| Back to the "Multiple platform build/check report" | A B C D E F G H I J K L M N O P Q [R] S T U V W X Y Z |
This page was generated on 2015-08-20 13:20:51 -0700 (Thu, 20 Aug 2015).
| Package 878/1069 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | |||||
| rols 1.11.6 Laurent Gatto
| zin1 | Linux (Ubuntu 14.04.2 LTS) / x86_64 | OK | OK | ERROR | ||||||
| moscato1 | Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 | OK | OK | [ ERROR ] | OK | ||||||
| perceval | Mac OS X Snow Leopard (10.6.8) / x86_64 | OK | OK | ERROR | OK | ||||||
| oaxaca | Mac OS X Mavericks (10.9.5) / x86_64 | OK | OK | ERROR | OK |
| Package: rols |
| Version: 1.11.6 |
| Command: rm -rf rols.buildbin-libdir rols.Rcheck && mkdir rols.buildbin-libdir rols.Rcheck && D:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=rols.buildbin-libdir rols_1.11.6.tar.gz >rols.Rcheck\00install.out 2>&1 && cp rols.Rcheck\00install.out rols-install.out && D:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD check --library=rols.buildbin-libdir --install="check:rols-install.out" --force-multiarch --no-vignettes --timings rols_1.11.6.tar.gz |
| StartedAt: 2015-08-20 09:50:19 -0700 (Thu, 20 Aug 2015) |
| EndedAt: 2015-08-20 09:55:10 -0700 (Thu, 20 Aug 2015) |
| EllapsedTime: 291.0 seconds |
| RetCode: 1 |
| Status: ERROR |
| CheckDir: rols.Rcheck |
| Warnings: NA |
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###
### Running command:
###
### rm -rf rols.buildbin-libdir rols.Rcheck && mkdir rols.buildbin-libdir rols.Rcheck && D:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=rols.buildbin-libdir rols_1.11.6.tar.gz >rols.Rcheck\00install.out 2>&1 && cp rols.Rcheck\00install.out rols-install.out && D:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD check --library=rols.buildbin-libdir --install="check:rols-install.out" --force-multiarch --no-vignettes --timings rols_1.11.6.tar.gz
###
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* using log directory 'D:/biocbld/bbs-3.2-bioc/meat/rols.Rcheck'
* using R version 3.2.2 (2015-08-14)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'rols/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'rols' version '1.11.6'
* 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 'rols' 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 ... NOTE
Found the following possibly unsafe calls:
File 'rols/R/queries.R':
unlockBinding("ontologies", .rolsEnv)
* 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' ... [36s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
allIds 5.26 0.00 7.15
CVParam-class 2.75 0.02 18.33
** running examples for arch 'x64' ... [37s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
allIds 6.33 0.00 8.31
CVParam-class 3.70 0.01 18.80
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
Running 'testthat.R' [82s]
[83s] OK
** running tests for arch 'x64' ...
Running 'testthat.R' [62s]
Warning message:
running command '"D:/biocbld/BBS-3˜1.2-B/R/bin/x64/R" CMD BATCH --vanilla "testthat.R" "testthat.Rout"' had status 1
ERROR
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
ns = character(0), nsuri = "http://www.ebi.ac.uk/ontology-lookup/OntologyQuery",
default = NULL, Rname = character(0), documentation = character(0))), .convert = .convert,
.header = c(Accept = "text/xml", Accept = "multipart/*", `Content-Type` = "text/xml; charset=utf-8",
SOAPAction = "\"getOntologyLoadDate\""), .opts = .opts, .literal = TRUE,
nameSpaces = nameSpaces, .elementFormQualified = TRUE, .returnNodeName = "getOntologyLoadDateResponse",
.soapHeader = .soapHeader)
testthat results ================================================================
OK: 59 SKIPPED: 0 FAILED: 1
1. Error: ontologyLoadDate/getOntologyLoadDate
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: 1 ERROR, 1 NOTE
See
'D:/biocbld/bbs-3.2-bioc/meat/rols.Rcheck/00check.log'
for details.
rols.Rcheck/tests_x64/testthat.Rout.fail:
R version 3.2.2 (2015-08-14) -- "Fire Safety"
Copyright (C) 2015 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.
> # setting R_TESTS to empty string because of
> # https://github.com/hadley/testthat/issues/144
> # revert this when that issue in R is fixed.
> Sys.setenv("R_TESTS" = "")
> library(testthat)
> library(rols)
This is 'rols' version 1.11.6
>
> test_check("rols")
[, , Hello, World]
Object of class "Map" with 5266 items:
Keys: MS:1001800, MS:1001801 , ...
Values: LECO instrument model, Pegasus HRT , ...
Empty object of class "Map"
Object of class "Map" with 2 items:
Keys: MS:1001800, MS:1001801 .
Values: LECO instrument model, Pegasus HRT .
Object of class "Map" with 1 items:
Key: MS:1001800.
Value: LECO instrument model.
exact_synonym_1: trans Golgi network
exact_synonym_2: TGN
related_synonym_1: late Golgi
definition: The network of interconnected tubular and cisternal
structures located within the Golgi apparatus on the side distal to
the endoplasmic reticulum, from which secretory vesicles emerge. The
trans-Golgi network is important in the later stages of protein
secretion where it is thought to play a key role in the sorting and
targeting of secreted proteins to the correct destination.
comment: There are different opinions about whether the TGN should be
considered part of the Golgi apparatus or not. We follow Alberts et
al, 1994 (ISBN:0815316194), who consider it to be a part.
related_synonym_3: Golgi trans-face
broad_synonym: trans face
related_synonym_2: maturing face
related_synonym_4: Golgi trans face
1. Error: ontologyLoadDate/getOntologyLoadDate ---------------------------------
java.lang.NullPointerException ves-hx-7d.ebi.ac.uk
1: withCallingHandlers(eval(code, new_test_environment), error = capture_calls, message = function(c) invokeRestart("muffleMessage"),
warning = function(c) invokeRestart("muffleWarning"))
2: eval(code, new_test_environment)
3: eval(expr, envir, enclos)
4: sapply(onms, ontologyLoadDate) at test_queries.R:45
5: lapply(X = X, FUN = FUN, ...)
6: FUN(X[[i]], ...)
7: getOntologyLoadDate(ontologyName = ontologyName, .convert = TRUE)
8: .SOAP(server, "getOntologyLoadDate", parameters = as(parameters, "ontologyName"),
action = "getOntologyLoadDate", xmlns = "http://www.ebi.ac.uk/ontology-lookup/OntologyQuery",
.types = list(parameters = new("Element", type = new("ClassDefinition", slotTypes = list(ontologyName = new("LocalElement",
count = c(1L, 1L), type = new("PrimitiveSOAPType", fromConverter = function() NULL,
toConverter = .Primitive("as.character"), count = c(1L, 1L), abstract = logical(0),
name = "string", ns = "xsd", nsuri = "http://www.w3.org/2001/XMLSchema",
default = NA_character_, Rname = character(0), documentation = character(0)),
name = "ontologyName", attributes = list(), xmlAttrs = character(0), ns = character(0),
nsuri = "http://www.ebi.ac.uk/ontology-lookup/OntologyQuery", default = NA_character_,
Rname = character(0), documentation = character(0))), isAttribute = FALSE,
uris = "http://www.ebi.ac.uk/ontology-lookup/OntologyQuery", fromConverter = function() NULL,
toConverter = function() NULL, count = numeric(0), abstract = logical(0),
name = "ontologyName", ns = character(0), nsuri = "http://www.ebi.ac.uk/ontology-lookup/OntologyQuery",
default = NA_character_, Rname = character(0), documentation = character(0)),
name = "getOntologyLoadDate", attributes = list(), xmlAttrs = character(0),
ns = character(0), nsuri = "http://www.ebi.ac.uk/ontology-lookup/OntologyQuery",
default = NULL, Rname = character(0), documentation = character(0))), .convert = .convert,
.header = c(Accept = "text/xml", Accept = "multipart/*", `Content-Type` = "text/xml; charset=utf-8",
SOAPAction = "\"getOntologyLoadDate\""), .opts = .opts, .literal = TRUE,
nameSpaces = nameSpaces, .elementFormQualified = TRUE, .returnNodeName = "getOntologyLoadDateResponse",
.soapHeader = .soapHeader)
testthat results ================================================================
OK: 59 SKIPPED: 0 FAILED: 1
1. Error: ontologyLoadDate/getOntologyLoadDate
Error: testthat unit tests failed
Execution halted
rols.Rcheck/00install.out:
install for i386 * installing *source* package 'rols' ... ** R ** inst ** preparing package for lazy loading Note: the specification for S3 class "connection" in package 'BiocGenerics' seems equivalent to one from package 'SSOAP': not turning on duplicate class definitions for this class. ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded Note: the specification for S3 class "connection" in package 'BiocGenerics' seems equivalent to one from package 'SSOAP': not turning on duplicate class definitions for this class. install for x64 * installing *source* package 'rols' ... ** testing if installed package can be loaded Note: the specification for S3 class "connection" in package 'BiocGenerics' seems equivalent to one from package 'SSOAP': not turning on duplicate class definitions for this class. * MD5 sums packaged installation of 'rols' as rols_1.11.6.zip * DONE (rols)
rols.Rcheck/examples_i386/rols-Ex.timings:
| name | user | system | elapsed | |
| CVParam-class | 2.75 | 0.02 | 18.33 | |
| allIds | 5.26 | 0.00 | 7.15 | |
| childrenRelations | 0.04 | 0.00 | 0.35 | |
| isIdObsolete | 0.22 | 0.00 | 1.85 | |
| olsQuery | 0.39 | 0.00 | 1.65 | |
| olsVersion | 0.01 | 0.00 | 0.33 | |
| ontologies | 0.03 | 0.00 | 0.03 | |
| ontologyLoadDate | 0.09 | 0.00 | 0.75 | |
| ontologyNames | 0.02 | 0.00 | 0.01 | |
| parents | 0.08 | 0.00 | 0.39 | |
| rootId | 0.17 | 0.00 | 1.13 | |
| term | 0.12 | 0.00 | 1.09 | |
| termMetadata | 0.21 | 0.00 | 0.83 | |
rols.Rcheck/examples_x64/rols-Ex.timings:
| name | user | system | elapsed | |
| CVParam-class | 3.70 | 0.01 | 18.80 | |
| allIds | 6.33 | 0.00 | 8.31 | |
| childrenRelations | 0.06 | 0.00 | 0.38 | |
| isIdObsolete | 0.22 | 0.02 | 1.81 | |
| olsQuery | 0.24 | 0.00 | 1.49 | |
| olsVersion | 0.03 | 0.00 | 0.35 | |
| ontologies | 0.01 | 0.00 | 0.01 | |
| ontologyLoadDate | 0.08 | 0.00 | 0.70 | |
| ontologyNames | 0.02 | 0.00 | 0.02 | |
| parents | 0.07 | 0.00 | 0.39 | |
| rootId | 0.21 | 0.00 | 1.14 | |
| term | 0.09 | 0.00 | 1.04 | |
| termMetadata | 0.14 | 0.00 | 0.80 | |