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### Running command:
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###   F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:ndexr.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings ndexr_1.28.0.tar.gz
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* using log directory 'F:/biocbuild/bbs-3.20-bioc/meat/ndexr.Rcheck'
* using R version 4.4.1 (2024-06-14 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 13.2.0
    GNU Fortran (GCC) 13.2.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'ndexr/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'ndexr' version '1.28.0'
* 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 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 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
  'F:/biocbuild/bbs-3.20-bioc/meat/ndexr.Rcheck/00check.log'
for details.