Package: ndexr

Version: 1.0.4

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings ndexr_1.0.4.tar.gz

StartedAt: 2018-04-12 07:02:19 -0400 (Thu, 12 Apr 2018)

EndedAt: 2018-04-12 07:03:29 -0400 (Thu, 12 Apr 2018)

EllapsedTime: 70.5 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 --no-vignettes --timings ndexr_1.0.4.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.6-bioc/meat/ndexr.Rcheck’
* using R version 3.4.4 (2018-03-15)
* 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 ‘1.0.4’
* 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 loading without being on the library search path ... 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’
ngraph_toRCX: no visible binding for global variable ‘po’
Undefined global functions or variables:
  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 meta-data column names (api Version_2.0)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 81 SKIPPED: 1 FAILED: 8
  1. Failure: Get list of networks from a server (ndex_find_networks) (@test_02_finding_networks.r#34) 
  2. Failure: Get list of networks from a server (ndex_find_networks) (@test_02_finding_networks.r#39) 
  3. Failure: Get list of networks from a server (ndex_find_networks) (@test_02_finding_networks.r#45) 
  4. Failure: Get list of networks from a server (ndex_find_networks) (@test_02_finding_networks.r#53) 
  5. Error: Get list of networks from a server (ndex_find_networks) (@test_02_finding_networks.r#55) 
  6. Failure: Get network summary from server (ndex_network_get_summary) (@test_03_simple_network_operations.r#75) 
  7. Failure: Get network summary from server (ndex_network_get_summary) (@test_03_simple_network_operations.r#75) 
  8. Failure: Get network meta-data (ndex_network_get_metadata) (@test_04_network_aspects_and_metadata.r#38) 
  
  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-3.6-bioc/meat/ndexr.Rcheck/00check.log’
for details.

* installing *source* package ‘ndexr’ ...
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (ndexr)

R version 3.4.4 (2018-03-15) -- "Someone to Lean On"
Copyright (C) 2018 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 using api Version_2.0

── 2. Failure: Get list of networks from a server (ndex_find_networks) (@test_02

Checking column names of found network list ("egfr") 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 ("egfr") of "ndextutorials" using api Version_2.0

── 4. 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

── 5. Error: Get list of networks from a server (ndex_find_networks) (@test_02_f
undefined columns selected
1: expect_identical(networks[, columnsToBeEqual], forLater[, columnsToBeEqual], info = paste0("The network list (start=1, size=5) should be the same as the excerpt [6:10] with standard parameter (start=0, size=100) using api ", 
       apiVersion)) at testthat/test_02_finding_networks.r:55
2: quasi_label(enquo(object), label)
3: eval_bare(get_expr(quo), get_env(quo))
4: networks[, columnsToBeEqual]
5: `[.data.frame`(networks, , columnsToBeEqual)
6: stop("undefined columns selected")

── 6. Failure: Get network summary from server (ndex_network_get_summary) (@test

Checking column names of found network (api Version_2.0)

── 7. Failure: Get network summary from server (ndex_network_get_summary) (@test

Checking column names of found network (api Version_1.3)

── 8. Failure: Get network meta-data (ndex_network_get_metadata) (@test_04_netwo

Checking meta-data column names (api Version_2.0)

══ testthat results  ═══════════════════════════════════════════════════════════
OK: 81 SKIPPED: 1 FAILED: 8
1. Failure: Get list of networks from a server (ndex_find_networks) (@test_02_finding_networks.r#34) 
2. Failure: Get list of networks from a server (ndex_find_networks) (@test_02_finding_networks.r#39) 
3. Failure: Get list of networks from a server (ndex_find_networks) (@test_02_finding_networks.r#45) 
4. Failure: Get list of networks from a server (ndex_find_networks) (@test_02_finding_networks.r#53) 
5. Error: Get list of networks from a server (ndex_find_networks) (@test_02_finding_networks.r#55) 
6. Failure: Get network summary from server (ndex_network_get_summary) (@test_03_simple_network_operations.r#75) 
7. Failure: Get network summary from server (ndex_network_get_summary) (@test_03_simple_network_operations.r#75) 
8. Failure: Get network meta-data (ndex_network_get_metadata) (@test_04_network_aspects_and_metadata.r#38) 

Error: testthat unit tests failed
Execution halted

name	user	system	elapsed
listToRCode	0.001	0.000	0.001
ndex_conf_header	0	0	0
ndex_config	0.001	0.000	0.000
ndex_connect	0.335	0.008	0.583
ndex_create_group	0	0	0
ndex_create_network	0.001	0.000	0.001
ndex_create_user	0.001	0.001	0.001
ndex_delete_group	0.001	0.000	0.001
ndex_delete_network	0.000	0.000	0.001
ndex_delete_user	0.001	0.001	0.001
ndex_find_groups	0.152	0.002	0.321
ndex_find_networks	0.094	0.002	0.517
ndex_find_user_byId	0.036	0.001	0.277
ndex_find_user_byName	0.010	0.000	0.171
ndex_find_users	0.012	0.000	0.173
ndex_get_group	0.019	0.001	0.264
ndex_get_network	0.266	0.010	0.621
ndex_group_delete_membership	0.001	0.000	0.001
ndex_group_list_networks	0.023	0.001	0.349
ndex_group_list_users	0.011	0.000	0.175
ndex_group_network_get_permission	0.014	0.001	0.259
ndex_group_set_membership	0.002	0.000	0.002
ndex_helper_encodeParams	0.004	0.000	0.005
ndex_helper_getApi	0.003	0.001	0.084
ndex_helper_httpResponseHandler	0.030	0.001	0.110
ndex_internal_addAspects	0.001	0.000	0.001
ndex_network_aspect_get_metadata	0.037	0.002	0.384
ndex_network_delete_permission	0.001	0.000	0.001
ndex_network_get_aspect	0.155	0.012	0.670
ndex_network_get_metadata	0.055	0.002	0.326
ndex_network_get_permission	0.001	0.000	0.001
ndex_network_get_provenance	0.054	0.002	0.318
ndex_network_get_summary	0.046	0.002	0.311
ndex_network_set_systemProperties	0.001	0.000	0.001
ndex_network_update_aspect	0.001	0.001	0.001
ndex_network_update_permission	0.001	0.000	0.001
ndex_network_update_profile	0.001	0.000	0.001
ndex_rest_DELETE	0.004	0.000	0.084
ndex_rest_GET	0.004	0.000	0.084
ndex_rest_POST	0.004	0.000	0.085
ndex_rest_PUT	0.004	0.000	0.085
ndex_update_group	0.001	0.000	0.001
ndex_update_network	0.001	0.000	0.001
ndex_update_user	0.001	0.001	0.001
ndex_user_change_password	0.001	0.000	0.001
ndex_user_forgot_password	0.001	0.000	0.001
ndex_user_get_networksummary	0.001	0.001	0.002
ndex_user_get_showcase	0.019	0.001	0.261
ndex_user_list_groups	0.001	0.000	0.001
ndex_user_list_permissions	0.001	0.001	0.005
ndex_user_mail_password	0.001	0.000	0.001
ndex_user_show_group	0.001	0.001	0.001
ndex_user_show_permission	0.001	0.000	0.001
ndex_verify_user	0.000	0.000	0.001
ndexr-package	0.001	0.000	0.001
ngraph_fromRCX	2.348	0.175	3.882
ngraph_toRCX	2.333	0.166	4.240
print.NDExConnection	0.010	0.001	0.172
print.RCX	0.006	0.000	0.005
rcx_asNewNetwork	0.086	0.002	0.589
rcx_aspect_toJSON	0.081	0.001	0.345
rcx_fromJSON	0.072	0.002	0.336
rcx_new	0.115	0.000	0.116
rcx_toJSON	0.214	0.002	0.482
rcx_toNGraph	1.981	0.162	3.510
rcx_updateMetaData	1.649	0.114	3.492