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###
### Running command:
###
###   /home/biocbuild/R/R-beta-2024-04-15_r86425/bin/R CMD check --install=check:ndexr.install-out.txt --library=/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library --no-vignettes --timings ndexr_1.26.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/ndexr.Rcheck’
* using R version 4.4.0 beta (2024-04-15 r86425)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
    gcc (GCC) 10.3.1
    GNU Fortran (GCC) 10.3.1
* running under: openEuler 22.03 (LTS-SP1)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘ndexr/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘ndexr’ version ‘1.26.0’
* 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
License stub is invalid DCF.
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code 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
Namespaces in Imports field not imported from:
  ‘plyr’ ‘tidyr’
  All declared Imports should be used.
Package in Depends field not imported from: ‘RCX’
  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’
Undefined global functions or variables:
  packageVersion tail
Consider adding
  importFrom("utils", "packageVersion", "tail")
to your NAMESPACE file.
* checking Rd files ... NOTE
checkRd: (-1) ndex_create_group.Rd:10: Lost braces
    10 | \item{ndexcon}{object of class NDExConnection link{ndex_connect}}
       |                                                   ^
checkRd: (-1) ndex_create_network.Rd:10: Lost braces
    10 | \item{ndexcon}{object of class NDExConnection link{ndex_connect}}
       |                                                   ^
checkRd: (-1) ndex_create_user.Rd:23: Lost braces
    23 | \item{ndexcon}{object of class NDExConnection link{ndex_connect}}
       |                                                   ^
checkRd: (-1) ndex_delete_group.Rd:10: Lost braces
    10 | \item{ndexcon}{object of class NDExConnection link{ndex_connect}}
       |                                                   ^
checkRd: (-1) ndex_delete_network.Rd:10: Lost braces
    10 | \item{ndexcon}{object of class NDExConnection link{ndex_connect}}
       |                                                   ^
checkRd: (-1) ndex_delete_user.Rd:10: Lost braces
    10 | \item{ndexcon}{object of class NDExConnection link{ndex_connect}}
       |                                                   ^
checkRd: (-1) ndex_find_groups.Rd:10: Lost braces
    10 | \item{ndexcon}{object of class NDExConnection link{ndex_connect}}
       |                                                   ^
checkRd: (-1) ndex_find_networks.Rd:10: Lost braces
    10 | \item{ndexcon}{object of class NDExConnection link{ndex_connect}}
       |                                                   ^
checkRd: (-1) ndex_find_user_byId.Rd:10: Lost braces
    10 | \item{ndexcon}{object of class NDExConnection link{ndex_connect}}
       |                                                   ^
checkRd: (-1) ndex_find_user_byName.Rd:10: Lost braces
    10 | \item{ndexcon}{object of class NDExConnection link{ndex_connect}}
       |                                                   ^
checkRd: (-1) ndex_find_users.Rd:10: Lost braces
    10 | \item{ndexcon}{object of class NDExConnection link{ndex_connect}}
       |                                                   ^
checkRd: (-1) ndex_get_group.Rd:10: Lost braces
    10 | \item{ndexcon}{object of class NDExConnection link{ndex_connect}}
       |                                                   ^
checkRd: (-1) ndex_get_network.Rd:10: Lost braces
    10 | \item{ndexcon}{object of class NDExConnection link{ndex_connect}}
       |                                                   ^
checkRd: (-1) ndex_group_delete_membership.Rd:10: Lost braces
    10 | \item{ndexcon}{object of class NDExConnection link{ndex_connect}}
       |                                                   ^
checkRd: (-1) ndex_group_list_networks.Rd:16: Lost braces
    16 | \item{ndexcon}{object of class NDExConnection link{ndex_connect}}
       |                                                   ^
checkRd: (-1) ndex_group_list_users.Rd:10: Lost braces
    10 | \item{ndexcon}{object of class NDExConnection link{ndex_connect}}
       |                                                   ^
checkRd: (-1) ndex_group_set_membership.Rd:10: Lost braces
    10 | \item{ndexcon}{object of class NDExConnection link{ndex_connect}}
       |                                                   ^
checkRd: (-1) ndex_network_aspect_get_metadata.Rd:10: Lost braces
    10 | \item{ndexcon}{object of class NDExConnection link{ndex_connect}}
       |                                                   ^
checkRd: (-1) ndex_network_delete_permission.Rd:10: Lost braces
    10 | \item{ndexcon}{object of class NDExConnection link{ndex_connect}}
       |                                                   ^
checkRd: (-1) ndex_network_get_aspect.Rd:10: Lost braces
    10 | \item{ndexcon}{object of class NDExConnection link{ndex_connect}}
       |                                                   ^
checkRd: (-1) ndex_network_get_metadata.Rd:10: Lost braces
    10 | \item{ndexcon}{object of class NDExConnection link{ndex_connect}}
       |                                                   ^
checkRd: (-1) ndex_network_get_permission.Rd:10: Lost braces
    10 | \item{ndexcon}{object of class NDExConnection link{ndex_connect}}
       |                                                   ^
checkRd: (-1) ndex_network_get_provenance.Rd:10: Lost braces
    10 | \item{ndexcon}{object of class NDExConnection link{ndex_connect}}
       |                                                   ^
checkRd: (-1) ndex_network_get_summary.Rd:10: Lost braces
    10 | \item{ndexcon}{object of class NDExConnection link{ndex_connect}}
       |                                                   ^
checkRd: (-1) ndex_network_set_systemProperties.Rd:16: Lost braces
    16 | \item{ndexcon}{object of class NDExConnection link{ndex_connect}}
       |                                                   ^
checkRd: (-1) ndex_network_update_aspect.Rd:16: Lost braces
    16 | \item{ndexcon}{object of class NDExConnection link{ndex_connect}}
       |                                                   ^
checkRd: (-1) ndex_network_update_permission.Rd:16: Lost braces
    16 | \item{ndexcon}{object of class NDExConnection link{ndex_connect}}
       |                                                   ^
checkRd: (-1) ndex_network_update_profile.Rd:16: Lost braces
    16 | \item{ndexcon}{object of class NDExConnection link{ndex_connect}}
       |                                                   ^
checkRd: (-1) ndex_update_group.Rd:18: Lost braces
    18 | \item{ndexcon}{object of class NDExConnection link{ndex_connect}}
       |                                                   ^
checkRd: (-1) ndex_update_network.Rd:10: Lost braces
    10 | \item{ndexcon}{object of class NDExConnection link{ndex_connect}}
       |                                                   ^
checkRd: (-1) ndex_update_user.Rd:22: Lost braces
    22 | \item{ndexcon}{object of class NDExConnection link{ndex_connect}}
       |                                                   ^
checkRd: (-1) ndex_user_change_password.Rd:10: Lost braces
    10 | \item{ndexcon}{object of class NDExConnection link{ndex_connect}}
       |                                                   ^
checkRd: (-1) ndex_user_forgot_password.Rd:10: Lost braces
    10 | \item{ndexcon}{object of class NDExConnection link{ndex_connect}}
       |                                                   ^
checkRd: (-1) ndex_user_get_networksummary.Rd:10: Lost braces
    10 | \item{ndexcon}{object of class NDExConnection link{ndex_connect}}
       |                                                   ^
checkRd: (-1) ndex_user_get_showcase.Rd:10: Lost braces
    10 | \item{ndexcon}{object of class NDExConnection link{ndex_connect}}
       |                                                   ^
checkRd: (-1) ndex_user_list_groups.Rd:10: Lost braces
    10 | \item{ndexcon}{object of class NDExConnection link{ndex_connect}}
       |                                                   ^
checkRd: (-1) ndex_user_list_permissions.Rd:17: Lost braces
    17 | \item{ndexcon}{object of class NDExConnection link{ndex_connect}}
       |                                                   ^
checkRd: (-1) ndex_user_mail_password.Rd:10: Lost braces
    10 | \item{ndexcon}{object of class NDExConnection link{ndex_connect}}
       |                                                   ^
checkRd: (-1) ndex_user_show_group.Rd:10: Lost braces
    10 | \item{ndexcon}{object of class NDExConnection link{ndex_connect}}
       |                                                   ^
checkRd: (-1) ndex_user_show_permission.Rd:10: Lost braces
    10 | \item{ndexcon}{object of class NDExConnection link{ndex_connect}}
       |                                                   ^
checkRd: (-1) ndex_verify_user.Rd:10: Lost braces
    10 | \item{ndexcon}{object of class NDExConnection link{ndex_connect}}
       |                                                   ^
* 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 files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 4 NOTEs
See
  ‘/home/biocbuild/bbs-3.19-bioc/meat/ndexr.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /home/biocbuild/R/R-beta-2024-04-15_r86425/bin/R CMD INSTALL ndexr
###
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* installing to library ‘/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library’
* installing *source* package ‘ndexr’ ...
** using staged installation
** R
** 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 4.4.0 beta (2024-04-15 r86425) -- "Puppy Cup"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: aarch64-unknown-linux-gnu

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: RCX
> 
> test_check("ndexr")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 124 ]
> 
> proc.time()
   user  system elapsed 
 22.851   0.502  56.720