Package: myvariant

Version: 1.12.0

Command: C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:myvariant.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings myvariant_1.12.0.tar.gz

StartedAt: 2019-04-13 04:06:37 -0400 (Sat, 13 Apr 2019)

EndedAt: 2019-04-13 04:12:17 -0400 (Sat, 13 Apr 2019)

EllapsedTime: 340.9 seconds

RetCode: 0

Status:  OK

CheckDir: myvariant.Rcheck

Warnings: 0

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### Running command:
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###   C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:myvariant.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings myvariant_1.12.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.8-bioc/meat/myvariant.Rcheck'
* using R version 3.5.3 (2019-03-11)
* 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 '1.12.0'
* checking package namespace information ... OK
* checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
  cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
 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
* 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
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
.convertColumn4csv: no visible binding for global variable 'is'
.df2DF: no visible binding for global variable 'as'
.getIndels: no visible binding for global variable 'REF'
.getIndels: no visible binding for global variable 'ALT'
.unnest.df : <anonymous>: no visible global function definition for
  'is'
.unnest.df : <anonymous>: no visible global function definition for
  'setNames'
MyVariant: no visible global function definition for 'new'
formatHgvs: no visible global function definition for
  'seqlevelsStyle<-'
validMyVariantObject: no visible global function definition for 'slot'
.request.get,MyVariant: no visible global function definition for
  'capture.output'
.request.post,MyVariant: no visible global function definition for
  'capture.output'
Undefined global functions or variables:
  ALT REF as capture.output is new seqlevelsStyle<- setNames slot
Consider adding
  importFrom("methods", "as", "is", "new", "slot")
  importFrom("stats", "setNames")
  importFrom("utils", "capture.output")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* 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 files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
** running examples for arch 'x64' ... 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:/Users/biocbuild/bbs-3.8-bioc/meat/myvariant.Rcheck/00check.log'
for details.

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.8/bioc/src/contrib/myvariant_1.12.0.tar.gz && rm -rf myvariant.buildbin-libdir && mkdir myvariant.buildbin-libdir && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=myvariant.buildbin-libdir myvariant_1.12.0.tar.gz && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL myvariant_1.12.0.zip && rm myvariant_1.12.0.tar.gz myvariant_1.12.0.zip
###
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  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100 17332  100 17332    0     0   429k      0 --:--:-- --:--:-- --:--:--  483k

install for i386

* installing *source* package 'myvariant' ...
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'myvariant'
    finding HTML links ... done
    MyVariant-class                         html  
    MyVariant                               html  
    formatHgvs                              html  
    finding level-2 HTML links ... done

    formatSingleHgvs                        html  
    getVariant                              html  
    getVariants                             html  
    metadata                                html  
    myvariant-package                       html  
    queryVariant                            html  
    queryVariants                           html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL

install for x64

* installing *source* package 'myvariant' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'myvariant' as myvariant_1.12.0.zip
* DONE (myvariant)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.8-bioc/R/library'
package 'myvariant' successfully unpacked and MD5 sums checked
In R CMD INSTALL