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This page was generated on 2024-12-23 12:06 -0500 (Mon, 23 Dec 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.1 LTS)x86_644.4.2 (2024-10-31) -- "Pile of Leaves" 4744
palomino8Windows Server 2022 Datacenterx644.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" 4487
merida1macOS 12.7.5 Montereyx86_644.4.2 (2024-10-31) -- "Pile of Leaves" 4515
kjohnson1macOS 13.6.6 Venturaarm644.4.2 (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

Package 1400/2289HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ndexr 1.28.0  (landing page)
Florian Auer
Snapshot Date: 2024-12-19 13:00 -0500 (Thu, 19 Dec 2024)
git_url: https://git.bioconductor.org/packages/ndexr
git_branch: RELEASE_3_20
git_last_commit: 575109b
git_last_commit_date: 2024-10-29 10:19:40 -0500 (Tue, 29 Oct 2024)
nebbiolo2Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino8Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 12.7.5 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.6 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published


CHECK results for ndexr on merida1

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: /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_1.28.0.tar.gz
StartedAt: 2024-12-20 06:49:58 -0500 (Fri, 20 Dec 2024)
EndedAt: 2024-12-20 06:51:45 -0500 (Fri, 20 Dec 2024)
EllapsedTime: 106.3 seconds
RetCode: 0
Status:   OK  
CheckDir: ndexr.Rcheck
Warnings: 0

Command output

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


* using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/ndexr.Rcheck’
* using R version 4.4.2 (2024-10-31)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* 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 ‘1.28.0’
* 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 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 0.066  0.014   6.409
* 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-3.20-bioc/meat/ndexr.Rcheck/00check.log’
for details.


Installation output

ndexr.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL ndexr
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/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-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 
 38.201   0.871  46.346 

Example timings

ndexr.Rcheck/ndexr-Ex.timings

nameusersystemelapsed
listToRCode0.0010.0010.001
ndex_conf_header0.0000.0000.001
ndex_config0.0020.0010.002
ndex_connect0.0660.0146.409
ndex_create_group0.0010.0010.001
ndex_create_network0.0000.0010.001
ndex_create_user0.0000.0000.001
ndex_delete_group0.0000.0000.001
ndex_delete_network0.0000.0010.001
ndex_delete_user0.0000.0010.000
ndex_find_groups0.0690.0060.192
ndex_find_networks0.1120.0050.362
ndex_find_user_byId0.0340.0020.199
ndex_find_user_byName0.0220.0010.132
ndex_find_users0.0260.0010.140
ndex_get_group0.0370.0020.206
ndex_get_network1.1780.0191.377
ndex_group_delete_membership0.0010.0010.001
ndex_group_list_networks0.0620.0030.288
ndex_group_list_users0.0270.0020.141
ndex_group_network_get_permission0.0430.0020.213
ndex_group_set_membership0.0010.0000.001
ndex_helper_encodeParams0.0030.0020.005
ndex_helper_getApi0.0100.0010.066
ndex_helper_httpResponseHandler0.0150.0010.071
ndex_network_aspect_get_metadata0.0390.0020.207
ndex_network_delete_permission0.0000.0010.001
ndex_network_get_aspect0.1060.0030.329
ndex_network_get_metadata0.0410.0030.209
ndex_network_get_permission0.0010.0010.001
ndex_network_get_provenance0.0930.0020.260
ndex_network_get_summary0.0380.0010.205
ndex_network_set_systemProperties0.0010.0010.001
ndex_network_update_aspect0.0010.0000.001
ndex_network_update_permission0.0000.0010.001
ndex_network_update_profile0.0000.0010.001
ndex_rest_DELETE0.0090.0000.064
ndex_rest_GET0.0090.0010.064
ndex_rest_POST0.0090.0000.064
ndex_rest_PUT0.0090.0010.064
ndex_update_group0.0000.0010.001
ndex_update_network000
ndex_update_user0.0000.0000.001
ndex_user_change_password0.0000.0000.001
ndex_user_forgot_password0.0000.0000.001
ndex_user_get_networksummary0.0010.0010.001
ndex_user_get_showcase0.0410.0050.210
ndex_user_list_groups0.0000.0010.001
ndex_user_list_permissions0.0000.0010.001
ndex_user_mail_password0.0000.0000.001
ndex_user_show_group0.0010.0010.001
ndex_user_show_permission0.0010.0010.001
ndex_verify_user0.0000.0000.001
ndexr-package0.0000.0020.002
print.NDExConnection0.0220.0030.133