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CHECK report for ndexr on tokay2

This page was generated on 2018-10-17 08:44:02 -0400 (Wed, 17 Oct 2018).

Package 983/1561HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ndexr 1.2.0
Florian Auer
Snapshot Date: 2018-10-15 16:45:08 -0400 (Mon, 15 Oct 2018)
URL: https://git.bioconductor.org/packages/ndexr
Branch: RELEASE_3_7
Last Commit: 2ef6588
Last Changed Date: 2018-04-30 10:35:47 -0400 (Mon, 30 Apr 2018)
malbec2 Linux (Ubuntu 16.04.1 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
merida2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: ndexr
Version: 1.2.0
Command: C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:ndexr.install-out.txt --library=C:\Users\biocbuild\bbs-3.7-bioc\R\library --no-vignettes --timings ndexr_1.2.0.tar.gz
StartedAt: 2018-10-17 03:37:31 -0400 (Wed, 17 Oct 2018)
EndedAt: 2018-10-17 03:40:02 -0400 (Wed, 17 Oct 2018)
EllapsedTime: 151.8 seconds
RetCode: 0
Status:  WARNINGS  
CheckDir: ndexr.Rcheck
Warnings: 1

Command output

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:ndexr.install-out.txt --library=C:\Users\biocbuild\bbs-3.7-bioc\R\library --no-vignettes --timings ndexr_1.2.0.tar.gz
###
##############################################################################
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* using log directory 'C:/Users/biocbuild/bbs-3.7-bioc/meat/ndexr.Rcheck'
* using R version 3.5.1 Patched (2018-07-24 r75005)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'ndexr/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'ndexr' version '1.2.0'
* 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 whether package 'ndexr' can be installed ... WARNING
Found the following significant warnings:
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpqGma5E/R.INSTALL15507db567fc/ndexr/man/ngraph_toRCX.Rd:153: file link 'igraph' in package 'igraph' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpqGma5E/R.INSTALL15507db567fc/ndexr/man/rcx_toNGraph.Rd:27: file link 'igraph' in package 'igraph' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpqGma5E/R.INSTALL15507db567fc/ndexr/man/rcx_toNGraph.Rd:163: file link 'igraph' in package 'igraph' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpqGma5E/R.INSTALL15507db567fc/ndexr/man/rcx_toRCXgraph.Rd:31: file link 'igraph' in package 'igraph' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpqGma5E/R.INSTALL15507db567fc/ndexr/man/rcx_toRCXgraph.Rd:148: file link 'igraph' in package 'igraph' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpqGma5E/R.INSTALL15507db567fc/ndexr/man/rcxgraph_toRCX.Rd:132: file link 'igraph' in package 'igraph' does not exist and so has been treated as a topic
See 'C:/Users/biocbuild/bbs-3.7-bioc/meat/ndexr.Rcheck/00install.out' for details.
* 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 ...
** running examples for arch 'i386' ... OK
** running examples for arch 'x64' ... OK
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'testthat.R'
 OK
** running tests for arch 'x64' ...
  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: 1 WARNING, 3 NOTEs
See
  'C:/Users/biocbuild/bbs-3.7-bioc/meat/ndexr.Rcheck/00check.log'
for details.



Installation output

ndexr.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.7/bioc/src/contrib/ndexr_1.2.0.tar.gz && rm -rf ndexr.buildbin-libdir && mkdir ndexr.buildbin-libdir && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=ndexr.buildbin-libdir ndexr_1.2.0.tar.gz && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL ndexr_1.2.0.zip && rm ndexr_1.2.0.tar.gz ndexr_1.2.0.zip
###
##############################################################################
##############################################################################


  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100  116k  100  116k    0     0  1765k      0 --:--:-- --:--:-- --:--:-- 1972k

install for i386

* installing *source* package 'ndexr' ...
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'ndexr'
    finding HTML links ... done
    listToRCode                             html  
    ndex_conf_header                        html  
    ndex_config                             html  
    ndex_connect                            html  
    ndex_create_group                       html  
    ndex_create_network                     html  
    ndex_create_user                        html  
    ndex_delete_group                       html  
    ndex_delete_network                     html  
    ndex_delete_user                        html  
    ndex_find_groups                        html  
    ndex_find_networks                      html  
    ndex_find_user_byId                     html  
    ndex_find_user_byName                   html  
    ndex_find_users                         html  
    ndex_get_group                          html  
    ndex_get_network                        html  
    ndex_group_delete_membership            html  
    ndex_group_list_networks                html  
    ndex_group_list_users                   html  
    ndex_group_network_get_permission       html  
    ndex_group_set_membership               html  
    ndex_helper_encodeParams                html  
    ndex_helper_getApi                      html  
    ndex_helper_httpResponseHandler         html  
    ndex_internal_addAspects                html  
    ndex_network_aspect_get_metadata        html  
    ndex_network_delete_permission          html  
    ndex_network_get_aspect                 html  
    ndex_network_get_metadata               html  
    ndex_network_get_permission             html  
    ndex_network_get_provenance             html  
    ndex_network_get_summary                html  
    ndex_network_set_systemProperties       html  
    ndex_network_update_aspect              html  
    ndex_network_update_permission          html  
    ndex_network_update_profile             html  
    ndex_rest_DELETE                        html  
    ndex_rest_GET                           html  
    ndex_rest_POST                          html  
    ndex_rest_PUT                           html  
    ndex_update_group                       html  
    ndex_update_network                     html  
    ndex_update_user                        html  
    ndex_user_change_password               html  
    ndex_user_forgot_password               html  
    ndex_user_get_networksummary            html  
    ndex_user_get_showcase                  html  
    ndex_user_list_groups                   html  
    ndex_user_list_permissions              html  
    ndex_user_mail_password                 html  
    ndex_user_show_group                    html  
    ndex_user_show_permission               html  
    ndex_verify_user                        html  
    ndexr-package                           html  
    ngraph_toRCX                            html  
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpqGma5E/R.INSTALL15507db567fc/ndexr/man/ngraph_toRCX.Rd:153: file link 'igraph' in package 'igraph' does not exist and so has been treated as a topic
    print.NDExConnection                    html  
    print.RCX                               html  
    rcx_asNewNetwork                        html  
    rcx_aspect_toJSON                       html  
    rcx_fromJSON                            html  
    rcx_new                                 html  
    rcx_toJSON                              html  
    rcx_toNGraph                            html  
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpqGma5E/R.INSTALL15507db567fc/ndexr/man/rcx_toNGraph.Rd:27: file link 'igraph' in package 'igraph' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpqGma5E/R.INSTALL15507db567fc/ndexr/man/rcx_toNGraph.Rd:163: file link 'igraph' in package 'igraph' does not exist and so has been treated as a topic
    rcx_toRCXgraph                          html  
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpqGma5E/R.INSTALL15507db567fc/ndexr/man/rcx_toRCXgraph.Rd:31: file link 'igraph' in package 'igraph' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpqGma5E/R.INSTALL15507db567fc/ndexr/man/rcx_toRCXgraph.Rd:148: file link 'igraph' in package 'igraph' does not exist and so has been treated as a topic
    rcx_updateMetaData                      html  
    rcxgraph_toRCX                          html  
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpqGma5E/R.INSTALL15507db567fc/ndexr/man/rcxgraph_toRCX.Rd:132: file link 'igraph' in package 'igraph' does not exist and so has been treated as a topic
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL

install for x64

* installing *source* package 'ndexr' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'ndexr' as ndexr_1.2.0.zip
* DONE (ndexr)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.7-bioc/R/library'
package 'ndexr' successfully unpacked and MD5 sums checked
In R CMD INSTALL

Tests output

ndexr.Rcheck/tests_i386/testthat.Rout


R version 3.5.1 Patched (2018-07-24 r75005) -- "Feather Spray"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-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: 141 SKIPPED: 0 FAILED: 0
> 
> proc.time()
   user  system elapsed 
  25.43    0.62   40.14 

ndexr.Rcheck/tests_x64/testthat.Rout


R version 3.5.1 Patched (2018-07-24 r75005) -- "Feather Spray"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (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: 141 SKIPPED: 0 FAILED: 0
> 
> proc.time()
   user  system elapsed 
  21.98    0.73   35.35 

Example timings

ndexr.Rcheck/examples_i386/ndexr-Ex.timings

nameusersystemelapsed
listToRCode000
ndex_conf_header000
ndex_config000
ndex_connect0.060.000.35
ndex_create_group000
ndex_create_network000
ndex_create_user000
ndex_delete_group000
ndex_delete_network000
ndex_delete_user0.020.000.02
ndex_find_groups0.060.000.25
ndex_find_networks0.080.000.56
ndex_find_user_byId0.000.010.29
ndex_find_user_byName0.000.000.21
ndex_find_users0.010.000.21
ndex_get_group0.030.000.31
ndex_get_network0.500.000.89
ndex_group_delete_membership000
ndex_group_list_networks0.050.000.42
ndex_group_list_users0.010.000.20
ndex_group_network_get_permission0.040.000.32
ndex_group_set_membership000
ndex_helper_encodeParams000
ndex_helper_getApi0.030.000.11
ndex_helper_httpResponseHandler0.000.020.11
ndex_internal_addAspects000
ndex_network_aspect_get_metadata0.100.000.48
ndex_network_delete_permission000
ndex_network_get_aspect0.120.010.65
ndex_network_get_metadata0.080.000.37
ndex_network_get_permission0.000.020.02
ndex_network_get_provenance0.090.000.39
ndex_network_get_summary0.080.000.37
ndex_network_set_systemProperties000
ndex_network_update_aspect000
ndex_network_update_permission0.020.000.02
ndex_network_update_profile000
ndex_rest_DELETE0.000.000.09
ndex_rest_GET0.010.000.11
ndex_rest_POST0.000.000.09
ndex_rest_PUT0.020.000.11
ndex_update_group000
ndex_update_network000
ndex_update_user000
ndex_user_change_password000
ndex_user_forgot_password000
ndex_user_get_networksummary000
ndex_user_get_showcase0.040.000.31
ndex_user_list_groups0.010.000.02
ndex_user_list_permissions000
ndex_user_mail_password000
ndex_user_show_group000
ndex_user_show_permission000
ndex_verify_user000
ndexr-package000
ngraph_toRCX000
print.NDExConnection0.010.010.22
print.RCX000
rcx_asNewNetwork0.020.000.02
rcx_aspect_toJSON000
rcx_fromJSON0.080.000.08
rcx_new0.010.000.01
rcx_toJSON000
rcx_toNGraph000
rcx_toRCXgraph0.010.000.01
rcx_updateMetaData0.020.000.02
rcxgraph_toRCX000

ndexr.Rcheck/examples_x64/ndexr-Ex.timings

nameusersystemelapsed
listToRCode000
ndex_conf_header000
ndex_config000
ndex_connect0.050.010.35
ndex_create_group000
ndex_create_network000
ndex_create_user000
ndex_delete_group0.010.000.01
ndex_delete_network000
ndex_delete_user000
ndex_find_groups0.050.020.25
ndex_find_networks0.080.010.58
ndex_find_user_byId0.010.020.31
ndex_find_user_byName0.020.000.21
ndex_find_users0.020.000.21
ndex_get_group0.050.000.32
ndex_get_network0.450.010.88
ndex_group_delete_membership000
ndex_group_list_networks0.030.000.44
ndex_group_list_users0.020.000.20
ndex_group_network_get_permission0.010.020.33
ndex_group_set_membership000
ndex_helper_encodeParams000
ndex_helper_getApi0.00.00.1
ndex_helper_httpResponseHandler0.000.020.11
ndex_internal_addAspects000
ndex_network_aspect_get_metadata0.070.020.49
ndex_network_delete_permission000
ndex_network_get_aspect0.160.000.65
ndex_network_get_metadata0.060.000.39
ndex_network_get_permission000
ndex_network_get_provenance0.080.010.39
ndex_network_get_summary0.080.000.37
ndex_network_set_systemProperties000
ndex_network_update_aspect000
ndex_network_update_permission000
ndex_network_update_profile000
ndex_rest_DELETE0.010.000.11
ndex_rest_GET0.000.010.11
ndex_rest_POST0.000.000.09
ndex_rest_PUT0.020.000.11
ndex_update_group000
ndex_update_network000
ndex_update_user000
ndex_user_change_password000
ndex_user_forgot_password000
ndex_user_get_networksummary000
ndex_user_get_showcase0.030.000.31
ndex_user_list_groups000
ndex_user_list_permissions000
ndex_user_mail_password000
ndex_user_show_group000
ndex_user_show_permission000
ndex_verify_user000
ndexr-package0.010.000.01
ngraph_toRCX000
print.NDExConnection0.040.000.22
print.RCX000
rcx_asNewNetwork000
rcx_aspect_toJSON000
rcx_fromJSON0.100.000.09
rcx_new0.010.000.02
rcx_toJSON000
rcx_toNGraph000
rcx_toRCXgraph0.020.000.01
rcx_updateMetaData000
rcxgraph_toRCX0.010.000.02