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CHECK report for myvariant on tokay2

This page was generated on 2019-10-16 12:33:53 -0400 (Wed, 16 Oct 2019).

Package 1078/1741HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
myvariant 1.14.0
Adam Mark, Chunlei Wu
Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019)
URL: https://git.bioconductor.org/packages/myvariant
Branch: RELEASE_3_9
Last Commit: 6a1503a
Last Changed Date: 2019-05-02 11:53:57 -0400 (Thu, 02 May 2019)
malbec2 Linux (Ubuntu 18.04.2 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository
celaya2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: myvariant
Version: 1.14.0
Command: C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:myvariant.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings myvariant_1.14.0.tar.gz
StartedAt: 2019-10-16 05:30:26 -0400 (Wed, 16 Oct 2019)
EndedAt: 2019-10-16 05:36:24 -0400 (Wed, 16 Oct 2019)
EllapsedTime: 358.5 seconds
RetCode: 0
Status:  OK  
CheckDir: myvariant.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:myvariant.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings myvariant_1.14.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.9-bioc/meat/myvariant.Rcheck'
* using R version 3.6.1 (2019-07-05)
* 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 '1.14.0'
* 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
* 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 : : no visible global function definition for
  'is'
.unnest.df : : 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-3.9-bioc/meat/myvariant.Rcheck/00check.log'
for details.



Installation output

myvariant.Rcheck/00install.out

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.9/bioc/src/contrib/myvariant_1.14.0.tar.gz && rm -rf myvariant.buildbin-libdir && mkdir myvariant.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=myvariant.buildbin-libdir myvariant_1.14.0.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL myvariant_1.14.0.zip && rm myvariant_1.14.0.tar.gz myvariant_1.14.0.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
  0 17644    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100 17644  100 17644    0     0   262k      0 --:--:-- --:--:-- --:--:--  292k

install for i386

* installing *source* package 'myvariant' ...
** using staged installation
** 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 from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path

install for x64

* installing *source* package 'myvariant' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'myvariant' as myvariant_1.14.0.zip
* DONE (myvariant)
* installing to library 'C:/Users/biocbuild/bbs-3.9-bioc/R/library'
package 'myvariant' successfully unpacked and MD5 sums checked

Tests output


Example timings

myvariant.Rcheck/examples_i386/myvariant-Ex.timings

nameusersystemelapsed
MyVariant-class000
MyVariant0.020.000.02
formatHgvs0.810.031.71
formatSingleHgvs000
getVariant0.090.010.38
getVariants0.070.000.20
metadata0.010.000.11
queryVariant0.040.000.38
queryVariants000

myvariant.Rcheck/examples_x64/myvariant-Ex.timings

nameusersystemelapsed
MyVariant-class000
MyVariant000
formatHgvs0.700.020.72
formatSingleHgvs000
getVariant0.060.010.34
getVariants0.100.000.24
metadata0.010.000.11
queryVariant0.080.000.39
queryVariants000