| 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 2016-10-13 12:52:34 -0700 (Thu, 13 Oct 2016).
| Package 957/1210 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | |||||
| RefNet 1.8.0 Paul Shannon
| zin2 | Linux (Ubuntu 14.04.2 LTS) / x86_64 | OK | OK | OK |  | |||||
| moscato2 | Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 | NotNeeded | OK | [ ERROR ] | OK | ||||||
| oaxaca | Mac OS X Mavericks (10.9.5) / x86_64 | NotNeeded | OK | OK | OK | |
| Package: RefNet |
| Version: 1.8.0 |
| Command: rm -rf RefNet.buildbin-libdir RefNet.Rcheck && mkdir RefNet.buildbin-libdir RefNet.Rcheck && E:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=RefNet.buildbin-libdir RefNet_1.8.0.tar.gz >RefNet.Rcheck\00install.out 2>&1 && cp RefNet.Rcheck\00install.out RefNet-install.out && E:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD check --library=RefNet.buildbin-libdir --install="check:RefNet-install.out" --force-multiarch --no-vignettes --timings RefNet_1.8.0.tar.gz |
| StartedAt: 2016-10-13 08:02:21 -0700 (Thu, 13 Oct 2016) |
| EndedAt: 2016-10-13 08:11:30 -0700 (Thu, 13 Oct 2016) |
| EllapsedTime: 548.6 seconds |
| RetCode: 1 |
| Status: ERROR |
| CheckDir: RefNet.Rcheck |
| Warnings: NA |
##############################################################################
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###
### Running command:
###
### rm -rf RefNet.buildbin-libdir RefNet.Rcheck && mkdir RefNet.buildbin-libdir RefNet.Rcheck && E:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=RefNet.buildbin-libdir RefNet_1.8.0.tar.gz >RefNet.Rcheck\00install.out 2>&1 && cp RefNet.Rcheck\00install.out RefNet-install.out && E:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD check --library=RefNet.buildbin-libdir --install="check:RefNet-install.out" --force-multiarch --no-vignettes --timings RefNet_1.8.0.tar.gz
###
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##############################################################################
* using log directory 'E:/biocbld/bbs-3.3-bioc/meat/RefNet.Rcheck'
* using R version 3.3.1 (2016-06-21)
* 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 '1.8.0'
* 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
** 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' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
RefNet-class 24.53 0.76 46.86
interactions 23.03 0.74 25.28
providerClasses 22.62 0.73 24.96
providers 20.31 0.61 22.69
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
RefNet-class 23.88 0.85 27.19
interactions 21.42 0.97 23.89
providerClasses 20.57 0.68 24.43
providers 19.78 0.74 22.35
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
Running 'runTests.R'
Warning message:
running command '"E:/biocbld/BBS-3˜1.3-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'
Warning message:
running command '"E:/biocbld/BBS-3˜1.3-B/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:
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
* 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 NOTE
See
'E:/biocbld/bbs-3.3-bioc/meat/RefNet.Rcheck/00check.log'
for details.
runTests.Rout.fail:
R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 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 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, cbind, colnames, do.call, duplicated, eval, evalq,
get, grep, grepl, intersect, is.unsorted, lapply, lengths, mapply,
match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank,
rbind, rownames, sapply, setdiff, sort, table, tapply, union,
unique, unsplit
Loading required package: S4Vectors
Loading required package: stats4
Attaching package: 'S4Vectors'
The following objects are masked from 'package:base':
colMeans, colSums, expand.grid, rowMeans, rowSums
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
[1] initializing PSICQUIC...
[1] initializing RefNet from AnnotationHub...
snapshotDate(): 2016-10-11
loading from cache 'C:/Users/biocbuild/AppData/.AnnotationHub/10364'
loading from cache 'C:/Users/biocbuild/AppData/.AnnotationHub/10365'
loading from cache 'C:/Users/biocbuild/AppData/.AnnotationHub/12810'
loading from cache 'C:/Users/biocbuild/AppData/.AnnotationHub/12814'
loading from cache 'C:/Users/biocbuild/AppData/.AnnotationHub/27766'
loading from cache 'C:/Users/biocbuild/AppData/.AnnotationHub/27767'
loading from cache 'C:/Users/biocbuild/AppData/.AnnotationHub/27768'
loading from cache 'C:/Users/biocbuild/AppData/.AnnotationHub/27769'
[1] RefNet ready.
checking for biomart access...
does 'http://www.ensembl.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(): 2016-10-11
loading from cache 'C:/Users/biocbuild/AppData/.AnnotationHub/10364'
loading from cache 'C:/Users/biocbuild/AppData/.AnnotationHub/10365'
loading from cache 'C:/Users/biocbuild/AppData/.AnnotationHub/12810'
loading from cache 'C:/Users/biocbuild/AppData/.AnnotationHub/12814'
loading from cache 'C:/Users/biocbuild/AppData/.AnnotationHub/27766'
loading from cache 'C:/Users/biocbuild/AppData/.AnnotationHub/27767'
loading from cache 'C:/Users/biocbuild/AppData/.AnnotationHub/27768'
loading from cache 'C:/Users/biocbuild/AppData/.AnnotationHub/27769'
[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 0 0.23
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 Oct 13 08:11:23 2016
***********************************************
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
runTests.Rout.fail:
R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 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, cbind, colnames, do.call, duplicated, eval, evalq,
get, grep, grepl, intersect, is.unsorted, lapply, lengths, mapply,
match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank,
rbind, rownames, sapply, setdiff, sort, table, tapply, union,
unique, unsplit
Loading required package: S4Vectors
Loading required package: stats4
Attaching package: 'S4Vectors'
The following objects are masked from 'package:base':
colMeans, colSums, expand.grid, rowMeans, rowSums
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
[1] initializing PSICQUIC...
[1] initializing RefNet from AnnotationHub...
snapshotDate(): 2016-10-11
loading from cache 'C:/Users/biocbuild/AppData/.AnnotationHub/10364'
loading from cache 'C:/Users/biocbuild/AppData/.AnnotationHub/10365'
loading from cache 'C:/Users/biocbuild/AppData/.AnnotationHub/12810'
loading from cache 'C:/Users/biocbuild/AppData/.AnnotationHub/12814'
loading from cache 'C:/Users/biocbuild/AppData/.AnnotationHub/27766'
loading from cache 'C:/Users/biocbuild/AppData/.AnnotationHub/27767'
loading from cache 'C:/Users/biocbuild/AppData/.AnnotationHub/27768'
loading from cache 'C:/Users/biocbuild/AppData/.AnnotationHub/27769'
[1] RefNet ready.
checking for biomart access...
does 'http://www.ensembl.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(): 2016-10-11
loading from cache 'C:/Users/biocbuild/AppData/.AnnotationHub/10364'
loading from cache 'C:/Users/biocbuild/AppData/.AnnotationHub/10365'
loading from cache 'C:/Users/biocbuild/AppData/.AnnotationHub/12810'
loading from cache 'C:/Users/biocbuild/AppData/.AnnotationHub/12814'
loading from cache 'C:/Users/biocbuild/AppData/.AnnotationHub/27766'
loading from cache 'C:/Users/biocbuild/AppData/.AnnotationHub/27767'
loading from cache 'C:/Users/biocbuild/AppData/.AnnotationHub/27768'
loading from cache 'C:/Users/biocbuild/AppData/.AnnotationHub/27769'
[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 0 0.25
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 Oct 13 08:10:15 2016
***********************************************
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_1.8.0.zip * DONE (RefNet)
RefNet.Rcheck/examples_i386/RefNet-Ex.timings:
| name | user | system | elapsed | |
| RefNet-class | 24.53 | 0.76 | 46.86 | |
| detectDuplicateInteractions | 0.01 | 0.00 | 0.02 | |
| interactions | 23.03 | 0.74 | 25.28 | |
| pickBestFromDupGroup | 0.03 | 0.00 | 0.03 | |
| providerClasses | 22.62 | 0.73 | 24.96 | |
| providers | 20.31 | 0.61 | 22.69 | |
| pubmedAbstract | 0.01 | 0.00 | 0.34 | |
RefNet.Rcheck/examples_x64/RefNet-Ex.timings:
| name | user | system | elapsed | |
| RefNet-class | 23.88 | 0.85 | 27.19 | |
| detectDuplicateInteractions | 0.03 | 0.00 | 0.03 | |
| interactions | 21.42 | 0.97 | 23.89 | |
| pickBestFromDupGroup | 0.02 | 0.02 | 0.03 | |
| providerClasses | 20.57 | 0.68 | 24.43 | |
| providers | 19.78 | 0.74 | 22.35 | |
| pubmedAbstract | 0.00 | 0.00 | 0.32 | |