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This page was generated on 2016-04-21 13:20:17 -0700 (Thu, 21 Apr 2016).
| Package 524/1210 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | |||||
| GSEABase 1.33.0 Bioconductor Package Maintainer
| zin2 | Linux (Ubuntu 14.04.2 LTS) / x86_64 | OK | OK | ERROR | ||||||
| moscato2 | Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 | OK | OK | ERROR | OK | ||||||
| morelia | Mac OS X Mavericks (10.9.5) / x86_64 | OK | OK | [ ERROR ] | OK |
| Package: GSEABase |
| Version: 1.33.0 |
| Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings GSEABase_1.33.0.tar.gz |
| StartedAt: 2016-04-21 03:40:20 -0700 (Thu, 21 Apr 2016) |
| EndedAt: 2016-04-21 03:43:34 -0700 (Thu, 21 Apr 2016) |
| EllapsedTime: 194.1 seconds |
| RetCode: 1 |
| Status: ERROR |
| CheckDir: GSEABase.Rcheck |
| Warnings: NA |
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### Running command:
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### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings GSEABase_1.33.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.3-bioc/meat/GSEABase.Rcheck’
* using R version 3.3.0 beta (2016-04-06 r70435)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘GSEABase/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘GSEABase’ version ‘1.33.0’
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘GSEABase’ can be installed ... [11s/16s] 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
* 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
goSlim,ExpressionSet-GOCollection: no visible binding for global
variable ‘sample.ExpressionSet’
Undefined global functions or variables:
sample.ExpressionSet
* 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [17s/17s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
GeneSetCollection-methods 8.048 0.177 8.358
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘unitTests.R’ [45s/46s]
ERROR
Running the tests in ‘tests/unitTests.R’ failed.
Last 13 lines of output:
Names: 1 string mismatch
Test files with failing tests
test_GeneIdentifierType.R
test_GeneIdentifierType_mapIdentifiers_map
test_GeneIdentifierType_mapIdentifiers_revMap
Error in BiocGenerics:::testPackage("GSEABase") :
unit tests failed for package GSEABase
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
‘/Users/biocbuild/bbs-3.3-bioc/meat/GSEABase.Rcheck/00check.log’
for details.
unitTests.Rout.fail:
R version 3.3.0 beta (2016-04-06 r70435) -- "Supposedly Educational"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin13.4.0 (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.
> BiocGenerics:::testPackage("GSEABase")
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
Welcome to Bioconductor
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
Attaching package: 'S4Vectors'
The following objects are masked from 'package:base':
colMeans, colSums, expand.grid, rowMeans, rowSums
Attaching package: 'graph'
The following object is masked from 'package:XML':
addNode
'select()' returned 1:many mapping between keys and columns
'select()' returned 1:many mapping between keys and columns
'select()' returned 1:many mapping between keys and columns
'select()' returned 1:many mapping between keys and columns
'select()' returned 1:many mapping between keys and columns
'select()' returned 1:many mapping between keys and columns
'select()' returned 1:many mapping between keys and columns
'select()' returned 1:many mapping between keys and columns
Timing stopped at: 0.023 0.001 0.023
Error in checkEquals(sids, f(aids, ai, si)) : 1 string mismatch
Timing stopped at: 0.272 0.001 0.273
Error in checkEquals(list(`exportin 1` = "XPO1", `lamin B receptor` = "LBR", :
Names: 1 string mismatch
RUNIT TEST PROTOCOL -- Thu Apr 21 03:43:30 2016
***********************************************
Number of test functions: 76
Number of errors: 0
Number of failures: 2
1 Test Suite :
GSEABase RUnit Tests - 76 test functions, 0 errors, 2 failures
FAILURE in test_GeneIdentifierType_mapIdentifiers_map: Error in checkEquals(sids, f(aids, ai, si)) : 1 string mismatch
FAILURE in test_GeneIdentifierType_mapIdentifiers_revMap: Error in checkEquals(list(`exportin 1` = "XPO1", `lamin B receptor` = "LBR", :
Names: 1 string mismatch
Test files with failing tests
test_GeneIdentifierType.R
test_GeneIdentifierType_mapIdentifiers_map
test_GeneIdentifierType_mapIdentifiers_revMap
Error in BiocGenerics:::testPackage("GSEABase") :
unit tests failed for package GSEABase
Execution halted
GSEABase.Rcheck/00install.out:
* installing *source* package ‘GSEABase’ ... ** R ** inst ** preparing package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded * DONE (GSEABase)
GSEABase.Rcheck/GSEABase-Ex.timings:
| name | user | system | elapsed | |
| CollectionType-class | 0.760 | 0.037 | 0.871 | |
| CollectionType-constructors | 0.256 | 0.008 | 0.265 | |
| GSEABase-package | 0.190 | 0.010 | 0.211 | |
| GeneColorSet-class | 0.188 | 0.008 | 0.198 | |
| GeneIdentifierType-class | 0.145 | 0.007 | 0.153 | |
| GeneIdentifierType-constructors | 0.343 | 0.011 | 0.385 | |
| GeneSet-class | 0.470 | 0.010 | 0.484 | |
| GeneSet-methods | 0.137 | 0.011 | 0.148 | |
| GeneSetCollection-class | 0.028 | 0.003 | 0.030 | |
| GeneSetCollection-methods | 8.048 | 0.177 | 8.358 | |
| OBOCollection-class | 0.163 | 0.002 | 0.166 | |
| getOBOCollection | 0.115 | 0.002 | 0.116 | |
| getObjects | 0.070 | 0.002 | 0.072 | |
| goSlim-methods | 0.760 | 0.036 | 0.842 | |
| incidence-methods | 0.031 | 0.001 | 0.031 | |