0.005 | 0.000 | 0.100 | |
| ndex_rest_PUT | 0.006 | 0.000 | 0.100 | |
| ndex_update_group | 0 | 0 | 0 | |
| ndex_update_network | 0 | 0 | 0 | |
| ndex_update_user | 0 | 0 | 0 | |
| ndex_user_change_password | 0 | 0 | 0 | |
| ndex_user_forgot_password | 0 | 0 | 0 | |
| ndex_user_get_networksummary | 0.001 | 0.000 | 0.001 | |
| ndex_user_get_showcase | 0.038 | 0.000 | 0.323 | |
| ndex_user_list_groups | 0 | 0 | 0 | |
| ndex_user_list_permissions | 0 | 0 | 0 | |
| ndex_user_mail_password | 0.001 | 0.000 | 0.000 | |
| ndex_user_show_group | 0.001 | 0.000 | 0.000 | |
| ndex_user_show_permission | 0.000 | 0.000 | 0.001 | |
| ndex_verify_user | 0.000 | 0.000 | 0.001 | |
| ndexr-package | 0 | 0 | 0 | |
| ngraph_toRCX | 0.002 | 0.002 | 0.004 | |
| print.NDExConnection | 0.013 | 0.000 | 0.202 | |
| print.RCX | 0.004 | 0.003 | 0.006 | |
| rcx_asNewNetwork | 0.002 | 0.000 | 0.003 | |
| rcx_aspect_toJSON | 0.004 | 0.000 | 0.004 | |
| rcx_fromJSON | 0.092 | 0.004 | 0.124 | |
| rcx_new | 0.018 | 0.000 | 0.017 | |
| rcx_toJSON | 0.005 | 0.000 | 0.005 | |
| rcx_toNGraph | 0.003 | 0.000 | 0.003 | |
| rcx_toRCXgraph | 0.008 | 0.004 | 0.012 | |
| rcx_updateMetaData | 0.004 | 0.000 | 0.004 | |
| rcxgraph_toRCX | 0.002 | 0.004 | 0.006 | |