Back to Multiple platform build/check report for BioC 3.8
ABCDEFGHIJKLM[N]OPQRSTUVWXYZ

CHECK report for ndexr on malbec1

This page was generated on 2019-04-16 11:52:48 -0400 (Tue, 16 Apr 2019).

Package 1043/1649HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ndexr 1.4.1
Florian Auer
Snapshot Date: 2019-04-15 17:01:12 -0400 (Mon, 15 Apr 2019)
URL: https://git.bioconductor.org/packages/ndexr
Branch: RELEASE_3_8
Last Commit: 23412f7
Last Changed Date: 2019-01-09 10:47:23 -0400 (Wed, 09 Jan 2019)
malbec1 Linux (Ubuntu 16.04.6 LTS) / x86_64  OK  OK [ OK ]UNNEEDED, same version exists in internal repository
merida1 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: ndexr
Version: 1.4.1
Command: /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD check --install=check:ndexr.install-out.txt --library=/home/biocbuild/bbs-3.8-bioc/R/library --no-vignettes --timings ndexr_1.4.1.tar.gz
StartedAt: 2019-04-16 01:44:58 -0400 (Tue, 16 Apr 2019)
EndedAt: 2019-04-16 01:45:50 -0400 (Tue, 16 Apr 2019)
EllapsedTime: 52.1 seconds
RetCode: 0
Status:  OK 
CheckDir: ndexr.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD check --install=check:ndexr.install-out.txt --library=/home/biocbuild/bbs-3.8-bioc/R/library --no-vignettes --timings ndexr_1.4.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.8-bioc/meat/ndexr.Rcheck’
* using R version 3.5.3 (2019-03-11)
* using platform: x86_64-pc-linux-gnu (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 ‘1.4.1’
* 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 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
  ‘/home/biocbuild/bbs-3.8-bioc/meat/ndexr.Rcheck/00check.log’
for details.



Installation output

ndexr.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD INSTALL ndexr
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.8-bioc/R/library’
* installing *source* package ‘ndexr’ ...
** 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
* DONE (ndexr)

Tests output

ndexr.Rcheck/tests/testthat.Rout


R version 3.5.3 (2019-03-11) -- "Great Truth"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (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 FAILED: 0
> 
> proc.time()
   user  system elapsed 
 14.344   0.140  22.774 

Example timings

ndexr.Rcheck/ndexr-Ex.timings

nameusersystemelapsed
listToRCode000
ndex_conf_header000
ndex_config0.0000.0000.002
ndex_connect0.1040.0120.351
ndex_create_group000
ndex_create_network000
ndex_create_user000
ndex_delete_group0.0000.0000.001
ndex_delete_network000
ndex_delete_user000
ndex_find_groups0.0480.0040.220
ndex_find_networks0.0760.0000.429
ndex_find_user_byId0.040.000.28
ndex_find_user_byName0.0200.0000.181
ndex_find_users0.0240.0000.185
ndex_get_group0.0400.0000.282
ndex_get_network0.3360.0000.612
ndex_group_delete_membership000
ndex_group_list_networks0.0600.0000.382
ndex_group_list_users0.0280.0000.196
ndex_group_network_get_permission0.0400.0000.284
ndex_group_set_membership000
ndex_helper_encodeParams0.0040.0000.002
ndex_helper_getApi0.0040.0000.089
ndex_helper_httpResponseHandler0.0160.0000.097
ndex_internal_addAspects000
ndex_network_aspect_get_metadata0.0880.0000.363
ndex_network_delete_permission000
ndex_network_get_aspect0.1920.0040.639
ndex_network_get_metadata0.0880.0040.366
ndex_network_get_permission0.0000.0000.001
ndex_network_get_provenance0.0800.0040.360
ndex_network_get_summary0.0880.0000.368
ndex_network_set_systemProperties000
ndex_network_update_aspect000
ndex_network_update_permission000
ndex_network_update_profile000
ndex_rest_DELETE0.0080.0000.086
ndex_rest_GET0.0080.0000.085
ndex_rest_POST0.0040.0000.084
ndex_rest_PUT0.0080.0000.085
ndex_update_group000
ndex_update_network000
ndex_update_user000
ndex_user_change_password0.0000.0000.001
ndex_user_forgot_password0.0000.0000.001
ndex_user_get_networksummary000
ndex_user_get_showcase0.040.000.28
ndex_user_list_groups0.0000.0000.001
ndex_user_list_permissions0.0000.0000.001
ndex_user_mail_password000
ndex_user_show_group000
ndex_user_show_permission000
ndex_verify_user000
ndexr-package0.0040.0000.000
ngraph_toRCX0.0040.0000.005
print.NDExConnection0.0120.0000.173
print.RCX0.0040.0000.006
rcx_asNewNetwork0.0040.0000.002
rcx_aspect_toJSON0.0040.0000.003
rcx_fromJSON0.0840.0000.085
rcx_new0.0200.0000.017
rcx_toJSON0.0040.0000.006
rcx_toNGraph0.0000.0000.002
rcx_toRCXgraph0.0120.0000.012
rcx_updateMetaData0.0040.0000.005
rcxgraph_toRCX0.0080.0000.007