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CHECK report for ndexr on tokay2

This page was generated on 2019-10-16 12:38:34 -0400 (Wed, 16 Oct 2019).

Package 1090/1741HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ndexr 1.6.1
Florian Auer
Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019)
URL: https://git.bioconductor.org/packages/ndexr
Branch: RELEASE_3_9
Last Commit: bba19ab
Last Changed Date: 2019-10-14 12:21:11 -0400 (Mon, 14 Oct 2019)
malbec2 Linux (Ubuntu 18.04.2 LTS) / x86_64  OK  OK  ERROR 
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK [ ERROR ] OK 
celaya2 OS X 10.11.6 El Capitan / x86_64  OK  OK  ERROR  OK 

Summary

Package: ndexr
Version: 1.6.1
Command: C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:ndexr.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings ndexr_1.6.1.tar.gz
StartedAt: 2019-10-16 05:33:25 -0400 (Wed, 16 Oct 2019)
EndedAt: 2019-10-16 05:36:01 -0400 (Wed, 16 Oct 2019)
EllapsedTime: 156.6 seconds
RetCode: 1
Status:  ERROR  
CheckDir: ndexr.Rcheck
Warnings: NA

Command output

##############################################################################
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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:ndexr.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings ndexr_1.6.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.9-bioc/meat/ndexr.Rcheck'
* using R version 3.6.1 (2019-07-05)
* 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 '1.6.1'
* 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 whether package 'ndexr' can be installed ... WARNING
Found the following significant warnings:
  Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpEnWLXg/R.INSTALL1f6c2893b07/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-3.9-bioc/tmpdir/RtmpEnWLXg/R.INSTALL1f6c2893b07/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-3.9-bioc/tmpdir/RtmpEnWLXg/R.INSTALL1f6c2893b07/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-3.9-bioc/tmpdir/RtmpEnWLXg/R.INSTALL1f6c2893b07/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-3.9-bioc/tmpdir/RtmpEnWLXg/R.INSTALL1f6c2893b07/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-3.9-bioc/tmpdir/RtmpEnWLXg/R.INSTALL1f6c2893b07/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-3.9-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'
 ERROR
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
  
  Checking column names of found network list (start=1, size=5) using api Version_2.0
  
  -- 3. Failure: Get list of networks from a server (ndex_find_networks) (@test_02
  
  Checking column names of found network list (start=1, size=5) using api Version_1.3
  
  == testthat results  ===========================================================
  [ OK: 137 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 3 ]
  1. Failure: Get list of networks from a server (ndex_find_networks) (@test_02_finding_networks.r#90) 
  2. Failure: Get list of networks from a server (ndex_find_networks) (@test_02_finding_networks.r#90) 
  3. Failure: Get list of networks from a server (ndex_find_networks) (@test_02_finding_networks.r#90) 
  
  Error: testthat unit tests failed
  Execution halted
** running tests for arch 'x64' ...
  Running 'testthat.R'
 ERROR
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
  
  Checking column names of found network list (start=1, size=5) using api Version_2.0
  
  -- 3. Failure: Get list of networks from a server (ndex_find_networks) (@test_02
  
  Checking column names of found network list (start=1, size=5) using api Version_1.3
  
  == testthat results  ===========================================================
  [ OK: 137 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 3 ]
  1. Failure: Get list of networks from a server (ndex_find_networks) (@test_02_finding_networks.r#90) 
  2. Failure: Get list of networks from a server (ndex_find_networks) (@test_02_finding_networks.r#90) 
  3. Failure: Get list of networks from a server (ndex_find_networks) (@test_02_finding_networks.r#90) 
  
  Error: testthat unit tests failed
  Execution halted
* 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: 2 ERRORs, 1 WARNING, 3 NOTEs
See
  'C:/Users/biocbuild/bbs-3.9-bioc/meat/ndexr.Rcheck/00check.log'
for details.

Installation output

ndexr.Rcheck/00install.out

##############################################################################
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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.9/bioc/src/contrib/ndexr_1.6.1.tar.gz && rm -rf ndexr.buildbin-libdir && mkdir ndexr.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=ndexr.buildbin-libdir ndexr_1.6.1.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL ndexr_1.6.1.zip && rm ndexr_1.6.1.tar.gz ndexr_1.6.1.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  374k  100  374k    0     0  5305k      0 --:--:-- --:--:-- --:--:-- 5943k

install for i386

* installing *source* package 'ndexr' ...
** using staged installation
** 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-3.9-bioc/tmpdir/RtmpEnWLXg/R.INSTALL1f6c2893b07/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-3.9-bioc/tmpdir/RtmpEnWLXg/R.INSTALL1f6c2893b07/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-3.9-bioc/tmpdir/RtmpEnWLXg/R.INSTALL1f6c2893b07/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-3.9-bioc/tmpdir/RtmpEnWLXg/R.INSTALL1f6c2893b07/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-3.9-bioc/tmpdir/RtmpEnWLXg/R.INSTALL1f6c2893b07/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-3.9-bioc/tmpdir/RtmpEnWLXg/R.INSTALL1f6c2893b07/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 from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path

install for x64

* installing *source* package 'ndexr' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'ndexr' as ndexr_1.6.1.zip
* DONE (ndexr)
* installing to library 'C:/Users/biocbuild/bbs-3.9-bioc/R/library'
package 'ndexr' successfully unpacked and MD5 sums checked

Tests output

ndexr.Rcheck/tests_i386/testthat.Rout.fail


R version 3.6.1 (2019-07-05) -- "Action of the Toes"
Copyright (C) 2019 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")
-- 1. Failure: Get list of networks from a server (ndex_find_networks) (@test_02

Checking column names of found network list (start=1, size=5) using api Version_2.1

-- 2. Failure: Get list of networks from a server (ndex_find_networks) (@test_02

Checking column names of found network list (start=1, size=5) using api Version_2.0

-- 3. Failure: Get list of networks from a server (ndex_find_networks) (@test_02

Checking column names of found network list (start=1, size=5) using api Version_1.3

== testthat results  ===========================================================
[ OK: 137 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 3 ]
1. Failure: Get list of networks from a server (ndex_find_networks) (@test_02_finding_networks.r#90) 
2. Failure: Get list of networks from a server (ndex_find_networks) (@test_02_finding_networks.r#90) 
3. Failure: Get list of networks from a server (ndex_find_networks) (@test_02_finding_networks.r#90) 

Error: testthat unit tests failed
Execution halted

ndexr.Rcheck/tests_x64/testthat.Rout.fail


R version 3.6.1 (2019-07-05) -- "Action of the Toes"
Copyright (C) 2019 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")
-- 1. Failure: Get list of networks from a server (ndex_find_networks) (@test_02

Checking column names of found network list (start=1, size=5) using api Version_2.1

-- 2. Failure: Get list of networks from a server (ndex_find_networks) (@test_02

Checking column names of found network list (start=1, size=5) using api Version_2.0

-- 3. Failure: Get list of networks from a server (ndex_find_networks) (@test_02

Checking column names of found network list (start=1, size=5) using api Version_1.3

== testthat results  ===========================================================
[ OK: 137 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 3 ]
1. Failure: Get list of networks from a server (ndex_find_networks) (@test_02_finding_networks.r#90) 
2. Failure: Get list of networks from a server (ndex_find_networks) (@test_02_finding_networks.r#90) 
3. Failure: Get list of networks from a server (ndex_find_networks) (@test_02_finding_networks.r#90) 

Error: testthat unit tests failed
Execution halted

Example timings

ndexr.Rcheck/examples_i386/ndexr-Ex.timings

nameusersystemelapsed
listToRCode000
ndex_conf_header000
ndex_config0.020.000.01
ndex_connect0.070.000.33
ndex_create_group000
ndex_create_network000
ndex_create_user000
ndex_delete_group000
ndex_delete_network000
ndex_delete_user000
ndex_find_groups0.080.000.25
ndex_find_networks0.190.000.55
ndex_find_user_byId0.030.010.28
ndex_find_user_byName0.020.000.17
ndex_find_users0.030.000.19
ndex_get_group0.060.000.29
ndex_get_network0.590.000.94
ndex_group_delete_membership000
ndex_group_list_networks0.040.000.39
ndex_group_list_users0.000.000.19
ndex_group_network_get_permission0.040.000.30
ndex_group_set_membership000
ndex_helper_encodeParams000
ndex_helper_getApi0.020.000.09
ndex_helper_httpResponseHandler0.010.000.09
ndex_internal_addAspects000
ndex_network_aspect_get_metadata0.190.000.57
ndex_network_delete_permission000
ndex_network_get_aspect0.130.000.45
ndex_network_get_metadata0.260.000.55
ndex_network_get_permission000
ndex_network_get_provenance0.220.000.51
ndex_network_get_summary0.230.000.53
ndex_network_set_systemProperties000
ndex_network_update_aspect000
ndex_network_update_permission000
ndex_network_update_profile000
ndex_rest_DELETE0.00.00.1
ndex_rest_GET0.020.000.09
ndex_rest_POST0.000.000.08
ndex_rest_PUT0.020.000.09
ndex_update_group000
ndex_update_network000
ndex_update_user000
ndex_user_change_password000
ndex_user_forgot_password000
ndex_user_get_networksummary000
ndex_user_get_showcase0.000.000.28
ndex_user_list_groups000
ndex_user_list_permissions000
ndex_user_mail_password000
ndex_user_show_group000
ndex_user_show_permission000
ndex_verify_user000
ndexr-package000
ngraph_toRCX000
print.NDExConnection0.020.000.19
print.RCX000
rcx_asNewNetwork000
rcx_aspect_toJSON0.010.000.01
rcx_fromJSON0.10.00.1
rcx_new0.010.000.01
rcx_toJSON000
rcx_toNGraph0.020.000.02
rcx_toRCXgraph0.010.000.01
rcx_updateMetaData000
rcxgraph_toRCX000

ndexr.Rcheck/examples_x64/ndexr-Ex.timings

nameusersystemelapsed
listToRCode000
ndex_conf_header000
ndex_config000
ndex_connect0.060.030.33
ndex_create_group000
ndex_create_network000
ndex_create_user000
ndex_delete_group000
ndex_delete_network000
ndex_delete_user000
ndex_find_groups0.030.020.23
ndex_find_networks0.160.010.54
ndex_find_user_byId0.010.000.28
ndex_find_user_byName0.050.000.21
ndex_find_users0.010.000.19
ndex_get_group0.050.000.29
ndex_get_network0.600.000.87
ndex_group_delete_membership000
ndex_group_list_networks0.030.000.39
ndex_group_list_users0.000.000.19
ndex_group_network_get_permission0.040.000.30
ndex_group_set_membership000
ndex_helper_encodeParams0.020.000.01
ndex_helper_getApi0.000.000.08
ndex_helper_httpResponseHandler0.020.000.09
ndex_internal_addAspects000
ndex_network_aspect_get_metadata0.230.030.55
ndex_network_delete_permission000
ndex_network_get_aspect0.180.000.54
ndex_network_get_metadata0.150.000.47
ndex_network_get_permission0.000.010.02
ndex_network_get_provenance0.190.000.51
ndex_network_get_summary0.160.020.54
ndex_network_set_systemProperties000
ndex_network_update_aspect000
ndex_network_update_permission000
ndex_network_update_profile000
ndex_rest_DELETE0.00.00.1
ndex_rest_GET0.020.000.10
ndex_rest_POST0.000.000.09
ndex_rest_PUT0.010.000.11
ndex_update_group000
ndex_update_network000
ndex_update_user000
ndex_user_change_password000
ndex_user_forgot_password000
ndex_user_get_networksummary000
ndex_user_get_showcase0.040.000.33
ndex_user_list_groups000
ndex_user_list_permissions000
ndex_user_mail_password000
ndex_user_show_group000
ndex_user_show_permission000
ndex_verify_user000
ndexr-package000
ngraph_toRCX000
print.NDExConnection0.020.000.19
print.RCX0.010.000.02
rcx_asNewNetwork000
rcx_aspect_toJSON000
rcx_fromJSON0.080.000.07
rcx_new0.020.000.02
rcx_toJSON0.010.000.02
rcx_toNGraph000
rcx_toRCXgraph0.020.000.01
rcx_updateMetaData000
rcxgraph_toRCX0.010.000.02