Package: ndexr

Version: 1.0.4

Command: rm -rf ndexr.buildbin-libdir ndexr.Rcheck && mkdir ndexr.buildbin-libdir ndexr.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=ndexr.buildbin-libdir ndexr_1.0.4.tar.gz >ndexr.Rcheck\00install.out 2>&1 && cp ndexr.Rcheck\00install.out ndexr-install.out && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=ndexr.buildbin-libdir --install="check:ndexr-install.out" --force-multiarch --no-vignettes --timings ndexr_1.0.4.tar.gz

StartedAt: 2018-04-12 01:46:10 -0400 (Thu, 12 Apr 2018)

EndedAt: 2018-04-12 01:50:11 -0400 (Thu, 12 Apr 2018)

EllapsedTime: 241.0 seconds

RetCode: 1

Status:  ERROR

CheckDir: ndexr.Rcheck

Warnings: NA

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###
### Running command:
###
###   rm -rf ndexr.buildbin-libdir ndexr.Rcheck && mkdir ndexr.buildbin-libdir ndexr.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=ndexr.buildbin-libdir ndexr_1.0.4.tar.gz >ndexr.Rcheck\00install.out 2>&1 && cp ndexr.Rcheck\00install.out ndexr-install.out  &&  C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=ndexr.buildbin-libdir --install="check:ndexr-install.out" --force-multiarch --no-vignettes --timings ndexr_1.0.4.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.6-bioc/meat/ndexr.Rcheck'
* using R version 3.4.4 (2018-03-15)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* 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 whether package 'ndexr' can be installed ... WARNING
Found the following significant warnings:
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpmWF4k1/R.INSTALL3068424f6ab1/ndexr/man/ngraph_fromRCX.Rd:22: missing file link 'igraph'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpmWF4k1/R.INSTALL3068424f6ab1/ndexr/man/ngraph_fromRCX.Rd:71: missing file link 'igraph'
See 'C:/Users/biocbuild/bbs-3.6-bioc/meat/ndexr.Rcheck/00install.out' for details.
* 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
* 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
** checking loading without being on the library search path ... 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 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 ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
                   user system elapsed
ngraph_fromRCX     4.28   0.21    9.30
ngraph_toRCX       3.48   0.24    9.68
rcx_toNGraph       3.35   0.16   26.79
rcx_updateMetaData 2.93   0.09   15.98
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                   user system elapsed
ngraph_toRCX       3.47   0.17   11.75
ngraph_fromRCX     3.40   0.14    6.20
rcx_toNGraph       3.27   0.13   18.01
rcx_updateMetaData 3.06   0.12   12.60
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'testthat.R'
Warning message:
running command '"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/bin/i386/R" CMD BATCH --vanilla  "testthat.R" "testthat.Rout"' had status 1 
 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
** running tests for arch 'x64' ...
  Running 'testthat.R'
Warning message:
running command '"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/bin/x64/R" CMD BATCH --vanilla  "testthat.R" "testthat.Rout"' had status 1 
 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: 2 ERRORs, 1 WARNING, 3 NOTEs
See
  'C:/Users/biocbuild/bbs-3.6-bioc/meat/ndexr.Rcheck/00check.log'
for details.

install for i386

* installing *source* package 'ndexr' ...
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
  converting help for package 'ndexr'
    finding HTML links ... done
    listToRCode                             html  
    ndex_conf_header                        html  
    ndex_config                             html  
    ndex_connect                            html  
    ndex_create_group                       html  
    ndex_create_network                     html  
    ndex_create_user                        html  
    ndex_delete_group                       html  
    ndex_delete_network                     html  
    ndex_delete_user                        html  
    ndex_find_groups                        html  
    ndex_find_networks                      html  
    ndex_find_user_byId                     html  
    ndex_find_user_byName                   html  
    ndex_find_users                         html  
    ndex_get_group                          html  
    ndex_get_network                        html  
    ndex_group_delete_membership            html  
    ndex_group_list_networks                html  
    ndex_group_list_users                   html  
    ndex_group_network_get_permission       html  
    ndex_group_set_membership               html  
    ndex_helper_encodeParams                html  
    ndex_helper_getApi                      html  
    ndex_helper_httpResponseHandler         html  
    ndex_internal_addAspects                html  
    ndex_network_aspect_get_metadata        html  
    ndex_network_delete_permission          html  
    ndex_network_get_aspect                 html  
    ndex_network_get_metadata               html  
    ndex_network_get_permission             html  
    ndex_network_get_provenance             html  
    ndex_network_get_summary                html  
    ndex_network_set_systemProperties       html  
    ndex_network_update_aspect              html  
    ndex_network_update_permission          html  
    ndex_network_update_profile             html  
    ndex_rest_DELETE                        html  
    ndex_rest_GET                           html  
    ndex_rest_POST                          html  
    ndex_rest_PUT                           html  
    ndex_update_group                       html  
    ndex_update_network                     html  
    ndex_update_user                        html  
    ndex_user_change_password               html  
    ndex_user_forgot_password               html  
    ndex_user_get_networksummary            html  
    ndex_user_get_showcase                  html  
    ndex_user_list_groups                   html  
    ndex_user_list_permissions              html  
    ndex_user_mail_password                 html  
    ndex_user_show_group                    html  
    ndex_user_show_permission               html  
    ndex_verify_user                        html  
    ndexr-package                           html  
    ngraph_fromRCX                          html  
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpmWF4k1/R.INSTALL3068424f6ab1/ndexr/man/ngraph_fromRCX.Rd:22: missing file link 'igraph'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpmWF4k1/R.INSTALL3068424f6ab1/ndexr/man/ngraph_fromRCX.Rd:71: missing file link 'igraph'
    ngraph_toRCX                            html  
    print.NDExConnection                    html  
    print.RCX                               html  
    rcx_asNewNetwork                        html  
    rcx_aspect_toJSON                       html  
    rcx_fromJSON                            html  
    rcx_new                                 html  
    rcx_toJSON                              html  
    rcx_toNGraph                            html  
    rcx_updateMetaData                      html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL

install for x64

* installing *source* package 'ndexr' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'ndexr' as ndexr_1.0.4.zip
* DONE (ndexr)
In R CMD INSTALL
In R CMD INSTALL

R version 3.4.4 (2018-03-15) -- "Someone to Lean On"
Copyright (C) 2018 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(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

R version 3.4.4 (2018-03-15) -- "Someone to Lean On"
Copyright (C) 2018 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(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