Back to Multiple platform build/check report for BioC 3.20:   simplified   long
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This page was generated on 2024-11-20 12:02 -0500 (Wed, 20 Nov 2024).

HostnameOSArch (*)R versionInstalled pkgs
teran2Linux (Ubuntu 24.04.1 LTS)x86_644.4.2 (2024-10-31) -- "Pile of Leaves" 4481
nebbiolo2Linux (Ubuntu 24.04.1 LTS)x86_644.4.2 (2024-10-31) -- "Pile of Leaves" 4479
palomino8Windows Server 2022 Datacenterx644.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" 4359
lconwaymacOS 12.7.1 Montereyx86_644.4.1 (2024-06-14) -- "Race for Your Life" 4539
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch644.4.1 (2024-06-14) -- "Race for Your Life" 4493
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: 2024-11-19 13:40 -0500 (Tue, 19 Nov 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)
teran2Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
nebbiolo2Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    OK  
palomino8Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kunpeng2Linux (openEuler 22.03 LTS-SP1) / aarch64  OK    OK    OK  


CHECK results for ndexr on teran2

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: 2024-11-20 06:38:30 -0500 (Wed, 20 Nov 2024)
EndedAt: 2024-11-20 06:39:14 -0500 (Wed, 20 Nov 2024)
EllapsedTime: 44.1 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 ‘/media/volume/teran2_disk/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 ... 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
  ‘/media/volume/teran2_disk/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 ‘/media/volume/teran2_disk/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 
 10.301   0.254  17.730 

Example timings

ndexr.Rcheck/ndexr-Ex.timings

nameusersystemelapsed
listToRCode000
ndex_conf_header000
ndex_config0.0010.0000.000
ndex_connect0.0240.0050.286
ndex_create_group000
ndex_create_network000
ndex_create_user000
ndex_delete_group000
ndex_delete_network000
ndex_delete_user000
ndex_find_groups0.0270.0010.142
ndex_find_networks0.0370.0000.282
ndex_find_user_byId0.0160.0000.182
ndex_find_user_byName0.0100.0010.130
ndex_find_users0.0110.0000.122
ndex_get_group0.0160.0010.190
ndex_get_network0.3300.0260.556
ndex_group_delete_membership000
ndex_group_list_networks0.0690.0030.294
ndex_group_list_users0.0120.0000.130
ndex_group_network_get_permission0.0180.0000.185
ndex_group_set_membership0.0000.0000.001
ndex_helper_encodeParams0.0010.0000.001
ndex_helper_getApi0.0030.0010.059
ndex_helper_httpResponseHandler0.0070.0000.070
ndex_network_aspect_get_metadata0.0180.0000.187
ndex_network_delete_permission000
ndex_network_get_aspect0.0350.0130.270
ndex_network_get_metadata0.0220.0030.192
ndex_network_get_permission000
ndex_network_get_provenance0.0190.0040.187
ndex_network_get_summary0.0230.0010.188
ndex_network_set_systemProperties000
ndex_network_update_aspect000
ndex_network_update_permission000
ndex_network_update_profile000
ndex_rest_DELETE0.0030.0000.057
ndex_rest_GET0.0030.0000.057
ndex_rest_POST0.0020.0010.057
ndex_rest_PUT0.0030.0000.057
ndex_update_group0.0010.0000.001
ndex_update_network000
ndex_update_user000
ndex_user_change_password000
ndex_user_forgot_password000
ndex_user_get_networksummary000
ndex_user_get_showcase0.0180.0010.184
ndex_user_list_groups000
ndex_user_list_permissions0.0000.0010.000
ndex_user_mail_password000
ndex_user_show_group000
ndex_user_show_permission000
ndex_verify_user000
ndexr-package000
print.NDExConnection0.0070.0020.118