Package: RBioinf

Version: 1.44.0

Command: /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:RBioinf.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings RBioinf_1.44.0.tar.gz

StartedAt: 2019-10-16 04:18:19 -0400 (Wed, 16 Oct 2019)

EndedAt: 2019-10-16 04:18:52 -0400 (Wed, 16 Oct 2019)

EllapsedTime: 33.1 seconds

RetCode: 0

Status:  OK

CheckDir: RBioinf.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:RBioinf.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings RBioinf_1.44.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.9-bioc/meat/RBioinf.Rcheck’
* using R version 3.6.1 (2019-07-05)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘RBioinf/DESCRIPTION’ ... OK
* this is package ‘RBioinf’ version ‘1.44.0’
* 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 ‘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 is not available
* 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
  ‘/home/biocbuild/bbs-3.9-bioc/meat/RBioinf.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 RBioinf
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* installing to library ‘/home/biocbuild/bbs-3.9-bioc/R/library’
* installing *source* package ‘RBioinf’ ...
** using staged installation
** libs
gcc -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG   -I/usr/local/include  -fpic  -g -O2  -Wall -c Rinit.c -o Rinit.o
gcc -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG   -I/usr/local/include  -fpic  -g -O2  -Wall -c rand.c -o rand.o
gcc -shared -L/home/biocbuild/bbs-3.9-bioc/R/lib -L/usr/local/lib -o RBioinf.so Rinit.o rand.o -L/home/biocbuild/bbs-3.9-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.9-bioc/R/library/00LOCK-RBioinf/00new/RBioinf/libs
** 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
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (RBioinf)

name	user	system	elapsed
Rcal	0.012	0.016	0.185
S4Help	0	0	0
asSimpleVector	0.001	0.000	0.001
classList2Graph	0.128	0.015	0.144
computeClassLinearization	0.063	0.008	0.072
printWithNumbers	0.001	0.000	0.001
randDNA	0	0	0
simplePVect	0	0	0
simpleRand	0.001	0.000	0.000
simpleSort	0.001	0.000	0.000
subClassNames	0.001	0.000	0.001
superClasses	0	0	0
traceMethods	0.001	0.000	0.000