genotypeeval 1.2.2
Jennifer Tom
| Snapshot Date: 2016-10-12 17:20:15 -0700 (Wed, 12 Oct 2016) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_3/madman/Rpacks/genotypeeval | | Last Changed Rev: 117513 / Revision: 122332 | | Last Changed Date: 2016-05-15 13:18:19 -0700 (Sun, 15 May 2016) |
| zin2 | Linux (Ubuntu 14.04.2 LTS) / x86_64 | NotNeeded | OK | WARNINGS | |  |
| moscato2 | Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 | NotNeeded | OK | [ WARNINGS ] | OK | |
| oaxaca | Mac OS X Mavericks (10.9.5) / x86_64 | NotNeeded | OK | WARNINGS | OK | |
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### Running command:
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### rm -rf genotypeeval.buildbin-libdir genotypeeval.Rcheck && mkdir genotypeeval.buildbin-libdir genotypeeval.Rcheck && E:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=genotypeeval.buildbin-libdir genotypeeval_1.2.2.tar.gz >genotypeeval.Rcheck\00install.out 2>&1 && cp genotypeeval.Rcheck\00install.out genotypeeval-install.out && E:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD check --library=genotypeeval.buildbin-libdir --install="check:genotypeeval-install.out" --force-multiarch --no-vignettes --timings genotypeeval_1.2.2.tar.gz
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* using log directory 'E:/biocbld/bbs-3.3-bioc/meat/genotypeeval.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 'genotypeeval/DESCRIPTION' ... OK
* this is package 'genotypeeval' version '1.2.2'
* 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 'genotypeeval' can be installed ... WARNING
Found the following significant warnings:
Warning: replacing previous import 'BiocGenerics::Position' by 'ggplot2::Position' when loading 'genotypeeval'
See 'E:/biocbld/bbs-3.3-bioc/meat/genotypeeval.Rcheck/00install.out' for details.
* 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 ... NOTE
ReadVCFDataChunk: no visible global function definition for
'read.table'
getCoefs: no visible global function definition for 'constrOptim'
Undefined global functions or variables:
constrOptim read.table
Consider adding
importFrom("stats", "constrOptim")
importFrom("utils", "read.table")
to your NAMESPACE file.
* 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
getPlots 7.41 0.03 7.44
ReadVCFDataChunk 5.46 0.01 5.48
VCFEvaluate 5.21 0.00 5.21
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
ReadVCFDataChunk 7.38 0.05 7.42
getPlots 6.96 0.00 6.95
didSamplePassOverall 6.20 0.00 6.20
didSamplePass 5.85 0.02 5.86
getName 5.53 0.00 5.54
VCFEvaluate 5.07 0.03 5.10
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
Running 'testthat.R'
OK
** running tests for arch 'x64' ...
Running 'testthat.R'
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 WARNING, 1 NOTE
See
'E:/biocbld/bbs-3.3-bioc/meat/genotypeeval.Rcheck/00check.log'
for details.
install for i386
* installing *source* package 'genotypeeval' ...
** R
** inst
** preparing package for lazy loading
Warning: replacing previous import 'BiocGenerics::Position' by 'ggplot2::Position' when loading 'genotypeeval'
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Warning: replacing previous import 'BiocGenerics::Position' by 'ggplot2::Position' when loading 'genotypeeval'
install for x64
* installing *source* package 'genotypeeval' ...
** testing if installed package can be loaded
Warning: replacing previous import 'BiocGenerics::Position' by 'ggplot2::Position' when loading 'genotypeeval'
* MD5 sums
packaged installation of 'genotypeeval' as genotypeeval_1.2.2.zip
* DONE (genotypeeval)