| 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 13:22:40 -0700 (Thu, 20 Aug 2015).
| Package 839/1069 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | |||||
| RefNet 1.5.0 Paul Shannon
| zin1 | Linux (Ubuntu 14.04.2 LTS) / x86_64 | OK | OK | OK |  | |||||
| 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 | OK | OK | | |||||
| oaxaca | Mac OS X Mavericks (10.9.5) / x86_64 | OK | OK | OK | OK | |
| Package: RefNet |
| Version: 1.5.0 |
| Command: rm -rf RefNet.buildbin-libdir RefNet.Rcheck && mkdir RefNet.buildbin-libdir RefNet.Rcheck && D:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=RefNet.buildbin-libdir RefNet_1.5.0.tar.gz >RefNet.Rcheck\00install.out 2>&1 && cp RefNet.Rcheck\00install.out RefNet-install.out && D:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD check --library=RefNet.buildbin-libdir --install="check:RefNet-install.out" --force-multiarch --no-vignettes --timings RefNet_1.5.0.tar.gz |
| StartedAt: 2015-08-20 09:27:20 -0700 (Thu, 20 Aug 2015) |
| EndedAt: 2015-08-20 09:36:01 -0700 (Thu, 20 Aug 2015) |
| EllapsedTime: 521.0 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 RefNet.Rcheck && mkdir RefNet.buildbin-libdir RefNet.Rcheck && D:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=RefNet.buildbin-libdir RefNet_1.5.0.tar.gz >RefNet.Rcheck\00install.out 2>&1 && cp RefNet.Rcheck\00install.out RefNet-install.out && D:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD check --library=RefNet.buildbin-libdir --install="check:RefNet-install.out" --force-multiarch --no-vignettes --timings RefNet_1.5.0.tar.gz
###
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* using log directory 'D:/biocbld/bbs-3.2-bioc/meat/RefNet.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 'RefNet/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'RefNet' version '1.5.0'
* 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 ... NOTE
Malformed Description field: should contain one or more complete sentences.
* 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 installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... [86s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
RefNet-class 15.12 0.62 34.32
interactions 13.97 0.56 16.13
providers 13.48 0.46 15.85
providerClasses 11.84 0.45 13.85
** running examples for arch 'x64' ... [67s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
RefNet-class 14.31 0.75 16.76
interactions 12.20 0.45 14.29
providerClasses 12.23 0.35 14.20
providers 11.39 0.43 14.10
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
Running 'runTests.R' [152s]
Warning message:
running command '"D:/biocbld/BBS-3˜1.2-B/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:
FAILURE in test_pubmedAbstract: Error in checkTrue(nchar(paste(text.lines, collapse = "")) > 1000) :
Test not TRUE
Test files with failing tests
test_RefNet.R
test_pubmedAbstract
Error in BiocGenerics:::testPackage("RefNet") :
unit tests failed for package RefNet
Execution halted
** running tests for arch 'x64' ...
Running 'runTests.R' [47s]
[48s] 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: 1 ERROR, 1 NOTE
See
'D:/biocbld/bbs-3.2-bioc/meat/RefNet.Rcheck/00check.log'
for details.
RefNet.Rcheck/tests_i386/runTests.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.
> 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 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
Loading required package: S4Vectors
Loading required package: stats4
Loading required package: PSICQUIC
Loading required package: biomaRt
Loading required package: httr
Loading required package: plyr
Attaching package: 'plyr'
The following object is masked from 'package:IRanges':
desc
The following object is masked from 'package:S4Vectors':
rename
Loading required package: AnnotationHub
Loading required package: RCurl
Loading required package: bitops
Loading required package: shiny
[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")'.
Attaching package: 'Biobase'
The following object is masked from 'package:AnnotationHub':
cache
The following object is masked from 'package:httr':
content
Loading required package: DBI
[1] initializing PSICQUIC...
[1] initializing RefNet from AnnotationHub...
snapshotDate(): 2015-08-17
[1] RefNet ready.
checking for biomart access...
does 'http://www.biomart.org' respond?
creating ensembl mart
hsapiens_gene_ensembl dataset provided?
connecting to biomart...
[1] "--- test_.combinations"
[1] "--- test_.filterOnColumnValue"
[1] "--- test_.findHits"
[1] "--- test_.smartRbind"
[1] "--- test_ctor"
[1] initializing PSICQUIC...
[1] initializing RefNet from AnnotationHub...
snapshotDate(): 2015-08-17
[1] RefNet ready.
[1] "--- test_detectDuplicateInteractions"
[1] "--- test_interactions"
[1] "--- test_pickBestFromDupGroup"
[1] "--- test_providerMix_PSICQUIC_and_native"
[1] "--- test_pubmedAbstract"
Timing stopped at: 0.02 0 30.33
Error in checkTrue(nchar(paste(text.lines, collapse = "")) > 1000) :
Test not TRUE
In addition: Warning messages:
1: In is.na(psicquic) :
is.na() applied to non-(list or vector) of type 'S4'
2: In is.na(refnet@psicquic) :
is.na() applied to non-(list or vector) of type 'S4'
3: In is.na(refnet@psicquic) :
is.na() applied to non-(list or vector) of type 'S4'
[1] "--- test_recon2Interactions"
RUNIT TEST PROTOCOL -- Thu Aug 20 09:35:08 2015
***********************************************
Number of test functions: 11
Number of errors: 0
Number of failures: 1
1 Test Suite :
RefNet RUnit Tests - 11 test functions, 0 errors, 1 failure
FAILURE in test_pubmedAbstract: Error in checkTrue(nchar(paste(text.lines, collapse = "")) > 1000) :
Test not TRUE
Test files with failing tests
test_RefNet.R
test_pubmedAbstract
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 ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded install for x64 * installing *source* package 'RefNet' ... ** testing if installed package can be loaded * MD5 sums packaged installation of 'RefNet' as RefNet_1.5.0.zip * DONE (RefNet)
RefNet.Rcheck/examples_i386/RefNet-Ex.timings:
| name | user | system | elapsed | |
| RefNet-class | 15.12 | 0.62 | 34.32 | |
| detectDuplicateInteractions | 0.02 | 0.00 | 0.01 | |
| interactions | 13.97 | 0.56 | 16.13 | |
| pickBestFromDupGroup | 0.02 | 0.00 | 0.02 | |
| providerClasses | 11.84 | 0.45 | 13.85 | |
| providers | 13.48 | 0.46 | 15.85 | |
| pubmedAbstract | 0.00 | 0.00 | 0.56 | |
RefNet.Rcheck/examples_x64/RefNet-Ex.timings:
| name | user | system | elapsed | |
| RefNet-class | 14.31 | 0.75 | 16.76 | |
| detectDuplicateInteractions | 0.03 | 0.00 | 0.03 | |
| interactions | 12.20 | 0.45 | 14.29 | |
| pickBestFromDupGroup | 0.01 | 0.00 | 0.01 | |
| providerClasses | 12.23 | 0.35 | 14.20 | |
| providers | 11.39 | 0.43 | 14.10 | |
| pubmedAbstract | 0.02 | 0.00 | 0.89 | |