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CHECK report for clipper on tokay1

This page was generated on 2021-05-05 12:11:32 -0400 (Wed, 05 May 2021).

To the developers/maintainers of the clipper package:
Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 312/1974HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
clipper 1.30.0  (landing page)
Paolo Martini
Snapshot Date: 2021-05-04 14:50:13 -0400 (Tue, 04 May 2021)
URL: https://git.bioconductor.org/packages/clipper
Branch: RELEASE_3_12
Last Commit: 3a1d234
Last Changed Date: 2020-10-27 10:48:58 -0400 (Tue, 27 Oct 2020)
malbec1Linux (Ubuntu 18.04.5 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version exists in internal repository
tokay1Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version exists in internal repository
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version exists in internal repository

Summary

Package: clipper
Version: 1.30.0
Command: C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:clipper.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings clipper_1.30.0.tar.gz
StartedAt: 2021-05-05 01:31:27 -0400 (Wed, 05 May 2021)
EndedAt: 2021-05-05 01:41:25 -0400 (Wed, 05 May 2021)
EllapsedTime: 598.5 seconds
RetCode: 0
Status:   OK   
CheckDir: clipper.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:clipper.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings clipper_1.30.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.12-bioc/meat/clipper.Rcheck'
* using R version 4.0.5 (2021-03-31)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'clipper/DESCRIPTION' ... OK
* this is package 'clipper' version '1.30.0'
* 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 'clipper' 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 files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                    user system elapsed
clipperAllRoots    18.21   0.43   18.71
clipper             8.57   0.59    9.16
pathwayTest         7.35   0.05    7.39
cliqueVarianceTest  5.19   0.14    5.32
cliquePairedTest    5.18   0.12    5.32
cliqueMeanTest      5.03   0.06    5.09
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                 user system elapsed
clipperAllRoots 14.34   0.06   14.40
clipper          6.14   0.30    6.45
pathwayTest      5.55   0.07    5.61
* 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

clipper.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://172.29.0.3/BBS/3.12/bioc/src/contrib/clipper_1.30.0.tar.gz && rm -rf clipper.buildbin-libdir && mkdir clipper.buildbin-libdir && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=clipper.buildbin-libdir clipper_1.30.0.tar.gz && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL clipper_1.30.0.zip && rm clipper_1.30.0.tar.gz clipper_1.30.0.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
 20  418k   20 88817    0     0   462k      0 --:--:-- --:--:-- --:--:--  463k
100  418k  100  418k    0     0  2197k      0 --:--:-- --:--:-- --:--:-- 2204k

install for i386

* installing *source* package 'clipper' ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
No methods found in package 'GenomicRanges' for request: 'c' when loading 'qpgraph'
** help
*** installing help indices
  converting help for package 'clipper'
    finding HTML links ... done
    clipper                                 html  
    clipperAllRoots                         html  
    cliqueMeanTest                          html  
    cliqueMixedTest                         html  
    cliquePairedTest                        html  
    cliqueVarianceTest                      html  
    deleteEdge                              html  
    easyClip                                html  
    easyLook                                html  
    getGraphEntryGenes                      html  
    getJunctionTreePaths                    html  
    nameCliques                             html  
    pathwayTest                             html  
    plotInCytoscape                         html  
    prunePaths                              html  
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
No methods found in package 'GenomicRanges' for request: 'c' when loading 'qpgraph'
** testing if installed package can be loaded from final location
No methods found in package 'GenomicRanges' for request: 'c' when loading 'qpgraph'
** testing if installed package keeps a record of temporary installation path

install for x64

* installing *source* package 'clipper' ...
** testing if installed package can be loaded
No methods found in package 'GenomicRanges' for request: 'c' when loading 'qpgraph'
* MD5 sums
packaged installation of 'clipper' as clipper_1.30.0.zip
* DONE (clipper)
* installing to library 'C:/Users/biocbuild/bbs-3.12-bioc/R/library'
package 'clipper' successfully unpacked and MD5 sums checked

Tests output

clipper.Rcheck/tests_i386/runTests.Rout


R version 4.0.5 (2021-03-31) -- "Shake and Throw"
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("clipper")

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

No methods found in package 'GenomicRanges' for request: 'c' when loading 'qpgraph'


RUNIT TEST PROTOCOL -- Wed May 05 01:40:53 2021 
*********************************************** 
Number of test functions: 10 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
clipper RUnit Tests - 10 test functions, 0 errors, 0 failures
Number of test functions: 10 
Number of errors: 0 
Number of failures: 0 
> 
> pattern="^test_.*\\.R$"
> 
> proc.time()
   user  system elapsed 
  19.12    1.43   24.28 

clipper.Rcheck/tests_x64/runTests.Rout


R version 4.0.5 (2021-03-31) -- "Shake and Throw"
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("clipper")

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

No methods found in package 'GenomicRanges' for request: 'c' when loading 'qpgraph'


RUNIT TEST PROTOCOL -- Wed May 05 01:41:16 2021 
*********************************************** 
Number of test functions: 10 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
clipper RUnit Tests - 10 test functions, 0 errors, 0 failures
Number of test functions: 10 
Number of errors: 0 
Number of failures: 0 
> 
> pattern="^test_.*\\.R$"
> 
> proc.time()
   user  system elapsed 
  20.85    0.75   23.20 

Example timings

clipper.Rcheck/examples_i386/clipper-Ex.timings

nameusersystemelapsed
clipper8.570.599.16
clipperAllRoots18.21 0.4318.71
cliqueMeanTest5.030.065.09
cliqueMixedTest4.690.054.73
cliquePairedTest5.180.125.32
cliqueVarianceTest5.190.145.32
deleteEdge1.070.061.14
easyClip4.190.104.28
getGraphEntryGenes1.460.011.47
getJunctionTreePaths1.530.021.55
nameCliques000
pathwayTest7.350.057.39
plotInCytoscape000
prunePaths000

clipper.Rcheck/examples_x64/clipper-Ex.timings

nameusersystemelapsed
clipper6.140.306.45
clipperAllRoots14.34 0.0614.40
cliqueMeanTest3.590.053.64
cliqueMixedTest3.740.063.80
cliquePairedTest4.920.024.93
cliqueVarianceTest2.780.062.85
deleteEdge0.690.000.68
easyClip2.780.082.86
getGraphEntryGenes0.750.000.75
getJunctionTreePaths0.680.010.69
nameCliques000
pathwayTest5.550.075.61
plotInCytoscape000
prunePaths000