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This page was generated on 2015-08-20 13:21:14 -0700 (Thu, 20 Aug 2015).
| Package 1044/1069 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | |||||
| UniProt.ws 2.9.2 Bioconductor Package Maintainer
| zin1 | Linux (Ubuntu 14.04.2 LTS) / x86_64 | OK | OK | WARNINGS |  | |||||
| 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 | WARNINGS | OK | | |||||
| oaxaca | Mac OS X Mavericks (10.9.5) / x86_64 | OK | OK | WARNINGS | OK | |
| Package: UniProt.ws |
| Version: 2.9.2 |
| Command: rm -rf UniProt.ws.buildbin-libdir UniProt.ws.Rcheck && mkdir UniProt.ws.buildbin-libdir UniProt.ws.Rcheck && D:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=UniProt.ws.buildbin-libdir UniProt.ws_2.9.2.tar.gz >UniProt.ws.Rcheck\00install.out 2>&1 && cp UniProt.ws.Rcheck\00install.out UniProt.ws-install.out && D:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD check --library=UniProt.ws.buildbin-libdir --install="check:UniProt.ws-install.out" --force-multiarch --no-vignettes --timings UniProt.ws_2.9.2.tar.gz |
| StartedAt: 2015-08-20 11:20:37 -0700 (Thu, 20 Aug 2015) |
| EndedAt: 2015-08-20 11:28:50 -0700 (Thu, 20 Aug 2015) |
| EllapsedTime: 492.7 seconds |
| RetCode: 1 |
| Status: ERROR |
| CheckDir: UniProt.ws.Rcheck |
| Warnings: NA |
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###
### Running command:
###
### rm -rf UniProt.ws.buildbin-libdir UniProt.ws.Rcheck && mkdir UniProt.ws.buildbin-libdir UniProt.ws.Rcheck && D:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=UniProt.ws.buildbin-libdir UniProt.ws_2.9.2.tar.gz >UniProt.ws.Rcheck\00install.out 2>&1 && cp UniProt.ws.Rcheck\00install.out UniProt.ws-install.out && D:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD check --library=UniProt.ws.buildbin-libdir --install="check:UniProt.ws-install.out" --force-multiarch --no-vignettes --timings UniProt.ws_2.9.2.tar.gz
###
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* using log directory 'D:/biocbld/bbs-3.2-bioc/meat/UniProt.ws.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 'UniProt.ws/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'UniProt.ws' version '2.9.2'
* 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 'UniProt.ws' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Package listed in more than one of Depends, Imports, Suggests, Enhances:
'BiocGenerics'
A package should be listed in only one of these fields.
* 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
Packages in Depends field not imported from:
'RCurl' 'RSQLite' 'methods'
These packages need to be imported from (in the NAMESPACE file)
for when this namespace is loaded but not attached.
Unexported objects imported by ':::' calls:
'AnnotationDbi:::.colsArgumentWarning' 'AnnotationDbi:::.resort'
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
.tryGetResult: no visible global function definition for 'getForm'
* 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 ... WARNING
Undocumented arguments in documentation object 'UniProt.ws-objects'
'object'
Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
* 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' ... [152s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
UniProtWS-class 10.10 1.62 106.80
colsAndKeytypes 6.25 1.12 41.22
** running examples for arch 'x64' ... ERROR
Running examples in 'UniProt.ws-Ex.R' failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: UniProt.ws-objects
> ### Title: UniProt.ws objects and their related methods and functions
> ### Aliases: UniProt.ws class:UniProt.ws UniProt.ws-class
> ### show,UniProt.ws-method species species,UniProt.ws-method taxId
> ### taxId,UniProt.ws-method taxId<- taxId<-,UniProt.ws-method cols
> ### columns columns,UniProt.ws-method keytypes keytypes,UniProt.ws-method
> ### keys keys,UniProt.ws-method select select,UniProt.ws-method
> ### availableUniprotSpecies lookupUniprotSpeciesFromTaxId
> ### Keywords: classes methods
>
> ### ** Examples
>
> ## Make a UniProt.ws object
> up <- UniProt.ws(taxId=9606)
Warning in file(con, "r") :
InternetOpenUrl failed: 'The HTTP redirect request failed'
Error in file(con, "r") : cannot open the connection
Calls: UniProt.ws -> .getUniprots -> readLines -> file
Execution halted
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
Running 'UniProt.ws_unit_tests.R' [12s]
Warning message:
running command '"D:/biocbld/BBS-3˜1.2-B/R/bin/i386/R" CMD BATCH --vanilla "UniProt.ws_unit_tests.R" "UniProt.ws_unit_tests.Rout"' had status 1
ERROR
Running the tests in 'tests/UniProt.ws_unit_tests.R' failed.
Last 13 lines of output:
1 Test Suite :
UniProt.ws RUnit Tests - 3 test functions, 1 error, 0 failures
ERROR in D:/biocbld/bbs-3.2-bioc/meat/UniProt.ws.buildbin-libdir/UniProt.ws/unitTests/test_select.R: Error while sourcing D:/biocbld/bbs-3.2-bioc/meat/UniProt.ws.buildbin-libdir/UniProt.ws/unitTests/test_select.R : Error in file(con, "r") : cannot open the connection
Test files with failing tests
test_select.R
D:/biocbld/bbs-3.2-bioc/meat/UniProt.ws.buildbin-libdir/UniProt.ws/unitTests/test_select.R
Error in BiocGenerics:::testPackage("UniProt.ws") :
unit tests failed for package UniProt.ws
Execution halted
** running tests for arch 'x64' ...
Running 'UniProt.ws_unit_tests.R' [207s]
[207s] OK
* 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
'D:/biocbld/bbs-3.2-bioc/meat/UniProt.ws.Rcheck/00check.log'
for details.
UniProt.ws.Rcheck/tests_i386/UniProt.ws_unit_tests.Rout.fail:
R version 3.2.2 (2015-08-14) -- "Fire Safety"
Copyright (C) 2015 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.
> BiocGenerics:::testPackage("UniProt.ws")
Attaching package: 'BiocGenerics'
The following objects are masked from 'package:parallel':
clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
clusterExport, clusterMap, parApply, parCapply, parLapply,
parLapplyLB, parRapply, parSapply, parSapplyLB
The following objects are masked from 'package:stats':
IQR, mad, xtabs
The following objects are masked from 'package:base':
Filter, Find, Map, Position, Reduce, anyDuplicated, append,
as.data.frame, as.vector, cbind, colnames, do.call, duplicated,
eval, evalq, get, grep, grepl, intersect, is.unsorted, lapply,
mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int,
rank, rbind, rep.int, rownames, sapply, setdiff, sort, table,
tapply, union, unique, unlist, unsplit
Error in file(con, "r") : cannot open the connection
In addition: Warning message:
In file(con, "r") :
InternetOpenUrl failed: 'The HTTP redirect request failed'
Getting extra data for P04217 P30443 NA etc
Getting extra data for P13368 P20806 Q9UM73 etc
Getting extra data for P13368 P20806 Q9UM73 etc
Getting mapping data for P13368 ... and P_REFSEQ_AC
Getting mapping data for 1 ... and ACC
Getting mapping data for P04217 ... and UNIGENE_ID
RUNIT TEST PROTOCOL -- Thu Aug 20 11:25:18 2015
***********************************************
Number of test functions: 3
Number of errors: 1
Number of failures: 0
1 Test Suite :
UniProt.ws RUnit Tests - 3 test functions, 1 error, 0 failures
ERROR in D:/biocbld/bbs-3.2-bioc/meat/UniProt.ws.buildbin-libdir/UniProt.ws/unitTests/test_select.R: Error while sourcing D:/biocbld/bbs-3.2-bioc/meat/UniProt.ws.buildbin-libdir/UniProt.ws/unitTests/test_select.R : Error in file(con, "r") : cannot open the connection
Test files with failing tests
test_select.R
D:/biocbld/bbs-3.2-bioc/meat/UniProt.ws.buildbin-libdir/UniProt.ws/unitTests/test_select.R
Error in BiocGenerics:::testPackage("UniProt.ws") :
unit tests failed for package UniProt.ws
Execution halted
UniProt.ws.Rcheck/00install.out:
install for i386 * installing *source* package 'UniProt.ws' ... ** R ** inst ** preparing package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded install for x64 * installing *source* package 'UniProt.ws' ... ** testing if installed package can be loaded * MD5 sums packaged installation of 'UniProt.ws' as UniProt.ws_2.9.2.zip * DONE (UniProt.ws)
UniProt.ws.Rcheck/examples_i386/UniProt.ws-Ex.timings:
| name | user | system | elapsed | |
| UniProtWS-class | 10.10 | 1.62 | 106.80 | |
| colsAndKeytypes | 6.25 | 1.12 | 41.22 | |
UniProt.ws.Rcheck/examples_x64/UniProt.ws-Ex.timings:
| name | user | system | elapsed |