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This page was generated on 2014-10-08 08:56:46 -0700 (Wed, 08 Oct 2014).
| Package 651/824 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||
| RefNet 1.0.4 Paul Shannon
| zin2 | Linux (Ubuntu 12.04.4 LTS) / x86_64 | NotNeeded | OK | OK | |||||
| moscato2 | Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 | NotNeeded | OK | [ ERROR ] | OK | |||||
| petty | Mac OS X Snow Leopard (10.6.8) / x86_64 | NotNeeded | OK | OK | OK | |||||
| morelia | Mac OS X Mavericks (10.9.5) / x86_64 | NotNeeded | OK | OK | OK |
| Package: RefNet |
| Version: 1.0.4 |
| Command: rm -rf RefNet.buildbin-libdir && mkdir RefNet.buildbin-libdir && E:\biocbld\bbs-2.14-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=RefNet.buildbin-libdir RefNet_1.0.4.tar.gz >RefNet-install.out 2>&1 && E:\biocbld\bbs-2.14-bioc\R\bin\R.exe CMD check --library=RefNet.buildbin-libdir --install="check:RefNet-install.out" --force-multiarch --no-vignettes --timings RefNet_1.0.4.tar.gz |
| StartedAt: 2014-10-08 04:27:17 -0700 (Wed, 08 Oct 2014) |
| EndedAt: 2014-10-08 04:41:42 -0700 (Wed, 08 Oct 2014) |
| EllapsedTime: 865.4 seconds |
| RetCode: 1 |
| Status: ERROR |
| CheckDir: RefNet.Rcheck |
| Warnings: NA |
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### Running command:
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### rm -rf RefNet.buildbin-libdir && mkdir RefNet.buildbin-libdir && E:\biocbld\bbs-2.14-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=RefNet.buildbin-libdir RefNet_1.0.4.tar.gz >RefNet-install.out 2>&1 && E:\biocbld\bbs-2.14-bioc\R\bin\R.exe CMD check --library=RefNet.buildbin-libdir --install="check:RefNet-install.out" --force-multiarch --no-vignettes --timings RefNet_1.0.4.tar.gz
###
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* using log directory 'E:/biocbld/bbs-2.14-bioc/meat/RefNet.Rcheck'
* using R version 3.1.1 (2014-07-10)
* using platform: i386-w64-mingw32 (32-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'RefNet/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'RefNet' version '1.0.4'
* 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 'RefNet' 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
** checking loading without being on the library search path ... 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 loading without being on the library search path ... 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 installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... [72s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
RefNet-class 9.32 0.09 15.85
interactions 8.53 0.02 14.78
providerClasses 6.71 0.03 13.85
providers 6.22 0.04 12.39
** running examples for arch 'x64' ... [66s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
RefNet-class 10.65 0.06 16.80
providerClasses 6.53 0.02 12.56
providers 6.48 0.01 12.55
interactions 5.87 0.04 11.84
* checking for unstated dependencies in tests ... OK
* checking tests ...
** running tests for arch 'i386' ...
Running 'runTests.R' [381s]
Warning message:
running command '"E:/biocbld/BBS-2˜1.14-/R/bin/i386/R" CMD BATCH --vanilla "runTests.R" "runTests.Rout"' had status 1
ERROR
Running the tests in 'tests/runTests.R' failed.
Last 13 lines of output:
1 Test Suite :
RefNet RUnit Tests - 1 test function, 1 error, 0 failures
ERROR in E:/biocbld/bbs-2.14-bioc/meat/RefNet.buildbin-libdir/RefNet/unitTests/test_RefNet.R: Error while sourcing E:/biocbld/bbs-2.14-bioc/meat/RefNet.buildbin-libdir/RefNet/unitTests/test_RefNet.R : Error : XML content does not seem to be XML:
Test files with failing tests
test_RefNet.R
E:/biocbld/bbs-2.14-bioc/meat/RefNet.buildbin-libdir/RefNet/unitTests/test_RefNet.R
Error in BiocGenerics:::testPackage("RefNet") :
unit tests failed for package RefNet
Execution halted
** running tests for arch 'x64' ...
Running 'runTests.R' [31s]
Warning message:
running command '"E:/biocbld/BBS-2˜1.14-/R/bin/x64/R" CMD BATCH --vanilla "runTests.R" "runTests.Rout"' had status 1
ERROR
Running the tests in 'tests/runTests.R' failed.
Last 13 lines of output:
1 Test Suite :
RefNet RUnit Tests - 1 test function, 1 error, 0 failures
ERROR in E:/biocbld/bbs-2.14-bioc/meat/RefNet.buildbin-libdir/RefNet/unitTests/test_RefNet.R: Error while sourcing E:/biocbld/bbs-2.14-bioc/meat/RefNet.buildbin-libdir/RefNet/unitTests/test_RefNet.R : Error : XML content does not seem to be XML:
Test files with failing tests
test_RefNet.R
E:/biocbld/bbs-2.14-bioc/meat/RefNet.buildbin-libdir/RefNet/unitTests/test_RefNet.R
Error in BiocGenerics:::testPackage("RefNet") :
unit tests failed for package RefNet
Execution halted
RefNet.Rcheck/tests_i386/runTests.Rout.fail:
R version 3.1.1 (2014-07-10) -- "Sock it to Me"
Copyright (C) 2014 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.
> require(RefNet) || stop("unable to load RefNet package")
Loading required package: RefNet
Loading required package: IRanges
Loading required package: BiocGenerics
Loading required package: parallel
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 object is masked from 'package:stats':
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, 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
Loading required package: PSICQUIC
Loading required package: biomaRt
Loading required package: AnnotationHub
Loading required package: RCurl
Loading required package: bitops
[1] TRUE
> BiocGenerics:::testPackage('RefNet')
Loading required package: AnnotationDbi
Loading required package: Biobase
Welcome to Bioconductor
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
Loading required package: GenomeInfoDb
Loading required package: DBI
connecting to biomart...
Request to BioMart web service failed. Verify if you are still connected to the internet. Alternatively the BioMart web service is temporarily down. Check http://www.biomart.org and verify if this website is available.
Error : XML content does not seem to be XML:
RUNIT TEST PROTOCOL -- Wed Oct 08 04:41:11 2014
***********************************************
Number of test functions: 1
Number of errors: 1
Number of failures: 0
1 Test Suite :
RefNet RUnit Tests - 1 test function, 1 error, 0 failures
ERROR in E:/biocbld/bbs-2.14-bioc/meat/RefNet.buildbin-libdir/RefNet/unitTests/test_RefNet.R: Error while sourcing E:/biocbld/bbs-2.14-bioc/meat/RefNet.buildbin-libdir/RefNet/unitTests/test_RefNet.R : Error : XML content does not seem to be XML:
Test files with failing tests
test_RefNet.R
E:/biocbld/bbs-2.14-bioc/meat/RefNet.buildbin-libdir/RefNet/unitTests/test_RefNet.R
Error in BiocGenerics:::testPackage("RefNet") :
unit tests failed for package RefNet
Execution halted
RefNet.Rcheck/tests_x64/runTests.Rout.fail:
R version 3.1.1 (2014-07-10) -- "Sock it to Me"
Copyright (C) 2014 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.
> require(RefNet) || stop("unable to load RefNet package")
Loading required package: RefNet
Loading required package: IRanges
Loading required package: BiocGenerics
Loading required package: parallel
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 object is masked from 'package:stats':
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, 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
Loading required package: PSICQUIC
Loading required package: biomaRt
Loading required package: AnnotationHub
Loading required package: RCurl
Loading required package: bitops
[1] TRUE
> BiocGenerics:::testPackage('RefNet')
Loading required package: AnnotationDbi
Loading required package: Biobase
Welcome to Bioconductor
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
Loading required package: GenomeInfoDb
Loading required package: DBI
connecting to biomart...
Request to BioMart web service failed. Verify if you are still connected to the internet. Alternatively the BioMart web service is temporarily down. Check http://www.biomart.org and verify if this website is available.
Error : XML content does not seem to be XML:
RUNIT TEST PROTOCOL -- Wed Oct 08 04:41:42 2014
***********************************************
Number of test functions: 1
Number of errors: 1
Number of failures: 0
1 Test Suite :
RefNet RUnit Tests - 1 test function, 1 error, 0 failures
ERROR in E:/biocbld/bbs-2.14-bioc/meat/RefNet.buildbin-libdir/RefNet/unitTests/test_RefNet.R: Error while sourcing E:/biocbld/bbs-2.14-bioc/meat/RefNet.buildbin-libdir/RefNet/unitTests/test_RefNet.R : Error : XML content does not seem to be XML:
Test files with failing tests
test_RefNet.R
E:/biocbld/bbs-2.14-bioc/meat/RefNet.buildbin-libdir/RefNet/unitTests/test_RefNet.R
Error in BiocGenerics:::testPackage("RefNet") :
unit tests failed for package RefNet
Execution halted
RefNet.Rcheck/00install.out:
install for i386 * installing *source* package 'RefNet' ... ** R ** inst ** preparing package for lazy loading Note: the specification for S3 class "AsIs" in package 'RJSONIO' seems equivalent to one from package 'BiocGenerics': 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 "AsIs" in package 'RJSONIO' seems equivalent to one from package 'BiocGenerics': not turning on duplicate class definitions for this class. install for x64 * installing *source* package 'RefNet' ... ** testing if installed package can be loaded Note: the specification for S3 class "AsIs" in package 'RJSONIO' seems equivalent to one from package 'BiocGenerics': not turning on duplicate class definitions for this class. * MD5 sums packaged installation of 'RefNet' as RefNet_1.0.4.zip * DONE (RefNet)
RefNet.Rcheck/examples_i386/RefNet-Ex.timings:
| name | user | system | elapsed | |
| RefNet-class | 9.32 | 0.09 | 15.85 | |
| detectDuplicateInteractions | 0.26 | 0.02 | 0.28 | |
| interactions | 8.53 | 0.02 | 14.78 | |
| pickBestFromDupGroup | 0.03 | 0.00 | 0.03 | |
| providerClasses | 6.71 | 0.03 | 13.85 | |
| providers | 6.22 | 0.04 | 12.39 | |
| pubmedAbstract | 0.02 | 0.00 | 0.61 | |
RefNet.Rcheck/examples_x64/RefNet-Ex.timings:
| name | user | system | elapsed | |
| RefNet-class | 10.65 | 0.06 | 16.80 | |
| detectDuplicateInteractions | 0.03 | 0.02 | 0.05 | |
| interactions | 5.87 | 0.04 | 11.84 | |
| pickBestFromDupGroup | 0.02 | 0.00 | 0.01 | |
| providerClasses | 6.53 | 0.02 | 12.56 | |
| providers | 6.48 | 0.01 | 12.55 | |
| pubmedAbstract | 0.00 | 0.00 | 0.81 | |