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This page was generated on 2023-01-02 09:00:34 -0500 (Mon, 02 Jan 2023).

HostnameOSArch (*)R versionInstalled pkgs
palomino5Windows Server 2022 Datacenterx64R Under development (unstable) (2022-12-25 r83502 ucrt) -- "Unsuffered Consequences" 4165
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

CHECK results for iBBiG on palomino5


To the developers/maintainers of the iBBiG package:
Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 925/2158HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
iBBiG 1.43.0  (landing page)
Aedin Culhane
Snapshot Date: 2022-12-28 11:00:06 -0500 (Wed, 28 Dec 2022)
git_url: https://git.bioconductor.org/packages/iBBiG
git_branch: master
git_last_commit: a133438
git_last_commit_date: 2022-11-01 11:06:51 -0500 (Tue, 01 Nov 2022)
palomino5Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  

Summary

Package: iBBiG
Version: 1.43.0
Command: F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:iBBiG.install-out.txt --library=F:\biocbuild\bbs-3.17-bioc\R\library --no-vignettes --timings iBBiG_1.43.0.tar.gz
StartedAt: 2022-12-29 00:34:58 -0500 (Thu, 29 Dec 2022)
EndedAt: 2022-12-29 00:36:57 -0500 (Thu, 29 Dec 2022)
EllapsedTime: 118.8 seconds
RetCode: 0
Status:   OK  
CheckDir: iBBiG.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:iBBiG.install-out.txt --library=F:\biocbuild\bbs-3.17-bioc\R\library --no-vignettes --timings iBBiG_1.43.0.tar.gz
###
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* using log directory 'F:/biocbuild/bbs-3.17-bioc-rtools43/meat/iBBiG.Rcheck'
* using R Under development (unstable) (2022-12-25 r83502 ucrt)
* using platform: x86_64-w64-mingw32 (64-bit)
* R was compiled by
    gcc.exe (GCC) 10.4.0
    GNU Fortran (GCC) 10.4.0
* running under: Windows Server x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'iBBiG/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'iBBiG' version '1.43.0'
* 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 'iBBiG' can be installed ... OK
* used C compiler: 'gcc.exe (GCC) 12.2.0'
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Description field: should contain one or more complete sentences.
* 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
'library' or 'require' call to 'biclust' which was already attached by Depends.
  Please remove these calls from your code.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
addSignal: no visible global function definition for 'runif'
iBBiG: no visible global function definition for 'new'
makeArtificial: no visible global function definition for 'runif'
makeArtificial: no visible global function definition for 'new'
Clusterscores,iBBiG: no visible global function definition for 'slot'
Clusterscores<-,iBBiG: no visible global function definition for
  'slot<-'
Clusterscores<-,iBBiG: no visible global function definition for
  'validObject'
Number,iBBiG: no visible global function definition for 'slot'
Number<-,iBBiG: no visible global function definition for 'slot<-'
Number<-,iBBiG: no visible global function definition for 'validObject'
NumberxCol,iBBiG: no visible global function definition for 'slot'
NumberxCol<-,iBBiG: no visible global function definition for 'slot<-'
NumberxCol<-,iBBiG: no visible global function definition for
  'validObject'
Parameters,iBBiG: no visible global function definition for 'slot'
Parameters<-,iBBiG: no visible global function definition for 'slot<-'
Parameters<-,iBBiG: no visible global function definition for
  'validObject'
RowScorexNumber,iBBiG: no visible global function definition for 'slot'
RowScorexNumber<-,iBBiG: no visible global function definition for
  'slot<-'
RowScorexNumber<-,iBBiG: no visible global function definition for
  'validObject'
RowxNumber,iBBiG: no visible global function definition for 'slot'
RowxNumber<-,iBBiG: no visible global function definition for 'slot<-'
RowxNumber<-,iBBiG: no visible global function definition for
  'validObject'
Seeddata,iBBiG: no visible global function definition for 'slot'
Seeddata<-,iBBiG: no visible global function definition for 'slot<-'
Seeddata<-,iBBiG: no visible global function definition for
  'validObject'
analyzeClust,Biclust-iBBiG: no visible global function definition for
  'as'
analyzeClust,list-iBBiG: no visible global function definition for
  'new'
coerce,Biclust-iBBiG: no visible global function definition for 'new'
info,iBBiG: no visible global function definition for 'slot'
info<-,iBBiG: no visible global function definition for 'slot<-'
info<-,iBBiG: no visible global function definition for 'validObject'
plot,iBBiG-ANY: no visible global function definition for 'layout'
plot,iBBiG-ANY: no visible global function definition for 'colors'
plot,iBBiG-ANY: no visible global function definition for 'image'
plot,iBBiG-ANY: no visible global function definition for 'legend'
plot,iBBiG-ANY: no visible binding for global variable 'title'
plot,iBBiG-ANY: no visible global function definition for 'title'
plot,iBBiG-ANY: no visible global function definition for 'barplot'
Undefined global functions or variables:
  as barplot colors image layout legend new runif slot slot<- title
  validObject
Consider adding
  importFrom("grDevices", "colors")
  importFrom("graphics", "barplot", "image", "layout", "legend", "title")
  importFrom("methods", "as", "new", "slot", "slot<-", "validObject")
  importFrom("stats", "runif")
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 'F:/biocbuild/bbs-3.17-bioc/R/library/iBBiG/libs/x64/iBBiG.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
  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 nor [v]sprintf. 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 sizes of PDF files under 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
               user system elapsed
iBBiG-class   24.19   0.06   24.27
iBBiG-package 23.22   0.11   23.33
iBBiG         19.53   0.06   19.82
* 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
  'F:/biocbuild/bbs-3.17-bioc-rtools43/meat/iBBiG.Rcheck/00check.log'
for details.

Installation output

iBBiG.Rcheck/00install.out

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###
### Running command:
###
###   F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD INSTALL iBBiG
###
##############################################################################
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* installing to library 'F:/biocbuild/bbs-3.17-bioc/R/library'
* installing *source* package 'iBBiG' ...
** using staged installation
** libs
using C compiler: 'gcc.exe (GCC) 12.2.0'
gcc  -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG     -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c R_init_iBBiG.c -o R_init_iBBiG.o
gcc  -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG     -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c iBBiG.c -o iBBiG.o
gcc -shared -s -static-libgcc -o iBBiG.dll tmp.def R_init_iBBiG.o iBBiG.o -Lc:/rtools42/x86_64-w64-mingw32.static.posix/lib/x64 -Lc:/rtools42/x86_64-w64-mingw32.static.posix/lib -LF:/biocbuild/bbs-3.17-bioc/R/bin/x64 -lR
installing to F:/biocbuild/bbs-3.17-bioc/R/library/00LOCK-iBBiG/00new/iBBiG/libs/x64
** R
** 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
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (iBBiG)

Tests output

Example timings

iBBiG.Rcheck/iBBiG-Ex.timings

nameusersystemelapsed
iBBiG-class24.19 0.0624.27
iBBiG-package23.22 0.1123.33
iBBiG19.53 0.0619.82
makeArtificial0.550.020.56