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### Running command:
###
###   D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:RBioinf.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings RBioinf_1.55.0.tar.gz
###
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* using log directory 'D:/biocbuild/bbs-3.15-bioc/meat/RBioinf.Rcheck'
* using R Under development (unstable) (2021-11-21 r81221)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'RBioinf/DESCRIPTION' ... OK
* this is package 'RBioinf' version '1.55.0'
* 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 'RBioinf' can be installed ... OK
* checking installed package size ... NOTE
  installed size is 12.5Mb
  sub-directories of 1Mb or more:
    extdata  12.3Mb
* 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
Packages in Depends field not imported from:
  'graph' 'methods'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Unexported object imported by a ':::' call: 'methods:::.getMethodsTable'
  See the note in ?`:::` about the use of this operator.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
class2Graph: warning in matrix(0, nr = nN, nc = nN): partial argument
  match of 'nr' to 'nrow'
class2Graph: warning in matrix(0, nr = nN, nc = nN): partial argument
  match of 'nc' to 'ncol'
LPO: no visible global function definition for 'getClass'
OLDcplList: no visible global function definition for
  'getAllSuperClasses'
OLDcplList: no visible global function definition for 'getClass'
S4Help: no visible global function definition for 'isClass'
S4Help: no visible global function definition for 'getAllSuperClasses'
S4Help: no visible global function definition for 'getClass'
S4Help: no visible global function definition for 'menu'
S4Help: no visible global function definition for 'isGeneric'
S4Help: no visible global function definition for 'getGeneric'
S4Help: no visible binding for global variable 'help'
candidateDirectSC: no visible global function definition for 'getClass'
class2Graph: no visible global function definition for 'is'
class2Graph: no visible global function definition for 'getClass'
class2Graph: no visible global function definition for
  'getAllSuperClasses'
class2Graph: no visible global function definition for 'new'
class2Graph: no visible global function definition for 'as'
classList2Graph: no visible global function definition for 'join'
computeClassLinearization: no visible global function definition for
  'getClass'
printWithNumbers: no visible global function definition for 'is'
subClassNames: no visible global function definition for 'isClassDef'
subClassNames: no visible global function definition for 'getClass'
superClassNames: no visible global function definition for 'isClassDef'
superClassNames: no visible global function definition for 'getClass'
superClasses: no visible global function definition for 'is'
traceMethods: no visible global function definition for 'isGeneric'
traceMethods: no visible global function definition for 'showMethods'
Undefined global functions or variables:
  as getAllSuperClasses getClass getGeneric help is isClass isClassDef
  isGeneric join menu new showMethods
Consider adding
  importFrom("methods", "as", "getAllSuperClasses", "getClass",
             "getGeneric", "is", "isClass", "isClassDef", "isGeneric",
             "new", "showMethods")
  importFrom("utils", "help", "menu")
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 line endings in C/C++/Fortran sources/headers ... OK
* checking compiled code ... NOTE
Note: information on .o files for x64 is not available
File 'D:/biocbuild/bbs-3.15-bioc/R/library/RBioinf/libs/x64/RBioinf.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
  Found 'printf', possibly from 'printf' (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 ... 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
  'D:/biocbuild/bbs-3.15-bioc/meat/RBioinf.Rcheck/00check.log'
for details.

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###
### Running command:
###
###   D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL RBioinf
###
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* installing to library 'D:/biocbuild/bbs-3.15-bioc/R/library'
* installing *source* package 'RBioinf' ...
** using staged installation
** libs
"C:/rtools40/mingw64/bin/"gcc  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c Rinit.c -o Rinit.o
"C:/rtools40/mingw64/bin/"gcc  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c rand.c -o rand.o
C:/rtools40/mingw64/bin/gcc -shared -s -static-libgcc -o RBioinf.dll tmp.def Rinit.o rand.o -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LD:/biocbuild/bbs-3.15-bioc/R/bin/x64 -lR
installing to D:/biocbuild/bbs-3.15-bioc/R/library/00LOCK-RBioinf/00new/RBioinf/libs/x64
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'RBioinf'
    finding HTML links ... done
    Rcal                                    html  
    S4Help                                  html  
    asSimpleVector                          html  
    classList2Graph                         html  
    computeClassLinearization               html  
    printWithNumbers                        html  
    randDNA                                 html  
    simplePVect                             html  
    simpleRand                              html  
    simpleSort                              html  
    subClassNames                           html  
    superClasses                            html  
    traceMethods                            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
* DONE (RBioinf)
Making 'packages.html' ...Warning in packageDescription(i, lib.loc = lib, fields = "Title", encoding = "UTF-8") :
  DESCRIPTION file of package 'SPEM' is missing or broken
 done