Florian Auer
| Snapshot Date: 2025-12-11 13:45 -0500 (Thu, 11 Dec 2025) |
| git_url: https://git.bioconductor.org/packages/ndexr |
| git_branch: RELEASE_3_22 |
| git_last_commit: 5dbac8e |
| git_last_commit_date: 2025-10-29 10:38:47 -0500 (Wed, 29 Oct 2025) |
| Back toMultiple platform build/check report for BioC 3.22: simplified long |
|
This page was generated on 2025-12-15 12:08 -0500 (Mon, 15 Dec 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble" | 4882 |
| merida1 | macOS 12.7.6 Monterey | x86_64 | 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble" | 4673 |
| kjohnson1 | macOS 13.7.5 Ventura | arm64 | 4.5.2 Patched (2025-11-04 r88984) -- "[Not] Part in a Rumble" | 4607 |
| taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4671 |
| 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 | ||||
| Package1448/2361 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| ndexr 1.32.0 (landing page) Florian Auer
| nebbiolo2 | 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 | | ||||||||
| taishan | 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. SeeTroubleshooting Build Report for more information. - Use the followingRenviron 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. SeeRenviron.bioc for more information. |
| Package: ndexr |
| Version: 1.32.0 |
| 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_1.32.0.tar.gz |
| StartedAt: 2025-12-13 15:37:56 -0500 (Sat, 13 Dec 2025) |
| EndedAt: 2025-12-13 15:39:22 -0500 (Sat, 13 Dec 2025) |
| EllapsedTime: 86.4 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_1.32.0.tar.gz###############################################################################################################################################################* using log directory ‘/Users/biocbuild/bbs-3.22-bioc/meat/ndexr.Rcheck’* using R version 4.5.2 Patched (2025-11-04 r88984)* using platform: aarch64-apple-darwin20* R was compiled by Apple clang version 16.0.0 (clang-1600.0.26.6) GNU Fortran (GCC) 14.2.0* running under: macOS Ventura 13.7.8* using session charset: UTF-8* using option ‘--no-vignettes’* checking for file ‘ndexr/DESCRIPTION’ ... OK* checking extension type ... Package* this is package ‘ndexr’ version ‘1.32.0’* 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 ... NOTELicense 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 ... NOTENamespaces 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 ... NOTEndex_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 tailConsider adding importFrom("utils", "packageVersion", "tail")to your NAMESPACE file.* checking Rd files ... NOTEcheckRd: (-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* DONEStatus: 4 NOTEsSee ‘/Users/biocbuild/bbs-3.22-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-arm64/Resources/library’* installing *source* package ‘ndexr’ ...** this is package ‘ndexr’ version ‘1.32.0’** 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 4.5.2 Patched (2025-11-04 r88984) -- "[Not] Part in a Rumble"Copyright (C) 2025 The R Foundation for Statistical ComputingPlatform: aarch64-apple-darwin20R 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 1 | PASS 124 ]══ Skipped tests (1) ═══════════════════════════════════════════════════════════• empty test (1):[ FAIL 0 | WARN 0 | SKIP 1 | PASS 124 ]> > proc.time() user system elapsed 16.016 0.583 37.582ndexr.Rcheck/ndexr-Ex.timings
| name | user | system | elapsed | |
| listToRCode | 0 | 0 | 0 | |
| ndex_conf_header | 0 | 0 | 0 | |
| ndex_config | 0.001 | 0.001 | 0.002 | |
| ndex_connect | 0.048 | 0.012 | 0.633 | |
| ndex_create_group | 0.000 | 0.000 | 0.001 | |
| ndex_create_network | 0.000 | 0.000 | 0.001 | |
| ndex_create_user | 0.000 | 0.000 | 0.001 | |
| ndex_delete_group | 0 | 0 | 0 | |
| ndex_delete_network | 0.000 | 0.001 | 0.000 | |
| ndex_delete_user | 0.001 | 0.000 | 0.000 | |
| ndex_find_groups | 0.046 | 0.004 | 0.338 | |
| ndex_find_networks | 0.047 | 0.003 | 0.629 | |
| ndex_find_user_byId | 0.027 | 0.002 | 0.450 | |
| ndex_find_user_byName | 0.015 | 0.002 | 0.304 | |
| ndex_find_users | 0.016 | 0.001 | 0.298 | |
| ndex_get_group | 0.026 | 0.001 | 0.459 | |
| ndex_get_network | 0.581 | 0.012 | 1.120 | |
| ndex_group_delete_membership | 0.000 | 0.000 | 0.001 | |
| ndex_group_list_networks | 0.036 | 0.002 | 0.612 | |
| ndex_group_list_users | 0.023 | 0.002 | 0.309 | |
| ndex_group_network_get_permission | 0.027 | 0.002 | 0.454 | |
| ndex_group_set_membership | 0.000 | 0.000 | 0.001 | |
| ndex_helper_encodeParams | 0.001 | 0.001 | 0.002 | |
| ndex_helper_getApi | 0.008 | 0.001 | 0.148 | |
| ndex_helper_httpResponseHandler | 0.010 | 0.001 | 0.150 | |
| ndex_network_aspect_get_metadata | 0.029 | 0.002 | 0.461 | |
| ndex_network_delete_permission | 0 | 0 | 0 | |
| ndex_network_get_aspect | 0.057 | 0.003 | 0.629 | |
| ndex_network_get_metadata | 0.031 | 0.002 | 0.462 | |
| ndex_network_get_permission | 0.000 | 0.000 | 0.001 | |
| ndex_network_get_provenance | 0.026 | 0.002 | 0.461 | |
| ndex_network_get_summary | 0.030 | 0.002 | 0.469 | |
| ndex_network_set_systemProperties | 0.000 | 0.000 | 0.001 | |
| ndex_network_update_aspect | 0.000 | 0.001 | 0.000 | |
| ndex_network_update_permission | 0.001 | 0.000 | 0.000 | |
| ndex_network_update_profile | 0.000 | 0.001 | 0.000 | |
| ndex_rest_DELETE | 0.007 | 0.001 | 0.146 | |
| ndex_rest_GET | 0.005 | 0.000 | 0.152 | |
| ndex_rest_POST | 0.006 | 0.001 | 0.147 | |
| ndex_rest_PUT | 0.005 | 0.001 | 0.153 | |
| ndex_update_group | 0.000 | 0.001 | 0.005 | |
| ndex_update_network | 0 | 0 | 0 | |
| ndex_update_user | 0.000 | 0.000 | 0.001 | |
| ndex_user_change_password | 0 | 0 | 0 | |
| ndex_user_forgot_password | 0.000 | 0.000 | 0.001 | |
| ndex_user_get_networksummary | 0.000 | 0.000 | 0.001 | |
| ndex_user_get_showcase | 0.028 | 0.002 | 0.465 | |
| ndex_user_list_groups | 0.000 | 0.000 | 0.001 | |
| ndex_user_list_permissions | 0.000 | 0.000 | 0.001 | |
| ndex_user_mail_password | 0.000 | 0.000 | 0.001 | |
| ndex_user_show_group | 0 | 0 | 0 | |
| ndex_user_show_permission | 0.000 | 0.001 | 0.000 | |
| ndex_verify_user | 0 | 0 | 0 | |
| ndexr-package | 0.000 | 0.001 | 0.001 | |
| print.NDExConnection | 0.016 | 0.002 | 0.312 | |