Florian Auer
| Snapshot Date: 2025-10-13 13:40 -0400 (Mon, 13 Oct 2025) |
| git_url: https://git.bioconductor.org/packages/ndexr |
| git_branch: RELEASE_3_21 |
| git_last_commit: 26b94e3 |
| git_last_commit_date: 2025-04-15 11:11:22 -0400 (Tue, 15 Apr 2025) |
| Back to Multiple platform build/check report for BioC 3.21: simplified long |
|
This page was generated on 2025-10-16 11:39 -0400 (Thu, 16 Oct 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4833 |
| merida1 | macOS 12.7.6 Monterey | x86_64 | 4.5.1 RC (2025-06-05 r88288) -- "Great Square Root" | 4614 |
| kjohnson1 | macOS 13.7.5 Ventura | arm64 | 4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" | 4555 |
| kunpeng2 | Linux (openEuler 24.03 LTS) | aarch64 | R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" | 4586 |
| Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X | ||||
| Package 1429/2341 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| ndexr 1.30.0 (landing page) Florian Auer
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| merida1 | macOS 12.7.6 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson1 | macOS 13.7.5 Ventura / arm64 | OK | OK | OK | OK | | ||||||||
| kunpeng2 | Linux (openEuler 24.03 LTS) / aarch64 | OK | OK | OK | ||||||||||
|
To the developers/maintainers of the ndexr package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/ndexr.git to reflect on this report. See Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
| Package: ndexr |
| Version: 1.30.0 |
| Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:ndexr.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings ndexr_1.30.0.tar.gz |
| StartedAt: 2025-10-14 07:24:33 -0400 (Tue, 14 Oct 2025) |
| EndedAt: 2025-10-14 07:26:36 -0400 (Tue, 14 Oct 2025) |
| EllapsedTime: 123.3 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: ndexr.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:ndexr.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings ndexr_1.30.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/ndexr.Rcheck’
* using R version 4.5.1 RC (2025-06-05 r88288)
* using platform: x86_64-apple-darwin20
* R was compiled by
Apple clang version 14.0.0 (clang-1400.0.29.202)
GNU Fortran (GCC) 14.2.0
* running under: macOS Monterey 12.7.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘ndexr/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘ndexr’ version ‘1.30.0’
* 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 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
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
ndex_connect 0.065 0.015 6.466
* 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
‘/Users/biocbuild/bbs-3.21-bioc/meat/ndexr.Rcheck/00check.log’
for details.
ndexr.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL ndexr ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library’ * installing *source* package ‘ndexr’ ... ** this is package ‘ndexr’ version ‘1.30.0’ ** 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)
ndexr.Rcheck/tests/testthat.Rout
R version 4.5.1 RC (2025-06-05 r88288) -- "Great Square Root"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20
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
36.539 0.798 44.506
ndexr.Rcheck/ndexr-Ex.timings
| name | user | system | elapsed | |
| listToRCode | 0.000 | 0.001 | 0.002 | |
| ndex_conf_header | 0.000 | 0.001 | 0.001 | |
| ndex_config | 0.001 | 0.001 | 0.003 | |
| ndex_connect | 0.065 | 0.015 | 6.466 | |
| ndex_create_group | 0.001 | 0.000 | 0.001 | |
| ndex_create_network | 0.001 | 0.001 | 0.001 | |
| ndex_create_user | 0.000 | 0.000 | 0.001 | |
| ndex_delete_group | 0.000 | 0.001 | 0.001 | |
| ndex_delete_network | 0.000 | 0.001 | 0.000 | |
| ndex_delete_user | 0.001 | 0.000 | 0.001 | |
| ndex_find_groups | 0.067 | 0.004 | 0.190 | |
| ndex_find_networks | 0.082 | 0.004 | 0.337 | |
| ndex_find_user_byId | 0.040 | 0.002 | 0.214 | |
| ndex_find_user_byName | 0.022 | 0.001 | 0.137 | |
| ndex_find_users | 0.026 | 0.002 | 0.144 | |
| ndex_get_group | 0.038 | 0.002 | 0.215 | |
| ndex_get_network | 1.206 | 0.021 | 1.415 | |
| ndex_group_delete_membership | 0.000 | 0.001 | 0.001 | |
| ndex_group_list_networks | 0.053 | 0.002 | 0.291 | |
| ndex_group_list_users | 0.031 | 0.001 | 0.152 | |
| ndex_group_network_get_permission | 0.038 | 0.002 | 0.216 | |
| ndex_group_set_membership | 0.000 | 0.000 | 0.001 | |
| ndex_helper_encodeParams | 0.002 | 0.002 | 0.005 | |
| ndex_helper_getApi | 0.011 | 0.001 | 0.068 | |
| ndex_helper_httpResponseHandler | 0.016 | 0.002 | 0.074 | |
| ndex_network_aspect_get_metadata | 0.043 | 0.002 | 0.219 | |
| ndex_network_delete_permission | 0.000 | 0.000 | 0.001 | |
| ndex_network_get_aspect | 0.101 | 0.002 | 0.335 | |
| ndex_network_get_metadata | 0.045 | 0.003 | 0.221 | |
| ndex_network_get_permission | 0.001 | 0.001 | 0.002 | |
| ndex_network_get_provenance | 0.038 | 0.001 | 0.212 | |
| ndex_network_get_summary | 0.043 | 0.002 | 0.218 | |
| ndex_network_set_systemProperties | 0.000 | 0.001 | 0.001 | |
| ndex_network_update_aspect | 0.000 | 0.001 | 0.000 | |
| ndex_network_update_permission | 0.000 | 0.000 | 0.001 | |
| ndex_network_update_profile | 0.001 | 0.001 | 0.001 | |
| ndex_rest_DELETE | 0.010 | 0.001 | 0.068 | |
| ndex_rest_GET | 0.009 | 0.001 | 0.067 | |
| ndex_rest_POST | 0.009 | 0.001 | 0.067 | |
| ndex_rest_PUT | 0.010 | 0.001 | 0.067 | |
| ndex_update_group | 0.000 | 0.001 | 0.001 | |
| ndex_update_network | 0.000 | 0.001 | 0.001 | |
| ndex_update_user | 0.000 | 0.000 | 0.001 | |
| ndex_user_change_password | 0.000 | 0.001 | 0.000 | |
| ndex_user_forgot_password | 0.000 | 0.001 | 0.001 | |
| ndex_user_get_networksummary | 0.000 | 0.001 | 0.001 | |
| ndex_user_get_showcase | 0.040 | 0.003 | 0.220 | |
| ndex_user_list_groups | 0.001 | 0.001 | 0.001 | |
| ndex_user_list_permissions | 0.000 | 0.001 | 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 | 0.000 | 0.000 | 0.001 | |
| ndexr-package | 0.001 | 0.001 | 0.002 | |
| print.NDExConnection | 0.022 | 0.002 | 0.138 | |