Package: ndexr

Version: 1.6.1

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:ndexr.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings ndexr_1.6.1.tar.gz

StartedAt: 2019-10-16 05:03:14 -0400 (Wed, 16 Oct 2019)

EndedAt: 2019-10-16 05:04:37 -0400 (Wed, 16 Oct 2019)

EllapsedTime: 83.1 seconds

RetCode: 1

Status:  ERROR

CheckDir: ndexr.Rcheck

Warnings: NA

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:ndexr.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings ndexr_1.6.1.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/ndexr.Rcheck’
* using R version 3.6.1 (2019-07-05)
* using platform: x86_64-apple-darwin15.6.0 (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
  ‘/Users/biocbuild/bbs-3.9-bioc/meat/ndexr.Rcheck/00check.log’
for details.

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### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL ndexr
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/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)

R version 3.6.1 (2019-07-05) -- "Action of the Toes"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin15.6.0 (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

name	user	system	elapsed
listToRCode	0.001	0.000	0.001
ndex_conf_header	0.000	0.000	0.001
ndex_config	0.002	0.001	0.003
ndex_connect	0.094	0.017	0.353
ndex_create_group	0	0	0
ndex_create_network	0.001	0.000	0.000
ndex_create_user	0	0	0
ndex_delete_group	0.000	0.000	0.001
ndex_delete_network	0.001	0.000	0.000
ndex_delete_user	0	0	0
ndex_find_groups	0.061	0.007	0.238
ndex_find_networks	0.100	0.008	0.462
ndex_find_user_byId	0.025	0.002	0.270
ndex_find_user_byName	0.022	0.001	0.185
ndex_find_users	0.022	0.002	0.186
ndex_get_group	0.031	0.002	0.280
ndex_get_network	0.355	0.019	0.657
ndex_group_delete_membership	0.000	0.000	0.001
ndex_group_list_networks	0.041	0.003	0.373
ndex_group_list_users	0.028	0.001	0.195
ndex_group_network_get_permission	0.028	0.002	0.277
ndex_group_set_membership	0.001	0.001	0.001
ndex_helper_encodeParams	0.005	0.001	0.007
ndex_helper_getApi	0.007	0.001	0.088
ndex_helper_httpResponseHandler	0.014	0.002	0.096
ndex_internal_addAspects	0.001	0.000	0.001
ndex_network_aspect_get_metadata	0.107	0.006	0.393
ndex_network_delete_permission	0.001	0.001	0.001
ndex_network_get_aspect	0.096	0.009	0.451
ndex_network_get_metadata	0.117	0.007	0.405
ndex_network_get_permission	0.001	0.000	0.002
ndex_network_get_provenance	0.194	0.006	0.483
ndex_network_get_summary	0.100	0.017	0.401
ndex_network_set_systemProperties	0.001	0.000	0.001
ndex_network_update_aspect	0.000	0.000	0.001
ndex_network_update_permission	0.000	0.000	0.001
ndex_network_update_profile	0.001	0.000	0.001
ndex_rest_DELETE	0.008	0.001	0.089
ndex_rest_GET	0.008	0.001	0.090
ndex_rest_POST	0.008	0.001	0.091
ndex_rest_PUT	0.008	0.002	0.090
ndex_update_group	0	0	0
ndex_update_network	0	0	0
ndex_update_user	0.001	0.000	0.001
ndex_user_change_password	0.000	0.001	0.000
ndex_user_forgot_password	0.000	0.001	0.001
ndex_user_get_networksummary	0.001	0.001	0.001
ndex_user_get_showcase	0.039	0.008	0.290
ndex_user_list_groups	0.001	0.000	0.001
ndex_user_list_permissions	0.000	0.001	0.001
ndex_user_mail_password	0.000	0.001	0.001
ndex_user_show_group	0.000	0.001	0.001
ndex_user_show_permission	0.001	0.000	0.001
ndex_verify_user	0	0	0
ndexr-package	0.001	0.000	0.001
ngraph_toRCX	0.006	0.001	0.007
print.NDExConnection	0.020	0.004	0.185
print.RCX	0.011	0.002	0.013
rcx_asNewNetwork	0.004	0.001	0.005
rcx_aspect_toJSON	0.012	0.001	0.012
rcx_fromJSON	0.075	0.001	0.076
rcx_new	0.017	0.000	0.017
rcx_toJSON	0.005	0.000	0.004
rcx_toNGraph	0.003	0.001	0.004
rcx_toRCXgraph	0.010	0.002	0.011
rcx_updateMetaData	0.003	0.001	0.004
rcxgraph_toRCX	0.005	0.000	0.005