Rariant 1.2.0
Julian Gehring
| Snapshot Date: 2015-04-09 16:20:12 -0700 (Thu, 09 Apr 2015) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_0/madman/Rpacks/Rariant | | Last Changed Rev: 95439 / Revision: 102249 | | Last Changed Date: 2014-10-13 14:38:33 -0700 (Mon, 13 Oct 2014) |
| zin1 | Linux (Ubuntu 12.04.4 LTS) / x86_64 | NotNeeded | OK | OK | |
| moscato1 | Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 | NotNeeded | OK | [ OK ] | OK |
| perceval | Mac OS X Snow Leopard (10.6.8) / x86_64 | NotNeeded | OK | OK | OK |
| oaxaca | Mac OS X Mavericks (10.9.5) / x86_64 | NotNeeded | OK | OK | OK |
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### Running command:
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### rm -rf Rariant.buildbin-libdir Rariant.Rcheck && mkdir Rariant.buildbin-libdir Rariant.Rcheck && D:\biocbld\bbs-3.0-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=Rariant.buildbin-libdir Rariant_1.2.0.tar.gz >Rariant.Rcheck\00install.out 2>&1 && cp Rariant.Rcheck\00install.out Rariant-install.out && D:\biocbld\bbs-3.0-bioc\R\bin\R.exe CMD check --library=Rariant.buildbin-libdir --install="check:Rariant-install.out" --force-multiarch --no-vignettes --timings Rariant_1.2.0.tar.gz
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* using log directory 'D:/biocbld/bbs-3.0-bioc/meat/Rariant.Rcheck'
* using R version 3.1.3 (2015-03-09)
* using platform: i386-w64-mingw32 (32-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'Rariant/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'Rariant' version '1.2.0'
* package encoding: UTF-8
* 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 'Rariant' can be installed ... OK
* checking installed package size ... NOTE
installed size is 6.5Mb
sub-directories of 1Mb or more:
doc 1.1Mb
extdata 5.2Mb
* 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
tallyBamRegion: no visible global function definition for 'PileupParam'
tallyBamRegion: no visible global function definition for
'ScanBamParam'
tallyBamRegion: no visible global function definition for 'pileup'
* 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' ... NOTE
The following files should probably not be installed:
'rariant-inspect-ci.png', 'rariant-inspect-shift.png'
Consider the use of a .Rinstignore file: see 'Writing R Extensions',
or move the vignette sources from 'inst/doc' to 'vignettes'.
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... [30s] OK
** running examples for arch 'x64' ... [34s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
mismatch-plot 5.49 0.04 5.6
* checking for unstated dependencies in tests ... OK
* checking tests ...
** running tests for arch 'i386' ...
Running 'test_all.R' [26s]
[26s] OK
** running tests for arch 'x64' ...
Running 'test_all.R' [30s]
[31s] 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
NOTE: There were 3 notes.
See
'D:/biocbld/bbs-3.0-bioc/meat/Rariant.Rcheck/00check.log'
for details.
install for i386
* installing *source* package 'Rariant' ...
** R
** inst
** byte-compile and prepare package for lazy loading
Note: the specification for S3 class "AsIs" in package 'RJSONIO' seems equivalent to one from package 'BiocGenerics': not turning on duplicate class definitions for this class.
Warning: replacing previous import by 'proxy::as.matrix' when loading 'SomaticSignatures'
Note: the specification for S3 class "cluster" in package 'NMF' seems equivalent to one from package 'BiocParallel': not turning on duplicate class definitions for this class.
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Note: the specification for S3 class "AsIs" in package 'RJSONIO' seems equivalent to one from package 'BiocGenerics': not turning on duplicate class definitions for this class.
Warning: replacing previous import by 'proxy::as.matrix' when loading 'SomaticSignatures'
Note: the specification for S3 class "cluster" in package 'NMF' seems equivalent to one from package 'BiocParallel': not turning on duplicate class definitions for this class.
install for x64
* installing *source* package 'Rariant' ...
** testing if installed package can be loaded
Note: the specification for S3 class "AsIs" in package 'RJSONIO' seems equivalent to one from package 'BiocGenerics': not turning on duplicate class definitions for this class.
Warning: replacing previous import by 'proxy::as.matrix' when loading 'SomaticSignatures'
Note: the specification for S3 class "cluster" in package 'NMF' seems equivalent to one from package 'BiocParallel': not turning on duplicate class definitions for this class.
* MD5 sums
packaged installation of 'Rariant' as Rariant_1.2.0.zip
* DONE (Rariant)