Back to Multiple platform build/check report for BioC 3.14
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This page was generated on 2021-09-21 12:06:17 -0400 (Tue, 21 Sep 2021).

CHECK results for RBioinf on riesling1

To the developers/maintainers of the RBioinf package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/RBioinf.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 1496/2029HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
RBioinf 1.53.0  (landing page)
Robert Gentleman
Snapshot Date: 2021-09-20 14:50:09 -0400 (Mon, 20 Sep 2021)
git_url: https://git.bioconductor.org/packages/RBioinf
git_branch: master
git_last_commit: 1337231
git_last_commit_date: 2021-05-19 11:40:41 -0400 (Wed, 19 May 2021)
nebbiolo2Linux (Ubuntu 20.04.2 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
riesling1Windows Server 2019 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: RBioinf
Version: 1.53.0
Command: D:\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:RBioinf.install-out.txt --library=D:\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings RBioinf_1.53.0.tar.gz
StartedAt: 2021-09-21 02:37:12 -0400 (Tue, 21 Sep 2021)
EndedAt: 2021-09-21 02:41:31 -0400 (Tue, 21 Sep 2021)
EllapsedTime: 258.7 seconds
RetCode: 0
Status:   OK  
CheckDir: RBioinf.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   D:\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:RBioinf.install-out.txt --library=D:\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings RBioinf_1.53.0.tar.gz
###
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* using log directory 'D:/biocbuild/bbs-3.14-bioc/meat/RBioinf.Rcheck'
* using R version 4.1.1 (2021-08-10)
* 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 '1.53.0'
* 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
* 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
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 i386 is not available
Note: information on .o files for x64 is not available
File 'D:/biocbuild/bbs-3.14-bioc/R/library/RBioinf/libs/i386/RBioinf.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
  Found 'printf', possibly from 'printf' (C)
File 'D:/biocbuild/bbs-3.14-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 ...
** 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: 4 NOTEs
See
  'D:/biocbuild/bbs-3.14-bioc/meat/RBioinf.Rcheck/00check.log'
for details.



Installation output

RBioinf.Rcheck/00install.out

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.14/bioc/src/contrib/RBioinf_1.53.0.tar.gz && rm -rf RBioinf.buildbin-libdir && mkdir RBioinf.buildbin-libdir && D:\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=RBioinf.buildbin-libdir RBioinf_1.53.0.tar.gz && D:\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL RBioinf_1.53.0.zip && rm RBioinf_1.53.0.tar.gz RBioinf_1.53.0.zip
###
##############################################################################
##############################################################################


  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
 27 3430k   27  940k    0     0  1938k      0  0:00:01 --:--:--  0:00:01 1934k
100 3430k  100 3430k    0     0  2786k      0  0:00:01  0:00:01 --:--:-- 2786k

install for i386

* installing *source* package 'RBioinf' ...
** using staged installation
** libs
"C:/rtools40/mingw32/bin/"gcc  -I"D:/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c Rinit.c -o Rinit.o
"C:/rtools40/mingw32/bin/"gcc  -I"D:/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c rand.c -o rand.o
C:/rtools40/mingw32/bin/gcc -shared -s -static-libgcc -o RBioinf.dll tmp.def Rinit.o rand.o -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LD:/biocbuild/bbs-3.14-bioc/R/bin/i386 -lR
installing to D:/biocbuild/bbs-3.14-bioc/meat/RBioinf.buildbin-libdir/00LOCK-RBioinf/00new/RBioinf/libs/i386
** 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

install for x64

* installing *source* package 'RBioinf' ...
** libs
"C:/rtools40/mingw64/bin/"gcc  -I"D:/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c Rinit.c -o Rinit.o
"C:/rtools40/mingw64/bin/"gcc  -I"D:/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -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-3.14-bioc/R/bin/x64 -lR
installing to D:/biocbuild/bbs-3.14-bioc/meat/RBioinf.buildbin-libdir/RBioinf/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'RBioinf' as RBioinf_1.53.0.zip
* DONE (RBioinf)
* installing to library 'D:/biocbuild/bbs-3.14-bioc/R/library'
package 'RBioinf' successfully unpacked and MD5 sums checked

Tests output


Example timings

RBioinf.Rcheck/examples_i386/RBioinf-Ex.timings

nameusersystemelapsed
Rcal000
S4Help000
asSimpleVector000
classList2Graph0.070.000.06
computeClassLinearization0.030.000.03
printWithNumbers000
randDNA000
simplePVect000
simpleRand000
simpleSort000
subClassNames000
superClasses000
traceMethods000

RBioinf.Rcheck/examples_x64/RBioinf-Ex.timings

nameusersystemelapsed
Rcal000
S4Help000
asSimpleVector000
classList2Graph0.060.000.06
computeClassLinearization0.030.000.03
printWithNumbers000
randDNA000
simplePVect000
simpleRand000
simpleSort000
subClassNames000
superClasses000
traceMethods000