Back to the "Multiple platform build/check report" A  B  C  D [E] F  G  H  I  J  K  L  M  N  O  P  Q  R  S  T  U  V  W  X  Y  Z 

BioC 3.5: CHECK report for ENVISIONQuery on tokay2

This page was generated on 2017-08-16 13:20:58 -0400 (Wed, 16 Aug 2017).

Package 405/1382HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ENVISIONQuery 1.24.0
Alex Lisovich , Roger Day
Snapshot Date: 2017-08-15 17:17:57 -0400 (Tue, 15 Aug 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_5/madman/Rpacks/ENVISIONQuery
Last Changed Rev: 129126 / Revision: 131943
Last Changed Date: 2017-04-24 15:25:24 -0400 (Mon, 24 Apr 2017)
malbec2 Linux (Ubuntu 16.04.1 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
veracruz2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: ENVISIONQuery
Version: 1.24.0
Command: rm -rf ENVISIONQuery.buildbin-libdir ENVISIONQuery.Rcheck && mkdir ENVISIONQuery.buildbin-libdir ENVISIONQuery.Rcheck && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=ENVISIONQuery.buildbin-libdir ENVISIONQuery_1.24.0.tar.gz >ENVISIONQuery.Rcheck\00install.out 2>&1 && cp ENVISIONQuery.Rcheck\00install.out ENVISIONQuery-install.out && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD check --library=ENVISIONQuery.buildbin-libdir --install="check:ENVISIONQuery-install.out" --force-multiarch --no-vignettes --timings ENVISIONQuery_1.24.0.tar.gz
StartedAt: 2017-08-15 23:32:45 -0400 (Tue, 15 Aug 2017)
EndedAt: 2017-08-15 23:33:45 -0400 (Tue, 15 Aug 2017)
EllapsedTime: 59.7 seconds
RetCode: 0
Status:  OK  
CheckDir: ENVISIONQuery.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf ENVISIONQuery.buildbin-libdir ENVISIONQuery.Rcheck && mkdir ENVISIONQuery.buildbin-libdir ENVISIONQuery.Rcheck && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=ENVISIONQuery.buildbin-libdir ENVISIONQuery_1.24.0.tar.gz >ENVISIONQuery.Rcheck\00install.out 2>&1 && cp ENVISIONQuery.Rcheck\00install.out ENVISIONQuery-install.out  &&  C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD check --library=ENVISIONQuery.buildbin-libdir --install="check:ENVISIONQuery-install.out" --force-multiarch --no-vignettes --timings ENVISIONQuery_1.24.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.5-bioc/meat/ENVISIONQuery.Rcheck'
* using R version 3.4.1 (2017-06-30)
* 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 '1.24.0'
* 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 installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
              user system elapsed
ENVISIONQuery 0.89   0.14    6.05
** 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-3.5-bioc/meat/ENVISIONQuery.Rcheck/00check.log'
for details.


ENVISIONQuery.Rcheck/00install.out:


install for i386

* installing *source* package 'ENVISIONQuery' ...
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
This is  ENVISIONQuery   1.24.0   2013-08-20 

install for x64

* installing *source* package 'ENVISIONQuery' ...
** testing if installed package can be loaded
This is  ENVISIONQuery   1.24.0   2013-08-20 
* MD5 sums
packaged installation of 'ENVISIONQuery' as ENVISIONQuery_1.24.0.zip
* DONE (ENVISIONQuery)

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

nameusersystemelapsed
ENVISIONQuery0.890.146.05
getInputTypes000
getService000
getServiceClient000
getServiceNames000
getServiceOptions0.030.020.13
getServices000
getTool000
getToolNames000

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

nameusersystemelapsed
ENVISIONQuery2.120.172.79
getInputTypes000
getService000
getServiceClient000
getServiceNames000
getServiceOptions0.040.000.05
getServices000
getTool0.020.000.02
getToolNames000