Back to Multiple platform build/check report for BioC 3.13
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This page was generated on 2021-07-21 15:05:21 -0400 (Wed, 21 Jul 2021).

CHECK results for fgga on tokay2

To the developers/maintainers of the fgga package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/fgga.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 630/2041HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
fgga 1.0.0  (landing page)
Spetale Flavio
Snapshot Date: 2021-07-20 04:50:13 -0400 (Tue, 20 Jul 2021)
URL: https://git.bioconductor.org/packages/fgga
Branch: RELEASE_3_13
Last Commit: aefd8a8
Last Changed Date: 2021-05-19 13:03:00 -0400 (Wed, 19 May 2021)
nebbiolo1Linux (Ubuntu 20.04.2 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    WARNINGS    OK  UNNEEDED, same version is already published

Summary

Package: fgga
Version: 1.0.0
Command: C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:fgga.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings fgga_1.0.0.tar.gz
StartedAt: 2021-07-20 23:51:45 -0400 (Tue, 20 Jul 2021)
EndedAt: 2021-07-20 23:54:32 -0400 (Tue, 20 Jul 2021)
EllapsedTime: 166.6 seconds
RetCode: 0
Status:   OK  
CheckDir: fgga.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:fgga.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings fgga_1.0.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.13-bioc/meat/fgga.Rcheck'
* using R version 4.1.0 (2021-05-18)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'fgga/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'fgga' version '1.0.0'
* package encoding: UTF-8
* 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 'fgga' can be installed ... OK
* checking installed package size ... OK
* 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* 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 contents of 'data' directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* 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
svmGO    8.57   0.09    8.67
svmTrain 8.41   0.11    8.52
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
         user system elapsed
svmTrain 7.72   0.03    7.75
svmGO    7.30   0.10    7.39
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'runTests.R'
 OK
** running tests for arch 'x64' ...
  Running 'runTests.R'
 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: OK


Installation output

fgga.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.165/BBS/3.13/bioc/src/contrib/fgga_1.0.0.tar.gz && rm -rf fgga.buildbin-libdir && mkdir fgga.buildbin-libdir && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=fgga.buildbin-libdir fgga_1.0.0.tar.gz && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL fgga_1.0.0.zip && rm fgga_1.0.0.tar.gz fgga_1.0.0.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
 54  994k   54  541k    0     0  1947k      0 --:--:-- --:--:-- --:--:-- 1949k
100  994k  100  994k    0     0  2233k      0 --:--:-- --:--:-- --:--:-- 2234k

install for i386

* installing *source* package 'fgga' ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'fgga'
    finding HTML links ... done
    CfData                                  html  
    createFolds                             html  
    fgga-package                            html  
    fgga                                    html  
    fgga2bipartite                          html  
    preCoreFG                               html  
    sumProduct                              html  
    svmGO                                   html  
    svmTrain                                html  
    tableTPG                                html  
    varianceGO                              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 'fgga' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'fgga' as fgga_1.0.0.zip
* DONE (fgga)
* installing to library 'C:/Users/biocbuild/bbs-3.13-bioc/R/library'
package 'fgga' successfully unpacked and MD5 sums checked

Tests output

fgga.Rcheck/tests_i386/runTests.Rout


R version 4.1.0 (2021-05-18) -- "Camp Pontanezen"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> BiocGenerics:::testPackage("fgga")

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, basename, cbind, colnames, dirname, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
    pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
    tapply, union, unique, unsplit, which.max, which.min

GO-term: GO:0000166
GO-term: GO:0003674
GO-term: GO:0003676
GO-term: GO:0003677
GO-term: GO:0003824
GO-term: GO:0004888
GO-term: GO:0005102
GO-term: GO:1901363
GO-term: GO:1902494
GO-term: GO:1990234
GO-term: GO:FES
GO-term:GO:0000166
GO-term:GO:0003674
GO-term:GO:0003676
GO-term:GO:0003677
GO-term:GO:0003824
GO-term:GO:0004888
GO-term:GO:0005102
GO-term:GO:1901363
GO-term:GO:1902494
GO-term:GO:1990234
GO-term:GO:FES
GO-term: GO:0001
GO-term: GO:0002
GO-term: GO:0003
GO-term: GO:0004
GO-term: GO:0005
GO-term: GO:FES
GO-term: GO:0007
GO-term: GO:0008
GO-term: GO:0009


RUNIT TEST PROTOCOL -- Tue Jul 20 23:54:17 2021 
*********************************************** 
Number of test functions: 8 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
fgga RUnit Tests - 8 test functions, 0 errors, 0 failures
Number of test functions: 8 
Number of errors: 0 
Number of failures: 0 
> 
> proc.time()
   user  system elapsed 
   4.81    0.39    5.18 

fgga.Rcheck/tests_x64/runTests.Rout


R version 4.1.0 (2021-05-18) -- "Camp Pontanezen"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> BiocGenerics:::testPackage("fgga")

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, basename, cbind, colnames, dirname, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
    pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
    tapply, union, unique, unsplit, which.max, which.min

GO-term: GO:0000166
GO-term: GO:0003674
GO-term: GO:0003676
GO-term: GO:0003677
GO-term: GO:0003824
GO-term: GO:0004888
GO-term: GO:0005102
GO-term: GO:1901363
GO-term: GO:1902494
GO-term: GO:1990234
GO-term: GO:FES
GO-term:GO:0000166
GO-term:GO:0003674
GO-term:GO:0003676
GO-term:GO:0003677
GO-term:GO:0003824
GO-term:GO:0004888
GO-term:GO:0005102
GO-term:GO:1901363
GO-term:GO:1902494
GO-term:GO:1990234
GO-term:GO:FES
GO-term: GO:0001
GO-term: GO:0002
GO-term: GO:0003
GO-term: GO:0004
GO-term: GO:0005
GO-term: GO:FES
GO-term: GO:0007
GO-term: GO:0008
GO-term: GO:0009


RUNIT TEST PROTOCOL -- Tue Jul 20 23:54:23 2021 
*********************************************** 
Number of test functions: 8 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
fgga RUnit Tests - 8 test functions, 0 errors, 0 failures
Number of test functions: 8 
Number of errors: 0 
Number of failures: 0 
> 
> proc.time()
   user  system elapsed 
   5.00    0.21    5.20 

Example timings

fgga.Rcheck/examples_i386/fgga-Ex.timings

nameusersystemelapsed
CfData0.140.000.14
createFolds0.140.030.18
fgga3.090.093.19
fgga2bipartite0.190.000.19
preCoreFG0.120.000.12
sumProduct2.020.082.09
svmGO8.570.098.67
svmTrain8.410.118.52
tableTPG000
varianceGO2.170.022.19

fgga.Rcheck/examples_x64/fgga-Ex.timings

nameusersystemelapsed
CfData0.080.020.09
createFolds0.110.000.11
fgga2.750.062.81
fgga2bipartite0.130.000.13
preCoreFG0.080.010.09
sumProduct1.730.081.81
svmGO7.300.107.39
svmTrain7.720.037.75
tableTPG000
varianceGO2.050.072.12