Klara Kaleb
| Snapshot Date: 2018-04-25 16:47:34 -0400 (Wed, 25 Apr 2018) |
| URL: https://git.bioconductor.org/packages/roma |
| Branch: master |
| Last Commit: a8efa46 |
| Last Changed Date: 2018-04-19 14:38:00 -0400 (Thu, 19 Apr 2018) |
| Back to Multiple platform build/check report for BioC 3.7 |
|
This page was generated on 2018-04-26 10:53:53 -0400 (Thu, 26 Apr 2018).
| Package 1266/1557 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| roma 0.99.11 Klara Kaleb
| malbec2 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | [ ERROR ] | OK |
| Package: roma |
| Version: 0.99.11 |
| Command: C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:roma.install-out.txt --library=C:\Users\biocbuild\bbs-3.7-bioc\R\library --no-vignettes --timings roma_0.99.11.tar.gz |
| StartedAt: 2018-04-26 05:22:59 -0400 (Thu, 26 Apr 2018) |
| EndedAt: 2018-04-26 05:26:08 -0400 (Thu, 26 Apr 2018) |
| EllapsedTime: 188.8 seconds |
| RetCode: 1 |
| Status: ERROR |
| CheckDir: roma.Rcheck |
| Warnings: NA |
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###
### Running command:
###
### C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:roma.install-out.txt --library=C:\Users\biocbuild\bbs-3.7-bioc\R\library --no-vignettes --timings roma_0.99.11.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.7-bioc/meat/roma.Rcheck'
* using R version 3.5.0 RC (2018-04-16 r74611)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'roma/DESCRIPTION' ... OK
* this is package 'roma' version '0.99.11'
* 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 'roma' 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 ... NOTE
Namespace in Imports field not imported from: 'ape'
All declared Imports should be used.
Missing or unexported object: 'topGO::annFUN.GO2gene'
* 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 ... WARNING
Undocumented code objects:
'group' 'hog' 'orthologs' 'pairs' 'protein' 'seq_protein'
'sequence_annotation' 'sequence_map' 'taxonomy' 'xref'
Undocumented data sets:
'group' 'hog' 'orthologs' 'pairs' 'protein' 'seq_protein'
'sequence_annotation' 'sequence_map' 'taxonomy' 'xref'
All user-level objects in a package should have documentation entries.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of 'data' directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... ERROR
Running examples in 'roma-Ex.R' failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: childrenMembers
> ### Title: Get Members of Children HOGs Function
> ### Aliases: childrenMembers
>
> ### ** Examples
>
> childrenMembers(getHOG(id = "YEAST590"))
THE OMA REST API request failed: https://omabrowser.org/api/hog/YEAST590/
Here's the original error message:
Error in httr::http_status(response) : object 'response' not found
Calls: childrenMembers ... tryCatchOne -> <Anonymous> -> <Anonymous> -> status_code
Execution halted
** running examples for arch 'x64' ... ERROR
Running examples in 'roma-Ex.R' failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: childrenMembers
> ### Title: Get Members of Children HOGs Function
> ### Aliases: childrenMembers
>
> ### ** Examples
>
> childrenMembers(getHOG(id = "YEAST590"))
THE OMA REST API request failed: https://omabrowser.org/api/hog/YEAST590/
Here's the original error message:
Error in httr::http_status(response) : object 'response' not found
Calls: childrenMembers ... tryCatchOne -> <Anonymous> -> <Anonymous> -> status_code
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:
response = httr::GET(url)
content_list = httr::content(response, as = "parsed")
column_names = names(content_list)
if (is.null(column_names)) {
if (length(content_list) == 1) {
column_names = names(content_list[[1]])
content_list = content_list[[1]]
return(objectFactory(column_names, content_list))
}
else if (length(content_list) != 1 && length(content_list) != 0) {
return(formatData(content_list))
}
else if (length(content_list) == 0) {
r
Execution halted
** running tests for arch 'x64' ...
Running 'testthat.R'
ERROR
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
response = httr::GET(url)
content_list = httr::content(response, as = "parsed")
column_names = names(content_list)
if (is.null(column_names)) {
if (length(content_list) == 1) {
column_names = names(content_list[[1]])
content_list = content_list[[1]]
return(objectFactory(column_names, content_list))
}
else if (length(content_list) != 1 && length(content_list) != 0) {
return(formatData(content_list))
}
else if (length(content_list) == 0) {
r
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 WARNING, 1 NOTE
See
'C:/Users/biocbuild/bbs-3.7-bioc/meat/roma.Rcheck/00check.log'
for details.
roma.Rcheck/00install.out
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###
### Running command:
###
### C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.7/bioc/src/contrib/roma_0.99.11.tar.gz && rm -rf roma.buildbin-libdir && mkdir roma.buildbin-libdir && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=roma.buildbin-libdir roma_0.99.11.tar.gz && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL roma_0.99.11.zip && rm roma_0.99.11.tar.gz roma_0.99.11.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 104k 100 104k 0 0 1727k 0 --:--:-- --:--:-- --:--:-- 1940k
install for i386
* installing *source* package 'roma' ...
** R
** data
*** moving datasets to lazyload DB
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'roma'
finding HTML links ... done
childrenMembers html
formatTopGO html
getAnnotation html
getAttribute html
getData html
getGRanges html
getGenomeAlignment html
getHOG html
getObjectAttributes html
getOntologies html
getSequences html
getTaxonomy html
getTopGO html
getXref html
mapSequence html
resolveURL html
roma-package html
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL
install for x64
* installing *source* package 'roma' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'roma' as roma_0.99.11.zip
* DONE (roma)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.7-bioc/R/library'
package 'roma' successfully unpacked and MD5 sums checked
In R CMD INSTALL
|
roma.Rcheck/tests_i386/testthat.Rout.fail
R version 3.5.0 RC (2018-04-16 r74611) -- "Joy in Playing"
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(roma)
Loading required package: httr
Loading required package: plyr
>
>
> test_that("Testing the correct format returned", {
+ expect_equal(class(getData("group","YEAST58")$members), "data.frame")
+ expect_equal(class(getXref(pattern="MAL")), "data.frame")
+ expect_equal(class(getData("genome","YEAST")), "list")
+ expect_equal(class(getGenomeAlignment("ASHGO","YEAST")), "data.frame")
+
+ })
Error: Test failed: 'Testing the correct format returned'
* object 'response' not found
1: expect_equal(class(getData("group", "YEAST58")$members), "data.frame")
2: quasi_label(enquo(object), label)
3: eval_bare(get_expr(quo), get_env(quo))
4: getData("group", "YEAST58")
5: requestFactory(url)
6: tryCatch({
if (pingr::is_online()) {
response = httr::GET(url)
content_list = httr::content(response, as = "parsed")
column_names = names(content_list)
if (is.null(column_names)) {
if (length(content_list) == 1) {
column_names = names(content_list[[1]])
content_list = content_list[[1]]
return(objectFactory(column_names, content_list))
}
else if (length(content_list) != 1 && length(content_list) != 0) {
return(formatData(content_list))
}
else if (length(content_list) == 0) {
r
Execution halted
|
roma.Rcheck/tests_x64/testthat.Rout.fail
R version 3.5.0 RC (2018-04-16 r74611) -- "Joy in Playing"
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(roma)
Loading required package: httr
Loading required package: plyr
>
>
> test_that("Testing the correct format returned", {
+ expect_equal(class(getData("group","YEAST58")$members), "data.frame")
+ expect_equal(class(getXref(pattern="MAL")), "data.frame")
+ expect_equal(class(getData("genome","YEAST")), "list")
+ expect_equal(class(getGenomeAlignment("ASHGO","YEAST")), "data.frame")
+
+ })
Error: Test failed: 'Testing the correct format returned'
* object 'response' not found
1: expect_equal(class(getData("group", "YEAST58")$members), "data.frame")
2: quasi_label(enquo(object), label)
3: eval_bare(get_expr(quo), get_env(quo))
4: getData("group", "YEAST58")
5: requestFactory(url)
6: tryCatch({
if (pingr::is_online()) {
response = httr::GET(url)
content_list = httr::content(response, as = "parsed")
column_names = names(content_list)
if (is.null(column_names)) {
if (length(content_list) == 1) {
column_names = names(content_list[[1]])
content_list = content_list[[1]]
return(objectFactory(column_names, content_list))
}
else if (length(content_list) != 1 && length(content_list) != 0) {
return(formatData(content_list))
}
else if (length(content_list) == 0) {
r
Execution halted
|
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roma.Rcheck/examples_i386/roma-Ex.timings
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roma.Rcheck/examples_x64/roma-Ex.timings
|