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CHECK report for ndexr on celaya2

This page was generated on 2020-01-16 13:48:06 -0500 (Thu, 16 Jan 2020).

Package 1136/1818HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ndexr 1.9.0
Florian Auer
Snapshot Date: 2020-01-15 16:46:30 -0500 (Wed, 15 Jan 2020)
URL: https://git.bioconductor.org/packages/ndexr
Branch: master
Last Commit: cd1b580
Last Changed Date: 2019-10-29 13:42:20 -0500 (Tue, 29 Oct 2019)
malbec2 Linux (Ubuntu 18.04.3 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository
celaya2 OS X 10.11.6 El Capitan / x86_64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: ndexr
Version: 1.9.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:ndexr.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings ndexr_1.9.0.tar.gz
StartedAt: 2020-01-16 06:56:10 -0500 (Thu, 16 Jan 2020)
EndedAt: 2020-01-16 06:57:41 -0500 (Thu, 16 Jan 2020)
EllapsedTime: 91.4 seconds
RetCode: 0
Status:  OK 
CheckDir: ndexr.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:ndexr.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings ndexr_1.9.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.11-bioc/meat/ndexr.Rcheck’
* using R Under development (unstable) (2019-12-14 r77572)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘ndexr/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘ndexr’ version ‘1.9.0’
* 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
Deprecated license: BSD
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R 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
Package in Depends field not imported from: ‘igraph’
  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’
rcx_fromRCXgraph: no visible binding for global variable ‘po’
rcx_toRCXgraph: no visible global function definition for ‘V’
rcx_toRCXgraph: no visible global function definition for ‘V<-’
rcx_toRCXgraph: no visible global function definition for ‘E’
rcx_toRCXgraph: no visible global function definition for ‘E<-’
rcxgraph_fromRCX: no visible global function definition for ‘V’
rcxgraph_fromRCX: no visible global function definition for ‘V<-’
rcxgraph_fromRCX: no visible global function definition for ‘E’
rcxgraph_fromRCX: no visible global function definition for ‘E<-’
rcxgraph_toRCX: no visible binding for global variable ‘po’
Undefined global functions or variables:
  E E<- V V<- packageVersion po tail
Consider adding
  importFrom("utils", "packageVersion", "tail")
to your NAMESPACE file.
* checking Rd files ... OK
* 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 installed files from ‘inst/doc’ ... 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 in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 3 NOTEs
See
  ‘/Users/biocbuild/bbs-3.11-bioc/meat/ndexr.Rcheck/00check.log’
for details.



Installation output

ndexr.Rcheck/00install.out

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


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/library’
* installing *source* package ‘ndexr’ ...
** using staged installation
** R
** inst
** 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 Under development (unstable) (2019-12-14 r77572) -- "Unsuffered Consequences"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin15.6.0 (64-bit)

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: igraph

Attaching package: 'igraph'

The following object is masked from 'package:testthat':

    compare

The following objects are masked from 'package:stats':

    decompose, spectrum

The following object is masked from 'package:base':

    union

> 
> test_check("ndexr")
══ testthat results  ═══════════════════════════════════════════════════════════
[ OK: 140 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
 21.385   1.413  32.698 

Example timings

ndexr.Rcheck/ndexr-Ex.timings

nameusersystemelapsed
listToRCode0.0010.0000.001
ndex_conf_header0.0010.0000.000
ndex_config0.0100.0010.010
ndex_connect0.0850.0200.354
ndex_create_group000
ndex_create_network0.0000.0010.001
ndex_create_user000
ndex_delete_group0.0010.0000.000
ndex_delete_network000
ndex_delete_user000
ndex_find_groups0.0650.0060.247
ndex_find_networks0.1320.0070.515
ndex_find_user_byId0.0370.0020.292
ndex_find_user_byName0.0180.0010.196
ndex_find_users0.0240.0010.201
ndex_get_group0.0350.0020.294
ndex_get_network0.4310.0230.770
ndex_group_delete_membership0.0000.0000.001
ndex_group_list_networks0.0470.0020.391
ndex_group_list_users0.0270.0010.200
ndex_group_network_get_permission0.0340.0020.292
ndex_group_set_membership0.0000.0010.000
ndex_helper_encodeParams0.0040.0010.005
ndex_helper_getApi0.0080.0010.092
ndex_helper_httpResponseHandler0.0230.0020.109
ndex_internal_addAspects0.0010.0010.001
ndex_network_aspect_get_metadata0.1210.0060.424
ndex_network_delete_permission0.0010.0010.001
ndex_network_get_aspect0.1950.0080.581
ndex_network_get_metadata0.1310.0170.447
ndex_network_get_permission0.0000.0010.001
ndex_network_get_provenance0.1890.0420.529
ndex_network_get_summary0.1340.0100.443
ndex_network_set_systemProperties0.0010.0000.001
ndex_network_update_aspect0.0000.0000.001
ndex_network_update_permission0.0000.0000.001
ndex_network_update_profile0.0010.0000.001
ndex_rest_DELETE0.0080.0010.091
ndex_rest_GET0.0070.0000.091
ndex_rest_POST0.0080.0000.092
ndex_rest_PUT0.0080.0010.092
ndex_update_group0.0010.0010.001
ndex_update_network0.0000.0010.000
ndex_update_user0.0000.0010.001
ndex_user_change_password0.0000.0010.001
ndex_user_forgot_password0.0010.0000.000
ndex_user_get_networksummary0.0010.0000.001
ndex_user_get_showcase0.0330.0020.287
ndex_user_list_groups0.0010.0010.000
ndex_user_list_permissions0.0000.0010.001
ndex_user_mail_password0.0000.0010.001
ndex_user_show_group0.0010.0010.001
ndex_user_show_permission0.0010.0010.001
ndex_verify_user0.0000.0010.000
ndexr-package0.0000.0010.001
ngraph_toRCX0.0050.0000.006
print.NDExConnection0.0150.0010.184
print.RCX0.0090.0000.009
rcx_asNewNetwork0.0040.0000.005
rcx_aspect_toJSON0.0060.0000.005
rcx_fromJSON0.1250.0000.126
rcx_new0.0190.0000.019
rcx_toJSON0.0070.0010.007
rcx_toNGraph0.0030.0010.005
rcx_toRCXgraph0.0150.0010.017
rcx_updateMetaData0.0070.0000.008
rcxgraph_toRCX0.0050.0000.006