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CHECK report for rWikiPathways on tokay1

This page was generated on 2019-04-13 11:29:09 -0400 (Sat, 13 Apr 2019).

Package 1375/1649HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
rWikiPathways 1.2.1
Egon Willighagen , Alexander Pico
Snapshot Date: 2019-04-12 17:01:30 -0400 (Fri, 12 Apr 2019)
URL: https://git.bioconductor.org/packages/rWikiPathways
Branch: RELEASE_3_8
Last Commit: 01cdd36
Last Changed Date: 2019-02-06 19:28:57 -0400 (Wed, 06 Feb 2019)
malbec1 Linux (Ubuntu 16.04.6 LTS) / x86_64  OK  OK  ERROR 
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK [ ERROR ] OK 
merida1 OS X 10.11.6 El Capitan / x86_64  OK  OK  ERROR  OK 

Summary

Package: rWikiPathways
Version: 1.2.1
Command: C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:rWikiPathways.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings rWikiPathways_1.2.1.tar.gz
StartedAt: 2019-04-13 05:17:17 -0400 (Sat, 13 Apr 2019)
EndedAt: 2019-04-13 05:20:50 -0400 (Sat, 13 Apr 2019)
EllapsedTime: 212.7 seconds
RetCode: 1
Status:  ERROR  
CheckDir: rWikiPathways.Rcheck
Warnings: NA

Command output

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:rWikiPathways.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings rWikiPathways_1.2.1.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.8-bioc/meat/rWikiPathways.Rcheck'
* using R version 3.5.3 (2019-03-11)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'rWikiPathways/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'rWikiPathways' version '1.2.1'
* checking package namespace information ... OK
* checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
  cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
 OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... NOTE
Found the following hidden files and directories:
  .travis.yml
These were most likely included in error. See section 'Package
structure' in the 'Writing R Extensions' manual.
* checking for portable file names ... OK
* checking whether package 'rWikiPathways' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... OK
* 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* 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 ...
** running examples for arch 'i386' ... ERROR
Running examples in 'rWikiPathways-Ex.R' failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: getColoredPathway
> ### Title: Get Colored Pathway
> ### Aliases: getColoredPathway
> 
> ### ** Examples
> 
> {
+   svg = getColoredPathway(pathway="WP554", graphId="ef1f3")
+   svg = getColoredPathway(pathway="WP554", graphId=c("ef1f3","e68e0"))
+   svg = getColoredPathway(pathway="WP554", graphId=c("ef1f3","e68e0"),
+                           color="00FF00")
+   svg = getColoredPathway(pathway="WP554", graphId=c("ef1f3","e68e0"),
+                           color=c("FF0000", "0000FF"))
+   # writeLines(svg, "pathway.svg")
+ }
Error in caTools::base64decode(res["data"], what = "character") : 
  base64decode: Input argument 'z' is suppose to be a string
Calls: getColoredPathway -> <Anonymous>
Execution halted
** running examples for arch 'x64' ... ERROR
Running examples in 'rWikiPathways-Ex.R' failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: getColoredPathway
> ### Title: Get Colored Pathway
> ### Aliases: getColoredPathway
> 
> ### ** Examples
> 
> {
+   svg = getColoredPathway(pathway="WP554", graphId="ef1f3")
+   svg = getColoredPathway(pathway="WP554", graphId=c("ef1f3","e68e0"))
+   svg = getColoredPathway(pathway="WP554", graphId=c("ef1f3","e68e0"),
+                           color="00FF00")
+   svg = getColoredPathway(pathway="WP554", graphId=c("ef1f3","e68e0"),
+                           color=c("FF0000", "0000FF"))
+   # writeLines(svg, "pathway.svg")
+ }
Error in caTools::base64decode(res["data"], what = "character") : 
  base64decode: Input argument 'z' is suppose to be a string
Calls: getColoredPathway -> <Anonymous>
Execution halted
* 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:
  "Q9UPY3" %in% xrefs isn't true.
  
  -- 5. Failure: get WP2338 (again) (@test-getXrefList.R#11)  --------------------
  "Q9UPY3" %in% xrefs isn't true.
  
  == testthat results  ===========================================================
  OK: 25 SKIPPED: 0 FAILED: 5
  1. Error: colored pathway (@test-getColoredPathway.R#5) 
  2. Error: green colored pathway (@test-getColoredPathway.R#10) 
  3. Error: colored pathway (vector) (@test-getColoredPathway.R#16) 
  4. Failure: get WP2338 Xrefs (@test-getXrefList.R#6) 
  5. Failure: get WP2338 (again) (@test-getXrefList.R#11) 
  
  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:
  "Q9UPY3" %in% xrefs isn't true.
  
  -- 5. Failure: get WP2338 (again) (@test-getXrefList.R#11)  --------------------
  "Q9UPY3" %in% xrefs isn't true.
  
  == testthat results  ===========================================================
  OK: 25 SKIPPED: 0 FAILED: 5
  1. Error: colored pathway (@test-getColoredPathway.R#5) 
  2. Error: green colored pathway (@test-getColoredPathway.R#10) 
  3. Error: colored pathway (vector) (@test-getColoredPathway.R#16) 
  4. Failure: get WP2338 Xrefs (@test-getXrefList.R#6) 
  5. Failure: get WP2338 (again) (@test-getXrefList.R#11) 
  
  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: 4 ERRORs, 1 NOTE
See
  'C:/Users/biocbuild/bbs-3.8-bioc/meat/rWikiPathways.Rcheck/00check.log'
for details.


Installation output

rWikiPathways.Rcheck/00install.out

##############################################################################
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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.8/bioc/src/contrib/rWikiPathways_1.2.1.tar.gz && rm -rf rWikiPathways.buildbin-libdir && mkdir rWikiPathways.buildbin-libdir && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=rWikiPathways.buildbin-libdir rWikiPathways_1.2.1.tar.gz && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL rWikiPathways_1.2.1.zip && rm rWikiPathways_1.2.1.tar.gz rWikiPathways_1.2.1.zip
###
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  % 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 1591k  100 1591k    0     0  30.3M      0 --:--:-- --:--:-- --:--:-- 33.0M

install for i386

* installing *source* package 'rWikiPathways' ...
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'rWikiPathways'
    finding HTML links ... done
    downloadPathwayArchive                  html  
    findPathwayIdsByLiterature              html  
    findPathwayIdsByText                    html  
    findPathwayIdsByXref                    html  
    findPathwayNamesByLiterature            html  
    findPathwayNamesByText                  html  
    findPathwayNamesByXref                  html  
    findPathwayUrlsByLiterature             html  
    findPathwayUrlsByText                   html  
    findPathwayUrlsByXref                   html  
    findPathwaysByLiterature                html  
    findPathwaysByText                      html  
    findPathwaysByXref                      html  
    getColoredPathway                       html  
    getCurationTagNames                     html  
    getCurationTags                         html  
    getEveryCurationTag                     html  
    getOntologyTermIds                      html  
    getOntologyTermNames                    html  
    getOntologyTerms                        html  
    getPathway                              html  
    getPathwayHistory                       html  
    getPathwayIdsByCurationTag              html  
    getPathwayIdsByOntologyTerm             html  
    getPathwayIdsByParentOntologyTerm       html  
    getPathwayInfo                          html  
    getPathwaysByCurationTag                html  
    getPathwaysByOntologyTerm               html  
    getPathwaysByParentOntologyTerm         html  
    getRecentChanges                        html  
    getRecentChangesIds                     html  
    getRecentChangesNames                   html  
    getXrefList                             html  
    listOrganisms                           html  
    listPathwayIds                          html  
    listPathwayNames                        html  
    listPathwayUrls                         html  
    listPathways                            html  
    wikipathwaysAPI                         html  
    wikipathwaysGET                         html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL

install for x64

* installing *source* package 'rWikiPathways' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'rWikiPathways' as rWikiPathways_1.2.1.zip
* DONE (rWikiPathways)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.8-bioc/R/library'
package 'rWikiPathways' successfully unpacked and MD5 sums checked
In R CMD INSTALL

Tests output

rWikiPathways.Rcheck/tests_i386/testthat.Rout.fail


R version 3.5.3 (2019-03-11) -- "Great Truth"
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(rWikiPathways)
> 
> test_check("rWikiPathways")
-- 1. Error: colored pathway (@test-getColoredPathway.R#5)  --------------------
base64decode: Input argument 'z' is suppose to be a string
1: getColoredPathway(pathway = "WP1842", graphId = c("dd68a", "a2c17")) at testthat/test-getColoredPathway.R:5
2: caTools::base64decode(res["data"], what = "character")
3: stop("base64decode: Input argument 'z' is suppose to be a string")

-- 2. Error: green colored pathway (@test-getColoredPathway.R#10)  -------------
base64decode: Input argument 'z' is suppose to be a string
1: getColoredPathway(pathway = "WP1842", graphId = c("dd68a", "a2c17"), color = "00FF00") at testthat/test-getColoredPathway.R:10
2: caTools::base64decode(res["data"], what = "character")
3: stop("base64decode: Input argument 'z' is suppose to be a string")

-- 3. Error: colored pathway (vector) (@test-getColoredPathway.R#16)  ----------
base64decode: Input argument 'z' is suppose to be a string
1: getColoredPathway(pathway = "WP1842", graphId = c("dd68a", "a2c17"), color = c("FF0000", 
       "00FF00")) at testthat/test-getColoredPathway.R:16
2: caTools::base64decode(res["data"], what = "character")
3: stop("base64decode: Input argument 'z' is suppose to be a string")

-- 4. Failure: get WP2338 Xrefs (@test-getXrefList.R#6)  -----------------------
"Q9UPY3" %in% xrefs isn't true.

-- 5. Failure: get WP2338 (again) (@test-getXrefList.R#11)  --------------------
"Q9UPY3" %in% xrefs isn't true.

== testthat results  ===========================================================
OK: 25 SKIPPED: 0 FAILED: 5
1. Error: colored pathway (@test-getColoredPathway.R#5) 
2. Error: green colored pathway (@test-getColoredPathway.R#10) 
3. Error: colored pathway (vector) (@test-getColoredPathway.R#16) 
4. Failure: get WP2338 Xrefs (@test-getXrefList.R#6) 
5. Failure: get WP2338 (again) (@test-getXrefList.R#11) 

Error: testthat unit tests failed
Execution halted

rWikiPathways.Rcheck/tests_x64/testthat.Rout.fail


R version 3.5.3 (2019-03-11) -- "Great Truth"
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(rWikiPathways)
> 
> test_check("rWikiPathways")
-- 1. Error: colored pathway (@test-getColoredPathway.R#5)  --------------------
base64decode: Input argument 'z' is suppose to be a string
1: getColoredPathway(pathway = "WP1842", graphId = c("dd68a", "a2c17")) at testthat/test-getColoredPathway.R:5
2: caTools::base64decode(res["data"], what = "character")
3: stop("base64decode: Input argument 'z' is suppose to be a string")

-- 2. Error: green colored pathway (@test-getColoredPathway.R#10)  -------------
base64decode: Input argument 'z' is suppose to be a string
1: getColoredPathway(pathway = "WP1842", graphId = c("dd68a", "a2c17"), color = "00FF00") at testthat/test-getColoredPathway.R:10
2: caTools::base64decode(res["data"], what = "character")
3: stop("base64decode: Input argument 'z' is suppose to be a string")

-- 3. Error: colored pathway (vector) (@test-getColoredPathway.R#16)  ----------
base64decode: Input argument 'z' is suppose to be a string
1: getColoredPathway(pathway = "WP1842", graphId = c("dd68a", "a2c17"), color = c("FF0000", 
       "00FF00")) at testthat/test-getColoredPathway.R:16
2: caTools::base64decode(res["data"], what = "character")
3: stop("base64decode: Input argument 'z' is suppose to be a string")

-- 4. Failure: get WP2338 Xrefs (@test-getXrefList.R#6)  -----------------------
"Q9UPY3" %in% xrefs isn't true.

-- 5. Failure: get WP2338 (again) (@test-getXrefList.R#11)  --------------------
"Q9UPY3" %in% xrefs isn't true.

== testthat results  ===========================================================
OK: 25 SKIPPED: 0 FAILED: 5
1. Error: colored pathway (@test-getColoredPathway.R#5) 
2. Error: green colored pathway (@test-getColoredPathway.R#10) 
3. Error: colored pathway (vector) (@test-getColoredPathway.R#16) 
4. Failure: get WP2338 Xrefs (@test-getXrefList.R#6) 
5. Failure: get WP2338 (again) (@test-getXrefList.R#11) 

Error: testthat unit tests failed
Execution halted

Example timings

rWikiPathways.Rcheck/examples_i386/rWikiPathways-Ex.timings

nameusersystemelapsed
downloadPathwayArchive000
findPathwayIdsByLiterature0.170.038.98
findPathwayIdsByText0.010.001.12
findPathwayIdsByXref0.030.001.05
findPathwayNamesByLiterature0.110.025.44
findPathwayNamesByText0.020.000.82
findPathwayNamesByXref0.030.000.52
findPathwayUrlsByLiterature0.130.025.41
findPathwayUrlsByText0.010.000.84
findPathwayUrlsByXref0.030.010.55
findPathwaysByLiterature0.210.065.56
findPathwaysByText0.030.000.76
findPathwaysByXref0.090.020.60

rWikiPathways.Rcheck/examples_x64/rWikiPathways-Ex.timings

nameusersystemelapsed
downloadPathwayArchive000
findPathwayIdsByLiterature0.140.015.86
findPathwayIdsByText0.000.000.77
findPathwayIdsByXref0.030.000.53
findPathwayNamesByLiterature0.090.025.44
findPathwayNamesByText0.020.000.76
findPathwayNamesByXref0.030.000.53
findPathwayUrlsByLiterature0.110.015.49
findPathwayUrlsByText0.000.020.75
findPathwayUrlsByXref0.030.000.55
findPathwaysByLiterature0.110.045.36
findPathwaysByText0.010.000.83
findPathwaysByXref0.050.020.59