Multiple platform build/check report for BioC 3.20 - CHECK results for ndexr on nebbiolo2

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo2	Linux (Ubuntu 24.04.1 LTS)	x86_64	4.4.2 (2024-10-31) -- "Pile of Leaves"	4744
palomino8	Windows Server 2022 Datacenter	x64	4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves"	4487
merida1	macOS 12.7.5 Monterey	x86_64	4.4.2 (2024-10-31) -- "Pile of Leaves"	4515
kjohnson1	macOS 13.6.6 Ventura	arm64	4.4.2 (2024-10-31) -- "Pile of Leaves"	4467
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*

CHECK results for ndexr on nebbiolo2

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.

raw results

Summary

Package: ndexr

Version: 1.28.0

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_1.28.0.tar.gz

StartedAt: 2024-12-20 03:31:51 -0500 (Fri, 20 Dec 2024)

EndedAt: 2024-12-20 03:36:33 -0500 (Fri, 20 Dec 2024)

EllapsedTime: 282.3 seconds

RetCode: 0

Status: OK

CheckDir: ndexr.Rcheck

Warnings: 0

Command output

##############################################################################
##############################################################################
###
### 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_1.28.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/ndexr.Rcheck’
* using R version 4.4.2 (2024-10-31)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0
    GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0
* running under: Ubuntu 24.04.1 LTS
* using session charset: UTF-8
* 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 ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
  cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
 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.

Installation output

ndexr.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD INSTALL ndexr
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.20-bioc/R/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)

Tests output

ndexr.Rcheck/tests/testthat.Rout


R version 4.4.2 (2024-10-31) -- "Pile of Leaves"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-pc-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 
 13.672   0.356  29.507

Example timings

ndexr.Rcheck/ndexr-Ex.timings

name	user	system	elapsed
listToRCode	0	0	0
ndex_conf_header	0	0	0
ndex_config	0.001	0.000	0.001
ndex_connect	0.038	0.007	0.484
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	0.000	0.000	0.001
ndex_delete_network	0.001	0.000	0.000
ndex_delete_user	0.001	0.000	0.000
ndex_find_groups	0.078	0.000	0.240
ndex_find_networks	0.098	0.000	0.616
ndex_find_user_byId	0.030	0.000	0.267
ndex_find_user_byName	0.024	0.000	0.179
ndex_find_users	0.030	0.001	0.189
ndex_get_group	0.055	0.000	0.296
ndex_get_network	0.535	0.048	1.065
ndex_group_delete_membership	0	0	0
ndex_group_list_networks	0.096	0.024	0.443
ndex_group_list_users	0.013	0.000	0.176
ndex_group_network_get_permission	0.030	0.002	0.272
ndex_group_set_membership	0	0	0
ndex_helper_encodeParams	0.001	0.000	0.001
ndex_helper_getApi	0.007	0.000	0.085
ndex_helper_httpResponseHandler	0.020	0.001	0.103
ndex_network_aspect_get_metadata	0.047	0.006	0.290
ndex_network_delete_permission	0.001	0.000	0.000
ndex_network_get_aspect	0.101	0.011	0.428
ndex_network_get_metadata	0.048	0.004	0.291
ndex_network_get_permission	0.001	0.000	0.000
ndex_network_get_provenance	0.047	0.004	0.288
ndex_network_get_summary	0.058	0.002	0.300
ndex_network_set_systemProperties	0	0	0
ndex_network_update_aspect	0	0	0
ndex_network_update_permission	0	0	0
ndex_network_update_profile	0	0	0
ndex_rest_DELETE	0.007	0.001	0.088
ndex_rest_GET	0.009	0.000	0.085
ndex_rest_POST	0.008	0.000	0.087
ndex_rest_PUT	0.009	0.000	0.087
ndex_update_group	0	0	0
ndex_update_network	0	0	0
ndex_update_user	0	0	0
ndex_user_change_password	0	0	0
ndex_user_forgot_password	0	0	0
ndex_user_get_networksummary	0	0	0
ndex_user_get_showcase	0.049	0.001	0.285
ndex_user_list_groups	0	0	0
ndex_user_list_permissions	0	0	0
ndex_user_mail_password	0	0	0
ndex_user_show_group	0	0	0
ndex_user_show_permission	0	0	0
ndex_verify_user	0	0	0
ndexr-package	0.000	0.001	0.000
print.NDExConnection	0.021	0.000	0.177