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BioC 3.2: CHECK report for myvariant on windows1.bioconductor.org

This page was generated on 2015-10-27 17:32:30 -0400 (Tue, 27 Oct 2015).

Package 691/1104HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
myvariant 1.0.1
Adam Mark, Chunlei Wu
Snapshot Date: 2015-10-26 19:24:07 -0400 (Mon, 26 Oct 2015)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_2/madman/Rpacks/myvariant
Last Changed Rev: 109637 / Revision: 109947
Last Changed Date: 2015-10-14 18:00:38 -0400 (Wed, 14 Oct 2015)
linux1.bioconductor.org Linux (Ubuntu 14.04.2 LTS) / x86_64  NotNeeded  OK  OK UNNEEDED, same version exists in internal repository
windows1.bioconductor.org Windows Server 2012 R2 Enterprise SP1 (64-bit) / x64  NotNeeded  OK [ OK ] OK UNNEEDED, same version exists in internal repository
perceval Mac OS X Snow Leopard (10.6.8) / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: myvariant
Version: 1.0.1
Command: rm -rf myvariant.buildbin-libdir myvariant.Rcheck && mkdir myvariant.buildbin-libdir myvariant.Rcheck && C:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=myvariant.buildbin-libdir myvariant_1.0.1.tar.gz >myvariant.Rcheck\00install.out 2>&1 && cp myvariant.Rcheck\00install.out myvariant-install.out && C:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD check --library=myvariant.buildbin-libdir --install="check:myvariant-install.out" --force-multiarch --no-vignettes --timings myvariant_1.0.1.tar.gz
StartedAt: 2015-10-27 03:57:29 -0400 (Tue, 27 Oct 2015)
EndedAt: 2015-10-27 04:01:50 -0400 (Tue, 27 Oct 2015)
EllapsedTime: 261.3 seconds
RetCode: 0
Status:  OK  
CheckDir: myvariant.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf myvariant.buildbin-libdir myvariant.Rcheck && mkdir myvariant.buildbin-libdir myvariant.Rcheck && C:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=myvariant.buildbin-libdir myvariant_1.0.1.tar.gz >myvariant.Rcheck\00install.out 2>&1 && cp myvariant.Rcheck\00install.out myvariant-install.out  && C:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD check --library=myvariant.buildbin-libdir --install="check:myvariant-install.out" --force-multiarch --no-vignettes --timings myvariant_1.0.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/biocbld/bbs-3.2-bioc/meat/myvariant.Rcheck'
* using R version 3.2.2 Patched (2015-08-16 r69094)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'myvariant/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'myvariant' version '1.0.1'
* 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 'myvariant' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Description field: should contain one or more complete sentences.
* 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 ... NOTE
package 'methods' is used but not declared
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
.getIndels: no visible binding for global variable 'REF'
.getIndels: no visible binding for global variable 'ALT'
formatHgvs: no visible global function definition for
  'seqlevelsStyle<-'
* 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' ... [11s] OK
** running examples for arch 'x64' ... [12s] 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: 3 NOTEs
See
  'C:/biocbld/bbs-3.2-bioc/meat/myvariant.Rcheck/00check.log'
for details.


myvariant.Rcheck/00install.out:


install for i386

* installing *source* package 'myvariant' ...
** R
** inst
** preparing package for lazy loading
Note: the specification for S3 class "AsIs" in package 'jsonlite' seems equivalent to one from package 'BiocGenerics': 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 'jsonlite' seems equivalent to one from package 'BiocGenerics': not turning on duplicate class definitions for this class.

install for x64

* installing *source* package 'myvariant' ...
** testing if installed package can be loaded
Note: the specification for S3 class "AsIs" in package 'jsonlite' seems equivalent to one from package 'BiocGenerics': not turning on duplicate class definitions for this class.
* MD5 sums
packaged installation of 'myvariant' as myvariant_1.0.1.zip
* DONE (myvariant)

myvariant.Rcheck/examples_i386/myvariant-Ex.timings:

nameusersystemelapsed
MyVariant-class000
MyVariant000
formatHgvs0.360.030.39
formatSingleHgvs000
getVariant0.080.000.31
getVariants0.150.090.44
metadata0.000.000.08
queryVariant0.220.021.81
queryVariants000

myvariant.Rcheck/examples_x64/myvariant-Ex.timings:

nameusersystemelapsed
MyVariant-class000
MyVariant000
formatHgvs0.470.020.48
formatSingleHgvs000
getVariant0.060.010.31
getVariants0.170.080.44
metadata0.000.000.08
queryVariant0.410.001.88
queryVariants000