Multiple platform build/check report for BioC 3.9 - CHECK report for ENVISIONQuery on tokay2

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### Running command:
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###   C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:ENVISIONQuery.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings ENVISIONQuery_1.31.0.tar.gz
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* using log directory 'C:/Users/biocbuild/bbs-3.9-bioc/meat/ENVISIONQuery.Rcheck'
* using R Under development (unstable) (2019-03-09 r76216)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'ENVISIONQuery/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'ENVISIONQuery' version '1.31.0'
* 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 ... NOTE
Found the following hidden files and directories:
  .BBSoptions
These were most likely included in error. See section 'Package
structure' in the 'Writing R Extensions' manual.
* checking for portable file names ... OK
* checking whether package 'ENVISIONQuery' 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
Packages in Depends field not imported from:
  'XML' 'rJava'
  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
NB: .First.lib is obsolete and will not be used in R >= 3.0.0
File 'ENVISIONQuery/R/zzz.R':
  .onAttach calls:
    cat("This is ", pkgname, " ", desc$Version, " ", desc$Date, "\n")

Package startup functions should use 'packageStartupMessage' to
  generate messages.
See section 'Good practice' in '?.onAttach'.

.First.lib: no visible global function definition for 'data'
.onAttach : getJavaVersion: no visible global function definition for
  '.jcall'
.onAttach : jpackage: no visible binding for global variable
  '.jniInitialized'
.onAttach : jpackage: no visible global function definition for
  '.jinit'
.onAttach : jpackage: no visible global function definition for
  '.jaddClassPath'
.onAttach : jpackage: no visible global function definition for
  '.jaddLibrary'
.onAttach: no visible global function definition for
  'packageDescription'
ENVISIONQuery.chunk: no visible global function definition for
  '.jarray'
formatIdMap: no visible global function definition for 'xmlTreeParse'
formatIdMap: no visible global function definition for 'xmlRoot'
formatIdMap: no visible global function definition for 'xmlChildren'
formatIntact: no visible global function definition for 'xmlTreeParse'
formatIntact: no visible global function definition for 'xmlRoot'
formatIntact: no visible global function definition for 'xmlChildren'
formatPicr: no visible global function definition for 'xmlTreeParse'
formatPicr: no visible global function definition for 'xmlRoot'
formatPicr: no visible global function definition for 'xmlChildren'
formatReactome: no visible global function definition for
  'xmlTreeParse'
formatReactome: no visible global function definition for 'xmlRoot'
formatReactome: no visible global function definition for 'xmlChildren'
getIdEntries: no visible global function definition for 'xmlChildren'
getIdEntries : <anonymous>: no visible global function definition for
  'xmlAttrs'
getIdMatchInfo: no visible global function definition for 'xmlChildren'
getIdMatchInfo : <anonymous>: no visible global function definition for
  'xmlAttrs'
getIdMatchInfo : <anonymous>: no visible global function definition for
  'xmlValue'
getIdMatchInfo : <anonymous>: no visible global function definition for
  'xmlChildren'
getInputIdEntries: no visible global function definition for
  'xmlChildren'
getInputIdEntries : <anonymous>: no visible global function definition
  for 'xmlAttrs'
getIntactMatchInfo: no visible global function definition for
  'xmlChildren'
getIntactMatchInfo : <anonymous>: no visible global function definition
  for 'xmlAttrs'
getIntactMatchInfo: no visible global function definition for
  'xmlAttrs'
getPicrMatchInfo: no visible global function definition for
  'xmlChildren'
getPicrMatchInfo : <anonymous>: no visible global function definition
  for 'xmlAttrs'
getPicrMatchInfo: no visible global function definition for 'xmlAttrs'
getPositiveResultSetIDs: no visible global function definition for
  'xmlChildren'
getPositiveResultSetIDs: no visible global function definition for
  'xmlAttrs'
getPositiveResultSetIDs : <anonymous>: no visible global function
  definition for 'xmlAttrs'
getReactomeMatchInfo: no visible global function definition for
  'xmlChildren'
getReactomeMatchInfo : <anonymous>: no visible global function
  definition for 'xmlAttrs'
getReactomeMatchInfo: no visible global function definition for
  'xmlValue'
getReactomeMatchInfo: no visible global function definition for
  'xmlAttrs'
getService: no visible global function definition for 'menu'
getServices: no visible global function definition for
  'assignInNamespace'
getTool: no visible global function definition for 'menu'
progressMsg: no visible global function definition for 'flush.console'
registerServices: no visible global function definition for 'new'
registerServices: no visible global function definition for 'J'
Undefined global functions or variables:
  .jaddClassPath .jaddLibrary .jarray .jcall .jinit .jniInitialized J
  assignInNamespace data flush.console menu new packageDescription
  xmlAttrs xmlChildren xmlRoot xmlTreeParse xmlValue
Consider adding
  importFrom("methods", "new")
  importFrom("utils", "assignInNamespace", "data", "flush.console",
             "menu", "packageDescription")
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: 4 NOTEs
See
  'C:/Users/biocbuild/bbs-3.9-bioc/meat/ENVISIONQuery.Rcheck/00check.log'
for details.

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###
### Running command:
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###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.9/bioc/src/contrib/ENVISIONQuery_1.31.0.tar.gz && rm -rf ENVISIONQuery.buildbin-libdir && mkdir ENVISIONQuery.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=ENVISIONQuery.buildbin-libdir ENVISIONQuery_1.31.0.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL ENVISIONQuery_1.31.0.zip && rm ENVISIONQuery_1.31.0.tar.gz ENVISIONQuery_1.31.0.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  542k  100  542k    0     0  8535k      0 --:--:-- --:--:-- --:--:-- 9680k

install for i386

* installing *source* package 'ENVISIONQuery' ...
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'ENVISIONQuery'
    finding HTML links ... done
    ENVISIONQuery-package                   html  
    ENVISIONQuery                           html  
    ENVISIONQuery.chunk                     html  
    ENVISIONQuery.loop                      html  
    ENVISIONServices                        html  
    formatIdMap                             html  
    formatIntact                            html  
    formatPicr                              html  
    formatReactome                          html  
    getFormatter                            html  
    getIdEntries                            html  
    getIdMatchInfo                          html  
    getInputIdEntries                       html  
    getInputTypes                           html  
    getIntactMatchInfo                      html  
    getMerger                               html  
    getPicrMatchInfo                        html  
    getPositiveResultSetIDs                 html  
    getReactomeMatchInfo                    html  
    getService                              html  
    getServiceClient                        html  
    getServiceNames                         html  
    getServiceOptions                       html  
    getServices                             html  
    getTool                                 html  
    getToolNames                            html  
    jgetOptions                             html  
    mergeFrameList                          html  
    mergeMatchRows                          html  
    progressMsg                             html  
    registerServices                        html  
    toChunks                                html  
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
This is  ENVISIONQuery   1.31.0   2013-08-20 
** testing if installed package can be loaded from final location
This is  ENVISIONQuery   1.31.0   2013-08-20 
** testing if installed package keeps a record of temporary installation path

install for x64

* installing *source* package 'ENVISIONQuery' ...
** testing if installed package can be loaded
This is  ENVISIONQuery   1.31.0   2013-08-20 
* MD5 sums
packaged installation of 'ENVISIONQuery' as ENVISIONQuery_1.31.0.zip
* DONE (ENVISIONQuery)
* installing to library 'C:/Users/biocbuild/bbs-3.9-bioc/R/library'
package 'ENVISIONQuery' successfully unpacked and MD5 sums checked

CHECK report for ENVISIONQuery on tokay2

Summary

Command output

Installation output

Tests output

Example timings