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This page was generated on 2022-04-13 12:06:43 -0400 (Wed, 13 Apr 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.1.3 (2022-03-10) -- "One Push-Up" 4324
tokay2Windows Server 2012 R2 Standardx644.1.3 (2022-03-10) -- "One Push-Up" 4077
machv2macOS 10.14.6 Mojavex86_644.1.3 (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

CHECK results for iBBiG on tokay2


To the developers/maintainers of the iBBiG package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/iBBiG.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? 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 899/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
iBBiG 1.38.0  (landing page)
Aedin Culhane
Snapshot Date: 2022-04-12 01:55:07 -0400 (Tue, 12 Apr 2022)
git_url: https://git.bioconductor.org/packages/iBBiG
git_branch: RELEASE_3_14
git_last_commit: 2d73690
git_last_commit_date: 2021-10-26 12:02:46 -0400 (Tue, 26 Oct 2021)
nebbiolo2Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: iBBiG
Version: 1.38.0
Command: C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:iBBiG.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings iBBiG_1.38.0.tar.gz
StartedAt: 2022-04-12 21:16:20 -0400 (Tue, 12 Apr 2022)
EndedAt: 2022-04-12 21:20:19 -0400 (Tue, 12 Apr 2022)
EllapsedTime: 238.4 seconds
RetCode: 0
Status:   OK  
CheckDir: iBBiG.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:iBBiG.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings iBBiG_1.38.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.14-bioc/meat/iBBiG.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 'iBBiG/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'iBBiG' version '1.38.0'
* 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 'iBBiG' can be installed ... OK
* 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
* 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
'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 i386 is not available
Note: information on .o files for x64 is not available
File 'C:/Users/biocbuild/bbs-3.14-bioc/R/library/iBBiG/libs/i386/iBBiG.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
  Found 'rand', possibly from 'rand' (C)
  Found 'srand', possibly from 'srand' (C)
File 'C:/Users/biocbuild/bbs-3.14-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. 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
Examples with CPU (user + system) or elapsed time > 5s
               user system elapsed
iBBiG         31.08   0.10   31.19
iBBiG-package 23.77   0.08   23.89
iBBiG-class   22.65   0.14   22.81
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
               user system elapsed
iBBiG-package 28.54   0.02   28.64
iBBiG         25.17   0.09   25.28
iBBiG-class   22.50   0.05   22.56
* 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
  'C:/Users/biocbuild/bbs-3.14-bioc/meat/iBBiG.Rcheck/00check.log'
for details.



Installation output

iBBiG.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.14/bioc/src/contrib/iBBiG_1.38.0.tar.gz && rm -rf iBBiG.buildbin-libdir && mkdir iBBiG.buildbin-libdir && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=iBBiG.buildbin-libdir iBBiG_1.38.0.tar.gz && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL iBBiG_1.38.0.zip && rm iBBiG_1.38.0.tar.gz iBBiG_1.38.0.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
 99 18822   99 18691    0     0   156k      0 --:--:-- --:--:-- --:--:--  156k
100 18822  100 18822    0     0  47651      0 --:--:-- --:--:-- --:--:-- 47650

install for i386

* installing *source* package 'iBBiG' ...
** using staged installation
** libs
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c R_init_iBBiG.c -o R_init_iBBiG.o
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c iBBiG.c -o iBBiG.o
C:/rtools40/mingw32/bin/gcc -shared -s -static-libgcc -o iBBiG.dll tmp.def R_init_iBBiG.o iBBiG.o -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.14-/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.14-bioc/meat/iBBiG.buildbin-libdir/00LOCK-iBBiG/00new/iBBiG/libs/i386
** R
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'iBBiG'
    finding HTML links ... done
    iBBiG-class                             html  
    finding level-2 HTML links ... done

    iBBiG-package                           html  
    iBBiG                                   html  
    makeArtificial                          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 'iBBiG' ...
** libs
"C:/rtools40/mingw64/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c R_init_iBBiG.c -o R_init_iBBiG.o
"C:/rtools40/mingw64/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c iBBiG.c -o iBBiG.o
C:/rtools40/mingw64/bin/gcc -shared -s -static-libgcc -o iBBiG.dll tmp.def R_init_iBBiG.o iBBiG.o -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.14-/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.14-bioc/meat/iBBiG.buildbin-libdir/iBBiG/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'iBBiG' as iBBiG_1.38.0.zip
* DONE (iBBiG)
* installing to library 'C:/Users/biocbuild/bbs-3.14-bioc/R/library'
package 'iBBiG' successfully unpacked and MD5 sums checked

Tests output


Example timings

iBBiG.Rcheck/examples_i386/iBBiG-Ex.timings

nameusersystemelapsed
iBBiG-class22.65 0.1422.81
iBBiG-package23.77 0.0823.89
iBBiG31.08 0.1031.19
makeArtificial0.590.030.62

iBBiG.Rcheck/examples_x64/iBBiG-Ex.timings

nameusersystemelapsed
iBBiG-class22.50 0.0522.56
iBBiG-package28.54 0.0228.64
iBBiG25.17 0.0925.28
makeArtificial0.520.030.55