gwascat 2.2.1
VJ Carey
| Snapshot Date: 2016-04-22 16:20:12 -0700 (Fri, 22 Apr 2016) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_2/madman/Rpacks/gwascat | | Last Changed Rev: 115772 / Revision: 116712 | | Last Changed Date: 2016-04-04 11:04:48 -0700 (Mon, 04 Apr 2016) |
| zin1 | Linux (Ubuntu 14.04.2 LTS) / x86_64 | OK | OK | WARNINGS | |  |
| moscato1 | Windows Server 2008 R2 Standard (64-bit) / x64 | OK | OK | [ WARNINGS ] | OK | |
| oaxaca | Mac OS X Mavericks (10.9.5) / x86_64 | OK | OK | WARNINGS | OK | |
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### Running command:
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### rm -rf gwascat.buildbin-libdir gwascat.Rcheck && mkdir gwascat.buildbin-libdir gwascat.Rcheck && D:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=gwascat.buildbin-libdir gwascat_2.2.1.tar.gz >gwascat.Rcheck\00install.out 2>&1 && cp gwascat.Rcheck\00install.out gwascat-install.out && D:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD check --library=gwascat.buildbin-libdir --install="check:gwascat-install.out" --force-multiarch --no-vignettes --timings gwascat_2.2.1.tar.gz
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* using log directory 'D:/biocbld/bbs-3.2-bioc/meat/gwascat.Rcheck'
* using R version 3.2.4 (2016-03-10)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'gwascat/DESCRIPTION' ... OK
* this is package 'gwascat' version '2.2.1'
* 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 'gwascat' can be installed ... WARNING
Found the following significant warnings:
Warning: replacing previous import 'ggplot2::Position' by 'S4Vectors::Position' when loading 'gwascat'
See 'D:/biocbld/bbs-3.2-bioc/meat/gwascat.Rcheck/00install.out' for details.
* checking installed package size ... NOTE
installed size is 38.5Mb
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
* 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 ... 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'
* 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 installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... [57s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
riskyAlleleCount 17.64 0.10 17.73
gwcex2gviz 7.94 0.22 8.44
** running examples for arch 'x64' ... [51s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
riskyAlleleCount 13.37 0.13 13.50
gwcex2gviz 6.71 0.28 7.42
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
Running 'test-all.R' [23s]
[24s] OK
** running tests for arch 'x64' ...
Running 'test-all.R' [22s]
[23s] 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, 3 NOTEs
See
'D:/biocbld/bbs-3.2-bioc/meat/gwascat.Rcheck/00check.log'
for details.
install for i386
* 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
Warning: replacing previous import 'ggplot2::Position' by 'BiocGenerics::Position' when loading 'ggbio'
Warning: replacing previous import 'ggplot2::Position' by 'S4Vectors::Position' when loading 'gwascat'
** 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
Warning: replacing previous import 'ggplot2::Position' by 'BiocGenerics::Position' when loading 'ggbio'
Warning: replacing previous import 'ggplot2::Position' by 'S4Vectors::Position' when loading 'gwascat'
install for x64
* installing *source* package 'gwascat' ...
** 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
Warning: replacing previous import 'ggplot2::Position' by 'BiocGenerics::Position' when loading 'ggbio'
Warning: replacing previous import 'ggplot2::Position' by 'S4Vectors::Position' when loading 'gwascat'
* MD5 sums
packaged installation of 'gwascat' as gwascat_2.2.1.zip
* DONE (gwascat)