| Back to Multiple platform build/check report for BioC 3.8 |
|
This page was generated on 2019-04-13 11:29:09 -0400 (Sat, 13 Apr 2019).
| Package 1375/1649 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| rWikiPathways 1.2.1 Egon Willighagen
| 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 |
| 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 |
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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.
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
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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
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rWikiPathways.Rcheck/examples_i386/rWikiPathways-Ex.timings
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rWikiPathways.Rcheck/examples_x64/rWikiPathways-Ex.timings
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