Multiple platform build/check report for BioC 3.14 - CHECK results for Rgraphviz on tokay2

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo2	Linux (Ubuntu 20.04.4 LTS)	x86_64	4.1.3 (2022-03-10) -- "One Push-Up"	4324
tokay2	Windows Server 2012 R2 Standard	x64	4.1.3 (2022-03-10) -- "One Push-Up"	4077
machv2	macOS 10.14.6 Mojave	x86_64	4.1.3 (2022-03-10) -- "One Push-Up"	4137
Click on any hostname to see more info about the system (e.g. compilers) () as reported by 'uname -p', except on Windows and Mac OS X*

Package: Rgraphviz

Version: 2.38.0

Command: C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:Rgraphviz.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings Rgraphviz_2.38.0.tar.gz

StartedAt: 2022-04-13 01:39:18 -0400 (Wed, 13 Apr 2022)

EndedAt: 2022-04-13 01:40:43 -0400 (Wed, 13 Apr 2022)

EllapsedTime: 85.0 seconds

RetCode: 0

Status: OK

CheckDir: Rgraphviz.Rcheck

Warnings: 0

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:Rgraphviz.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings Rgraphviz_2.38.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.14-bioc/meat/Rgraphviz.Rcheck'
* using R version 4.1.3 (2022-03-10)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'Rgraphviz/DESCRIPTION' ... OK
* this is package 'Rgraphviz' version '2.38.0'
* 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 'Rgraphviz' 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
There are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
  '.graphviz_build_version'
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* 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 line endings in shell scripts ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking use of PKG_*FLAGS in Makefiles ... OK
* checking include directives in Makefiles ... OK
* checking compiled code ... NOTE
Note: information on .o files for i386 is not available
Note: information on .o files for x64 is not available
File 'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rgraphviz/libs/i386/Rgraphviz.dll':
  Found '_exit', possibly from '_exit' (C)
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
  Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
  Found 'printf', possibly from 'printf' (C)
  Found 'putchar', possibly from 'putchar' (C)
  Found 'puts', possibly from 'printf' (C), 'puts' (C)
  Found 'rand', possibly from 'rand' (C)
  Found 'srand', possibly from 'srand' (C)
File 'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rgraphviz/libs/x64/Rgraphviz.dll':
  Found '_exit', possibly from '_exit' (C)
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
  Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
  Found 'printf', possibly from 'printf' (C)
  Found 'putchar', possibly from 'putchar' (C)
  Found 'puts', possibly from 'printf' (C), 'puts' (C)
  Found 'rand', possibly from 'rand' (C)
  Found 'srand', possibly from 'srand' (C)

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs. The detected symbols are linked into the code but
might come from libraries and not actually be called.

See 'Writing portable packages' in the 'Writing R Extensions' manual.
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
** running examples for arch 'x64' ... OK
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'runTests.R'
 OK
** running tests for arch 'x64' ...
  Running 'runTests.R'
 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-3.14-bioc/meat/Rgraphviz.Rcheck/00check.log'
for details.

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.14/bioc/src/contrib/Rgraphviz_2.38.0.tar.gz && rm -rf Rgraphviz.buildbin-libdir && mkdir Rgraphviz.buildbin-libdir && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=Rgraphviz.buildbin-libdir Rgraphviz_2.38.0.tar.gz && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL Rgraphviz_2.38.0.zip && rm Rgraphviz_2.38.0.tar.gz Rgraphviz_2.38.0.zip
###
##############################################################################
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  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
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  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
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 81 6786k   81 5505k    0     0  2037k      0  0:00:03  0:00:02  0:00:01 2037k
100 6786k  100 6786k    0     0  2210k      0  0:00:03  0:00:03 --:--:-- 2210k

install for i386

* installing *source* package 'Rgraphviz' ...
** using staged installation

   **********************************************
   WARNING: this package has a configure script
         It probably needs manual configuration
   **********************************************


** libs
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG     -I"C:/extsoft/include"  -Ilibwin/i386/include/graphviz -DHAVE_STDBOOL_H=1 -DHAVE_BOOL=1 -DGRAPHVIZ_MAJOR=2 -DGRAPHVIZ_MINOR=28 -DGRAPHVIZ_STATIC   -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c LL_funcs.c -o LL_funcs.o
LL_funcs.c: In function 'Rgraphviz_agopenSimple':
LL_funcs.c:430:29: warning: variable 'curNode' set but not used [-Wunused-but-set-variable]
     Agnode_t *head, *tail, *curNode;
                             ^~~~~~~
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG     -I"C:/extsoft/include"  -Ilibwin/i386/include/graphviz -DHAVE_STDBOOL_H=1 -DHAVE_BOOL=1 -DGRAPHVIZ_MAJOR=2 -DGRAPHVIZ_MINOR=28 -DGRAPHVIZ_STATIC   -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c Rgraphviz.c -o Rgraphviz.o
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG     -I"C:/extsoft/include"  -Ilibwin/i386/include/graphviz -DHAVE_STDBOOL_H=1 -DHAVE_BOOL=1 -DGRAPHVIZ_MAJOR=2 -DGRAPHVIZ_MINOR=28 -DGRAPHVIZ_STATIC   -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c RgraphvizInit.c -o RgraphvizInit.o
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG     -I"C:/extsoft/include"  -Ilibwin/i386/include/graphviz -DHAVE_STDBOOL_H=1 -DHAVE_BOOL=1 -DGRAPHVIZ_MAJOR=2 -DGRAPHVIZ_MINOR=28 -DGRAPHVIZ_STATIC   -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c agopen.c -o agopen.o
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG     -I"C:/extsoft/include"  -Ilibwin/i386/include/graphviz -DHAVE_STDBOOL_H=1 -DHAVE_BOOL=1 -DGRAPHVIZ_MAJOR=2 -DGRAPHVIZ_MINOR=28 -DGRAPHVIZ_STATIC   -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c agread.c -o agread.o
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG     -I"C:/extsoft/include"  -Ilibwin/i386/include/graphviz -DHAVE_STDBOOL_H=1 -DHAVE_BOOL=1 -DGRAPHVIZ_MAJOR=2 -DGRAPHVIZ_MINOR=28 -DGRAPHVIZ_STATIC   -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c agwrite.c -o agwrite.o
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG     -I"C:/extsoft/include"  -Ilibwin/i386/include/graphviz -DHAVE_STDBOOL_H=1 -DHAVE_BOOL=1 -DGRAPHVIZ_MAJOR=2 -DGRAPHVIZ_MINOR=28 -DGRAPHVIZ_STATIC   -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c bezier.c -o bezier.o
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG     -I"C:/extsoft/include"  -Ilibwin/i386/include/graphviz -DHAVE_STDBOOL_H=1 -DHAVE_BOOL=1 -DGRAPHVIZ_MAJOR=2 -DGRAPHVIZ_MINOR=28 -DGRAPHVIZ_STATIC   -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c buildEdgeList.c -o buildEdgeList.o
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG     -I"C:/extsoft/include"  -Ilibwin/i386/include/graphviz -DHAVE_STDBOOL_H=1 -DHAVE_BOOL=1 -DGRAPHVIZ_MAJOR=2 -DGRAPHVIZ_MINOR=28 -DGRAPHVIZ_STATIC   -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c buildNodeList.c -o buildNodeList.o
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG     -I"C:/extsoft/include"  -Ilibwin/i386/include/graphviz -DHAVE_STDBOOL_H=1 -DHAVE_BOOL=1 -DGRAPHVIZ_MAJOR=2 -DGRAPHVIZ_MINOR=28 -DGRAPHVIZ_STATIC   -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c doLayout.c -o doLayout.o
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG     -I"C:/extsoft/include"  -Ilibwin/i386/include/graphviz -DHAVE_STDBOOL_H=1 -DHAVE_BOOL=1 -DGRAPHVIZ_MAJOR=2 -DGRAPHVIZ_MINOR=28 -DGRAPHVIZ_STATIC   -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c graphvizVersion.c -o graphvizVersion.o
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG     -I"C:/extsoft/include"  -Ilibwin/i386/include/graphviz -DHAVE_STDBOOL_H=1 -DHAVE_BOOL=1 -DGRAPHVIZ_MAJOR=2 -DGRAPHVIZ_MINOR=28 -DGRAPHVIZ_STATIC   -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c init.c -o init.o
C:/rtools40/mingw32/bin/gcc -shared -s -static-libgcc -o Rgraphviz.dll tmp.def LL_funcs.o Rgraphviz.o RgraphvizInit.o agopen.o agread.o agwrite.o bezier.o buildEdgeList.o buildNodeList.o doLayout.o graphvizVersion.o init.o libwin/i386/lib/libxdot.a libwin/i386/lib/libgvplugin_dot_layout.a libwin/i386/lib/libgvplugin_neato_layout.a libwin/i386/lib/libgvplugin_core.a libwin/i386/lib/libgvc.a libwin/i386/lib/libpathplan.a libwin/i386/lib/libgraph.a libwin/i386/lib/libcdt.a -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.14-/R/bin/i386 -lR
sed "s!@GRAPHVIZ_VERSION@!"2.28.0"!" ../R/graphviz_build_version.R.in |\
  sed "s!@GRAPHVIZ_BUNDLED@!TRUE!" > ../R/graphviz_build_version.R
installing to C:/Users/biocbuild/bbs-3.14-bioc/meat/Rgraphviz.buildbin-libdir/00LOCK-Rgraphviz/00new/Rgraphviz/libs/i386
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'Rgraphviz'
    finding HTML links ... done
    AgEdge-class                            html  
    AgNode-class                            html  
    AgTextLabel-class                       html  
    BezierCurve-class                       html  
    GraphvizAttributes                      html  
    GraphvizLayouts                         html  
    Ragraph-class                           html  
    agopen                                  html  
    agopenSimple                            html  
    agwrite                                 html  
    boundingBox-class                       html  
    buildNodeList                           html  
    clusterData-methods                     html  
    getDefaultAttrs                         html  
    graphData-methods                       html  
    graphDataDefaults-methods               html  
    graphLayout                             html  
    graphvizCapabilities                    html  
    graphvizVersion                         html  
    layoutGraph                             html  
    makeNodeAttrs                           html  
    pEdge-class                             html  
    pNode-class                             html  
    pieGlyph                                html  
    plot-methods                            html  
    removedEdges                            html  
    renderGraph                             html  
    toDot-methods                           html  
    toFile                                  html  
    xyPoint-class                           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 'Rgraphviz' ...

   **********************************************
   WARNING: this package has a configure script
         It probably needs manual configuration
   **********************************************


** libs
"C:/rtools40/mingw64/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG     -I"C:/extsoft/include"  -Ilibwin/x64/include/graphviz -DHAVE_STDBOOL_H=1 -DHAVE_BOOL=1 -DGRAPHVIZ_MAJOR=2 -DGRAPHVIZ_MINOR=28 -DGRAPHVIZ_STATIC   -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c LL_funcs.c -o LL_funcs.o
LL_funcs.c: In function 'Rgraphviz_agopenSimple':
LL_funcs.c:430:29: warning: variable 'curNode' set but not used [-Wunused-but-set-variable]
     Agnode_t *head, *tail, *curNode;
                             ^~~~~~~
"C:/rtools40/mingw64/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG     -I"C:/extsoft/include"  -Ilibwin/x64/include/graphviz -DHAVE_STDBOOL_H=1 -DHAVE_BOOL=1 -DGRAPHVIZ_MAJOR=2 -DGRAPHVIZ_MINOR=28 -DGRAPHVIZ_STATIC   -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c Rgraphviz.c -o Rgraphviz.o
"C:/rtools40/mingw64/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG     -I"C:/extsoft/include"  -Ilibwin/x64/include/graphviz -DHAVE_STDBOOL_H=1 -DHAVE_BOOL=1 -DGRAPHVIZ_MAJOR=2 -DGRAPHVIZ_MINOR=28 -DGRAPHVIZ_STATIC   -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c RgraphvizInit.c -o RgraphvizInit.o
"C:/rtools40/mingw64/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG     -I"C:/extsoft/include"  -Ilibwin/x64/include/graphviz -DHAVE_STDBOOL_H=1 -DHAVE_BOOL=1 -DGRAPHVIZ_MAJOR=2 -DGRAPHVIZ_MINOR=28 -DGRAPHVIZ_STATIC   -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c agopen.c -o agopen.o
"C:/rtools40/mingw64/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG     -I"C:/extsoft/include"  -Ilibwin/x64/include/graphviz -DHAVE_STDBOOL_H=1 -DHAVE_BOOL=1 -DGRAPHVIZ_MAJOR=2 -DGRAPHVIZ_MINOR=28 -DGRAPHVIZ_STATIC   -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c agread.c -o agread.o
"C:/rtools40/mingw64/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG     -I"C:/extsoft/include"  -Ilibwin/x64/include/graphviz -DHAVE_STDBOOL_H=1 -DHAVE_BOOL=1 -DGRAPHVIZ_MAJOR=2 -DGRAPHVIZ_MINOR=28 -DGRAPHVIZ_STATIC   -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c agwrite.c -o agwrite.o
"C:/rtools40/mingw64/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG     -I"C:/extsoft/include"  -Ilibwin/x64/include/graphviz -DHAVE_STDBOOL_H=1 -DHAVE_BOOL=1 -DGRAPHVIZ_MAJOR=2 -DGRAPHVIZ_MINOR=28 -DGRAPHVIZ_STATIC   -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c bezier.c -o bezier.o
"C:/rtools40/mingw64/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG     -I"C:/extsoft/include"  -Ilibwin/x64/include/graphviz -DHAVE_STDBOOL_H=1 -DHAVE_BOOL=1 -DGRAPHVIZ_MAJOR=2 -DGRAPHVIZ_MINOR=28 -DGRAPHVIZ_STATIC   -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c buildEdgeList.c -o buildEdgeList.o
"C:/rtools40/mingw64/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG     -I"C:/extsoft/include"  -Ilibwin/x64/include/graphviz -DHAVE_STDBOOL_H=1 -DHAVE_BOOL=1 -DGRAPHVIZ_MAJOR=2 -DGRAPHVIZ_MINOR=28 -DGRAPHVIZ_STATIC   -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c buildNodeList.c -o buildNodeList.o
"C:/rtools40/mingw64/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG     -I"C:/extsoft/include"  -Ilibwin/x64/include/graphviz -DHAVE_STDBOOL_H=1 -DHAVE_BOOL=1 -DGRAPHVIZ_MAJOR=2 -DGRAPHVIZ_MINOR=28 -DGRAPHVIZ_STATIC   -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c doLayout.c -o doLayout.o
"C:/rtools40/mingw64/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG     -I"C:/extsoft/include"  -Ilibwin/x64/include/graphviz -DHAVE_STDBOOL_H=1 -DHAVE_BOOL=1 -DGRAPHVIZ_MAJOR=2 -DGRAPHVIZ_MINOR=28 -DGRAPHVIZ_STATIC   -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c graphvizVersion.c -o graphvizVersion.o
"C:/rtools40/mingw64/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG     -I"C:/extsoft/include"  -Ilibwin/x64/include/graphviz -DHAVE_STDBOOL_H=1 -DHAVE_BOOL=1 -DGRAPHVIZ_MAJOR=2 -DGRAPHVIZ_MINOR=28 -DGRAPHVIZ_STATIC   -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c init.c -o init.o
C:/rtools40/mingw64/bin/gcc -shared -s -static-libgcc -o Rgraphviz.dll tmp.def LL_funcs.o Rgraphviz.o RgraphvizInit.o agopen.o agread.o agwrite.o bezier.o buildEdgeList.o buildNodeList.o doLayout.o graphvizVersion.o init.o libwin/x64/lib/libxdot.a libwin/x64/lib/libgvplugin_dot_layout.a libwin/x64/lib/libgvplugin_neato_layout.a libwin/x64/lib/libgvplugin_core.a libwin/x64/lib/libgvc.a libwin/x64/lib/libpathplan.a libwin/x64/lib/libgraph.a libwin/x64/lib/libcdt.a -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.14-/R/bin/x64 -lR
sed "s!@GRAPHVIZ_VERSION@!"2.28.0"!" ../R/graphviz_build_version.R.in |\
  sed "s!@GRAPHVIZ_BUNDLED@!TRUE!" > ../R/graphviz_build_version.R
installing to C:/Users/biocbuild/bbs-3.14-bioc/meat/Rgraphviz.buildbin-libdir/Rgraphviz/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'Rgraphviz' as Rgraphviz_2.38.0.zip
* DONE (Rgraphviz)
* installing to library 'C:/Users/biocbuild/bbs-3.14-bioc/R/library'
package 'Rgraphviz' successfully unpacked and MD5 sums checked


R version 4.1.3 (2022-03-10) -- "One Push-Up"
Copyright (C) 2022 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> require("Rgraphviz") || stop("unable to load Rgraphviz")
Loading required package: Rgraphviz
Loading required package: graph
Loading required package: BiocGenerics

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, basename, cbind, colnames, dirname, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
    pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
    tapply, union, unique, unsplit, which.max, which.min

Loading required package: grid
[1] TRUE
> BiocGenerics:::testPackage("Rgraphviz")
plotting different layout types
   dot  .... done
   circo  .... done
   fdp  .... done
   neato  .... done
   osage  .... done
   twopi  .... done
using toFile with various device types
   canon . done
   cmap . done
   cmapx . done
   cmapx_np . done
   dot . done
   eps . done
   fig . done
   gv . done
   imap . done
   imap_np . done
   ismap . done
   plain . done
   plain-ext . done
   ps . done
   ps2 . done
   svg . done
   tk . done
   vml . done
   xdot . done


RUNIT TEST PROTOCOL -- Wed Apr 13 01:40:32 2022 
*********************************************** 
Number of test functions: 4 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
Rgraphviz RUnit Tests - 4 test functions, 0 errors, 0 failures
Number of test functions: 4 
Number of errors: 0 
Number of failures: 0 
> 
> proc.time()
   user  system elapsed 
   1.76    0.04    1.79


R version 4.1.3 (2022-03-10) -- "One Push-Up"
Copyright (C) 2022 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> require("Rgraphviz") || stop("unable to load Rgraphviz")
Loading required package: Rgraphviz
Loading required package: graph
Loading required package: BiocGenerics

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, basename, cbind, colnames, dirname, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
    pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
    tapply, union, unique, unsplit, which.max, which.min

Loading required package: grid
[1] TRUE
> BiocGenerics:::testPackage("Rgraphviz")
plotting different layout types
   dot  .... done
   circo  .... done
   fdp  .... done
   neato  .... done
   osage  .... done
   twopi  .... done
using toFile with various device types
   canon . done
   cmap . done
   cmapx . done
   cmapx_np . done
   dot . done
   eps . done
   fig . done
   gv . done
   imap . done
   imap_np . done
   ismap . done
   plain . done
   plain-ext . done
   ps . done
   ps2 . done
   svg . done
   tk . done
   vml . done
   xdot . done


RUNIT TEST PROTOCOL -- Wed Apr 13 01:40:34 2022 
*********************************************** 
Number of test functions: 4 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
Rgraphviz RUnit Tests - 4 test functions, 0 errors, 0 failures
Number of test functions: 4 
Number of errors: 0 
Number of failures: 0 
> 
> proc.time()
   user  system elapsed 
   1.67    0.09    1.76

name	user	system	elapsed
AgEdge-class	0.04	0.00	0.03
AgNode-class	0	0	0
AgTextLabel-class	0.02	0.00	0.01
BezierCurve-class	0.00	0.01	0.02
GraphvizLayouts	0	0	0
Ragraph-class	0.01	0.00	0.02
agopen	0.02	0.00	0.01
agopenSimple	0.06	0.00	0.06
agwrite	0	0	0
boundingBox-class	0.02	0.00	0.02
buildNodeList	0	0	0
clusterData-methods	0.17	0.00	0.20
getDefaultAttrs	0	0	0
graphLayout	0	0	0
graphvizCapabilities	0.01	0.00	0.02
graphvizVersion	0	0	0
layoutGraph	0.29	0.00	0.28
makeNodeAttrs	0	0	0
pEdge-class	0.01	0.00	0.02
pNode-class	0	0	0
pieGlyph	0.02	0.00	0.01
plot-methods	0	0	0
removedEdges	0	0	0
renderGraph	0.08	0.02	0.10
toDot-methods	0.01	0.00	0.01
toFile	0.05	0.00	0.05
xyPoint-class	0	0	0

name	user	system	elapsed
AgEdge-class	0.05	0.00	0.05
AgNode-class	0	0	0
AgTextLabel-class	0.02	0.00	0.02
BezierCurve-class	0	0	0
GraphvizLayouts	0	0	0
Ragraph-class	0.03	0.00	0.03
agopen	0.01	0.00	0.02
agopenSimple	0.07	0.00	0.06
agwrite	0.01	0.00	0.01
boundingBox-class	0	0	0
buildNodeList	0	0	0
clusterData-methods	0.19	0.02	0.47
getDefaultAttrs	0	0	0
graphLayout	0.02	0.00	0.02
graphvizCapabilities	0	0	0
graphvizVersion	0	0	0
layoutGraph	0.32	0.00	0.33
makeNodeAttrs	0	0	0
pEdge-class	0.02	0.00	0.01
pNode-class	0	0	0
pieGlyph	0.02	0.00	0.02
plot-methods	0	0	0
removedEdges	0.01	0.00	0.02
renderGraph	0.10	0.00	0.09
toDot-methods	0.01	0.00	0.01
toFile	0.05	0.00	0.05
xyPoint-class	0.01	0.00	0.02

CHECK results for Rgraphviz on tokay2

Summary

Command output

Installation output

Tests output

Example timings