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CHECK report for SBMLR on tokay1

This page was generated on 2019-04-13 11:19:32 -0400 (Sat, 13 Apr 2019).

Package 1387/1649HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
SBMLR 1.78.0
Tomas Radivoyevitch
Snapshot Date: 2019-04-12 17:01:30 -0400 (Fri, 12 Apr 2019)
URL: https://git.bioconductor.org/packages/SBMLR
Branch: RELEASE_3_8
Last Commit: 1985c63
Last Changed Date: 2018-10-30 11:41:42 -0400 (Tue, 30 Oct 2018)
malbec1 Linux (Ubuntu 16.04.6 LTS) / x86_64  OK  OK  OK 
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository
merida1 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: SBMLR
Version: 1.78.0
Command: C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:SBMLR.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings SBMLR_1.78.0.tar.gz
StartedAt: 2019-04-13 05:19:17 -0400 (Sat, 13 Apr 2019)
EndedAt: 2019-04-13 05:21:00 -0400 (Sat, 13 Apr 2019)
EllapsedTime: 102.8 seconds
RetCode: 0
Status:  OK  
CheckDir: SBMLR.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:SBMLR.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings SBMLR_1.78.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.8-bioc/meat/SBMLR.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 'SBMLR/DESCRIPTION' ... OK
* this is package 'SBMLR' version '1.78.0'
* 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 '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
* 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
'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 ...
** 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: 2 NOTEs
See
  'C:/Users/biocbuild/bbs-3.8-bioc/meat/SBMLR.Rcheck/00check.log'
for details.



Installation output

SBMLR.Rcheck/00install.out

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.8/bioc/src/contrib/SBMLR_1.78.0.tar.gz && rm -rf SBMLR.buildbin-libdir && mkdir SBMLR.buildbin-libdir && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=SBMLR.buildbin-libdir SBMLR_1.78.0.tar.gz && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL SBMLR_1.78.0.zip && rm SBMLR_1.78.0.tar.gz SBMLR_1.78.0.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 75834  100 75834    0     0  2200k      0 --:--:-- --:--:-- --:--:-- 2468k

install for i386

* installing *source* package 'SBMLR' ...
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'SBMLR'
    finding HTML links ... done
    Ops.SBMLR                               html  
    S4toS3                                  html  
    readSBML                                html  
    readSBMLR                               html  
    saveSBML                                html  
    saveSBMLR                               html  
    sim                                     html  
    summary.SBMLR                           html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL

install for x64

* installing *source* package 'SBMLR' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'SBMLR' as SBMLR_1.78.0.zip
* DONE (SBMLR)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.8-bioc/R/library'
package 'SBMLR' successfully unpacked and MD5 sums checked
In R CMD INSTALL

Tests output


Example timings

SBMLR.Rcheck/examples_i386/SBMLR-Ex.timings

nameusersystemelapsed
Ops.SBMLR0.550.000.62
S4toS30.730.011.27
readSBML0.380.000.38
readSBMLR0.440.000.43
saveSBML0.530.050.58
saveSBMLR0.590.000.59
sim3.750.063.86
summary.SBMLR0.280.020.30

SBMLR.Rcheck/examples_x64/SBMLR-Ex.timings

nameusersystemelapsed
Ops.SBMLR0.710.000.72
S4toS30.820.001.16
readSBML0.420.010.44
readSBMLR0.450.030.48
saveSBML0.610.020.63
saveSBMLR0.670.000.67
sim4.040.054.08
summary.SBMLR0.320.000.32