Package: SBMLR

Version: 1.79.0

Command: /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:SBMLR.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings SBMLR_1.79.0.tar.gz

StartedAt: 2019-04-09 03:27:33 -0400 (Tue, 09 Apr 2019)

EndedAt: 2019-04-09 03:28:19 -0400 (Tue, 09 Apr 2019)

EllapsedTime: 45.3 seconds

RetCode: 0

Status:  OK

CheckDir: SBMLR.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:SBMLR.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings SBMLR_1.79.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.9-bioc/meat/SBMLR.Rcheck’
* using R Under development (unstable) (2019-03-18 r76245)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘SBMLR/DESCRIPTION’ ... OK
* this is package ‘SBMLR’ version ‘1.79.0’
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘SBMLR’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* 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
* 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
'library' or 'require' call to ‘XML’ which was already attached by Depends.
  Please remove these calls from your code.
'library' or 'require' call to ‘rsbml’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Packages in Depends field not imported from:
  ‘XML’ ‘deSolve’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
There are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
  ‘R2MathML’ ‘getRuleLeaves’ ‘makeLaw’
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
R2MathML: no visible global function definition for ‘xmlOutputDOM’
S4toS3: no visible global function definition for ‘model’
S4toS3: no visible global function definition for ‘id’
S4toS3: no visible global function definition for ‘size’
S4toS3: no visible global function definition for
  ‘initialConcentration’
S4toS3: no visible global function definition for ‘compartment’
S4toS3: no visible global function definition for ‘boundaryCondition’
S4toS3: no visible binding for global variable ‘value’
S4toS3: no visible binding for global variable ‘id’
S4toS3: no visible global function definition for ‘math’
S4toS3: no visible global function definition for ‘variable’
S4toS3: no visible global function definition for ‘kineticLaw’
S4toS3: no visible global function definition for ‘reactants’
S4toS3: no visible global function definition for ‘modifiers’
S4toS3: no visible global function definition for ‘products’
S4toS3: no visible global function definition for ‘reversible’
S4toS3: no visible global function definition for ‘notes’
getRuleLeaves: no visible global function definition for ‘xmlName’
getRuleLeaves: no visible global function definition for ‘xmlValue’
readSBML : mathml2R.XMLNode: no visible global function definition for
  ‘xmlName’
readSBML: no visible global function definition for ‘xmlEventParse’
readSBML: no visible global function definition for ‘xmlTreeParse’
readSBMLR: no visible global function definition for ‘xmlOutputDOM’
readSBMLR: no visible global function definition for ‘xmlTextNode’
saveSBML: no visible global function definition for ‘saveXML’
sim: no visible global function definition for ‘ode’
Undefined global functions or variables:
  boundaryCondition compartment id initialConcentration kineticLaw math
  model modifiers notes ode products reactants reversible saveXML size
  value variable xmlEventParse xmlName xmlOutputDOM xmlTextNode
  xmlTreeParse xmlValue
* 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 ... OK
Examples with CPU or elapsed time > 5s
     user system elapsed
sim 6.312  0.028   6.525
* 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: 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.9-bioc/meat/SBMLR.Rcheck/00check.log’
for details.

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### Running command:
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###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD INSTALL SBMLR
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* installing to library ‘/home/biocbuild/bbs-3.9-bioc/R/library’
* installing *source* package ‘SBMLR’ ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** 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
* DONE (SBMLR)

name	user	system	elapsed
Ops.SBMLR	0.641	0.000	0.689
S4toS3	1.118	0.015	1.203
readSBML	0.597	0.000	0.599
readSBMLR	0.619	0.016	0.644
saveSBML	0.773	0.008	0.805
saveSBMLR	1.110	0.008	1.200
sim	6.312	0.028	6.525
summary.SBMLR	0.504	0.004	0.519