gwascat 2.3.0
VJ Carey
| Snapshot Date: 2015-10-21 20:20:05 -0400 (Wed, 21 Oct 2015) | | URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/gwascat | | Last Changed Rev: 109592 / Revision: 109826 | | Last Changed Date: 2015-10-13 15:59:53 -0400 (Tue, 13 Oct 2015) |
| linux2.bioconductor.org | Linux (Ubuntu 14.04.2 LTS) / x86_64 | OK | OK | ERROR | | |
| windows2.bioconductor.org | Windows Server 2012 R2 Enterprise SP1 (64-bit) / x64 | OK | OK | ERROR | OK | |
| morelia | Mac OS X Mavericks (10.9.5) / x86_64 | OK | OK | [ ERROR ] | OK | |
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### Running command:
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### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings gwascat_2.3.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.3-bioc/meat/gwascat.Rcheck’
* using R Under development (unstable) (2015-10-08 r69496)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘gwascat/DESCRIPTION’ ... OK
* this is package ‘gwascat’ version ‘2.3.0’
* 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 ‘gwascat’ can be installed ... [26s/26s] OK
* checking installed package size ... NOTE
installed size is 38.6Mb
sub-directories of 1Mb or more:
data 30.8Mb
obo 3.0Mb
olddata 2.2Mb
tab 1.1Mb
* 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 ... NOTE
Namespace in Imports field not imported from: ‘VariantAnnotation’
All declared Imports should be used.
Package in Depends field not imported from: ‘Homo.sapiens’
These packages need to be imported from (in the NAMESPACE file)
for when this namespace is loaded but not attached.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
bindcadd_snv: no visible global function definition for ‘findOverlaps’
chklocs: no visible binding for global variable ‘gwrngs19’
chklocs: no visible global function definition for ‘getSNPlocs’
gwcex2gviz: no visible global function definition for ‘mapIds’
ldtagr: no visible global function definition for ‘rowRanges’
ldtagr: no visible global function definition for ‘col.summary’
lo38to19: no visible binding for global variable ‘si.hs.37’
makeCurrentGwascat: no visible binding for global variable ‘si.hs.38’
makeCurrentGwascat.legacy: no visible binding for global variable
‘si.hs.38’
snpGenos: no visible global function definition for ‘getSNPlocs’
tfilt: no visible binding for global variable ‘phr’
tpad: no visible binding for global variable ‘phr’
traitsManh: no visible binding for global variable ‘PVALUE_MLOG’
variantProps: no visible binding for global variable ‘gwrngs’
Undefined global functions or variables:
PVALUE_MLOG col.summary findOverlaps getSNPlocs gwrngs gwrngs19
mapIds phr rowRanges si.hs.37 si.hs.38
* 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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [33s/33s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
riskyAlleleCount 11.516 0.051 11.567
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘test-all.R’ [15s/15s]
ERROR
Running the tests in ‘tests/test-all.R’ failed.
Last 13 lines of output:
ERROR in /Users/biocbuild/bbs-3.3-bioc/meat/gwascat.Rcheck/gwascat/unitTests/test_gwascat.R: Error while sourcing /Users/biocbuild/bbs-3.3-bioc/meat/gwascat.Rcheck/gwascat/unitTests/test_gwascat.R : Error in checkTrue(identical(topTraits(ebicat38), tt38saved)) :
Test not TRUE
Test files with failing tests
test_gwascat.R
/Users/biocbuild/bbs-3.3-bioc/meat/gwascat.Rcheck/gwascat/unitTests/test_gwascat.R
Error in BiocGenerics:::testPackage("gwascat") :
unit tests failed for package gwascat
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, 3 NOTEs
See
‘/Users/biocbuild/bbs-3.3-bioc/meat/gwascat.Rcheck/00check.log’
for details.
* installing *source* package ‘gwascat’ ...
** R
** data
** inst
** preparing package for lazy loading
Now getting the GODb Object directly
Now getting the OrgDb Object directly
Now getting the TxDb Object directly
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Now getting the GODb Object directly
Now getting the OrgDb Object directly
Now getting the TxDb Object directly
* DONE (gwascat)