| Back to Multiple platform build/check report for BioC 3.6 |
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This page was generated on 2018-04-12 13:16:18 -0400 (Thu, 12 Apr 2018).
| Package 932/1472 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| ndexr 1.0.4 Florian Auer
| malbec1 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | NotNeeded | OK | [ ERROR ] | |||||||
| tokay1 | Windows Server 2012 R2 Standard / x64 | NotNeeded | OK | ERROR | OK | |||||||
| veracruz1 | OS X 10.11.6 El Capitan / x86_64 | NotNeeded | OK | ERROR | OK |
| Package: ndexr |
| Version: 1.0.4 |
| Command: /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings ndexr_1.0.4.tar.gz |
| StartedAt: 2018-04-12 01:26:57 -0400 (Thu, 12 Apr 2018) |
| EndedAt: 2018-04-12 01:27:55 -0400 (Thu, 12 Apr 2018) |
| EllapsedTime: 58.1 seconds |
| RetCode: 1 |
| Status: ERROR |
| CheckDir: ndexr.Rcheck |
| Warnings: NA |
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###
### Running command:
###
### /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings ndexr_1.0.4.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.6-bioc/meat/ndexr.Rcheck’
* using R version 3.4.4 (2018-03-15)
* 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 ‘1.0.4’
* 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
‘/home/biocbuild/bbs-3.6-bioc/meat/ndexr.Rcheck/00check.log’
for details.
ndexr.Rcheck/00install.out
* 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)
ndexr.Rcheck/tests/testthat.Rout.fail
R version 3.4.4 (2018-03-15) -- "Someone to Lean On"
Copyright (C) 2018 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 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
ndexr.Rcheck/ndexr-Ex.timings
| name | user | system | elapsed | |
| listToRCode | 0 | 0 | 0 | |
| ndex_conf_header | 0 | 0 | 0 | |
| ndex_config | 0.000 | 0.000 | 0.001 | |
| ndex_connect | 0.496 | 0.000 | 0.759 | |
| ndex_create_group | 0.000 | 0.000 | 0.001 | |
| ndex_create_network | 0.000 | 0.000 | 0.001 | |
| ndex_create_user | 0.004 | 0.000 | 0.001 | |
| ndex_delete_group | 0.000 | 0.000 | 0.001 | |
| ndex_delete_network | 0.004 | 0.000 | 0.001 | |
| ndex_delete_user | 0.004 | 0.000 | 0.001 | |
| ndex_find_groups | 0.188 | 0.004 | 0.374 | |
| ndex_find_networks | 0.124 | 0.000 | 0.581 | |
| ndex_find_user_byId | 0.056 | 0.000 | 0.318 | |
| ndex_find_user_byName | 0.016 | 0.000 | 0.194 | |
| ndex_find_users | 0.020 | 0.000 | 0.201 | |
| ndex_get_group | 0.036 | 0.000 | 0.308 | |
| ndex_get_network | 0.288 | 0.000 | 0.664 | |
| ndex_group_delete_membership | 0.000 | 0.004 | 0.001 | |
| ndex_group_list_networks | 0.052 | 0.000 | 0.408 | |
| ndex_group_list_users | 0.024 | 0.000 | 0.202 | |
| ndex_group_network_get_permission | 0.036 | 0.000 | 0.301 | |
| ndex_group_set_membership | 0.000 | 0.000 | 0.001 | |
| ndex_helper_encodeParams | 0.004 | 0.000 | 0.003 | |
| ndex_helper_getApi | 0.004 | 0.000 | 0.092 | |
| ndex_helper_httpResponseHandler | 0.032 | 0.000 | 0.122 | |
| ndex_internal_addAspects | 0 | 0 | 0 | |
| ndex_network_aspect_get_metadata | 0.052 | 0.000 | 0.339 | |
| ndex_network_delete_permission | 0.000 | 0.000 | 0.001 | |
| ndex_network_get_aspect | 0.180 | 0.008 | 0.737 | |
| ndex_network_get_metadata | 0.068 | 0.000 | 0.357 | |
| ndex_network_get_permission | 0.004 | 0.000 | 0.001 | |
| ndex_network_get_provenance | 0.052 | 0.000 | 0.338 | |
| ndex_network_get_summary | 0.052 | 0.000 | 0.337 | |
| ndex_network_set_systemProperties | 0.000 | 0.000 | 0.001 | |
| ndex_network_update_aspect | 0.004 | 0.000 | 0.001 | |
| ndex_network_update_permission | 0.000 | 0.000 | 0.001 | |
| ndex_network_update_profile | 0 | 0 | 0 | |
| ndex_rest_DELETE | 0.004 | 0.000 | 0.092 | |
| ndex_rest_GET | 0.004 | 0.000 | 0.093 | |
| ndex_rest_POST | 0.004 | 0.000 | 0.093 | |
| ndex_rest_PUT | 0.004 | 0.000 | 0.093 | |
| ndex_update_group | 0.004 | 0.000 | 0.001 | |
| ndex_update_network | 0 | 0 | 0 | |
| ndex_update_user | 0 | 0 | 0 | |
| ndex_user_change_password | 0.000 | 0.000 | 0.001 | |
| ndex_user_forgot_password | 0.000 | 0.000 | 0.001 | |
| ndex_user_get_networksummary | 0 | 0 | 0 | |
| ndex_user_get_showcase | 0.036 | 0.000 | 0.298 | |
| ndex_user_list_groups | 0 | 0 | 0 | |
| ndex_user_list_permissions | 0.004 | 0.000 | 0.001 | |
| ndex_user_mail_password | 0 | 0 | 0 | |
| ndex_user_show_group | 0.000 | 0.000 | 0.001 | |
| ndex_user_show_permission | 0.000 | 0.000 | 0.001 | |
| ndex_verify_user | 0 | 0 | 0 | |
| ndexr-package | 0 | 0 | 0 | |
| ngraph_fromRCX | 1.740 | 0.092 | 2.760 | |
| ngraph_toRCX | 1.752 | 0.032 | 2.862 | |
| print.NDExConnection | 0.008 | 0.004 | 0.187 | |
| print.RCX | 0.008 | 0.000 | 0.006 | |
| rcx_asNewNetwork | 0.076 | 0.000 | 0.454 | |
| rcx_aspect_toJSON | 0.092 | 0.000 | 0.379 | |
| rcx_fromJSON | 0.084 | 0.000 | 0.370 | |
| rcx_new | 0.088 | 0.000 | 0.089 | |
| rcx_toJSON | 0.200 | 0.004 | 0.490 | |
| rcx_toNGraph | 1.908 | 0.044 | 2.820 | |
| rcx_updateMetaData | 1.136 | 0.032 | 2.253 | |