############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:ndexr.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings ndexr_1.27.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/ndexr.Rcheck’ * using R version 4.4.0 RC (2024-04-16 r86468) * using platform: x86_64-pc-linux-gnu * R was compiled by gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 * running under: Ubuntu 22.04.4 LTS * using session charset: UTF-8 * checking for file ‘ndexr/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘ndexr’ version ‘1.27.0’ * 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 re-building of vignette outputs ... OK * checking PDF version of manual ... OK * DONE Status: 4 NOTEs See ‘/home/biocbuild/bbs-3.20-bioc/meat/ndexr.Rcheck/00check.log’ for details.