Back to Multiple platform build/check report for BioC 3.15
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This page was generated on 2022-03-18 11:08:26 -0400 (Fri, 18 Mar 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 20.04.4 LTS)x86_64R Under development (unstable) (2022-02-17 r81757) -- "Unsuffered Consequences" 4334
riesling1Windows Server 2019 Standardx64R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences" 4097
palomino3Windows Server 2022 Datacenterx64R Under development (unstable) (2022-02-17 r81757 ucrt) -- "Unsuffered Consequences" 4083
merida1macOS 10.14.6 Mojavex86_64R Under development (unstable) (2022-03-02 r81842) -- "Unsuffered Consequences" 4134
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 RCM on riesling1


To the developers/maintainers of the RCM package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/RCM.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 1553/2090HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
RCM 1.11.2  (landing page)
Stijn Hawinkel
Snapshot Date: 2022-03-17 13:55:23 -0400 (Thu, 17 Mar 2022)
git_url: https://git.bioconductor.org/packages/RCM
git_branch: master
git_last_commit: 167c723
git_last_commit_date: 2022-03-02 04:43:43 -0400 (Wed, 02 Mar 2022)
nebbiolo1Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
riesling1Windows Server 2019 Standard / x64  OK    OK    OK    OK  
palomino3Windows Server 2022 Datacenter / 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: RCM
Version: 1.11.2
Command: D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:RCM.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings RCM_1.11.2.tar.gz
StartedAt: 2022-03-17 20:01:23 -0400 (Thu, 17 Mar 2022)
EndedAt: 2022-03-17 20:06:18 -0400 (Thu, 17 Mar 2022)
EllapsedTime: 295.1 seconds
RetCode: 0
Status:   OK  
CheckDir: RCM.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:RCM.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings RCM_1.11.2.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'D:/biocbuild/bbs-3.15-bioc/meat/RCM.Rcheck'
* using R Under development (unstable) (2021-11-21 r81221)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'RCM/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'RCM' version '1.11.2'
* 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 'RCM' 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
* 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
Package in Depends field not imported from: 'DBI'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
* 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 LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in 'vignettes' ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                  user system elapsed
getDevianceRes    7.31   0.04    7.34
RCM               6.25   0.61    6.86
plotRespFun       6.45   0.11    6.56
addOrthProjection 5.51   0.66    6.17
extractCoord      5.60   0.32    5.92
RCM_NB            4.98   0.66    5.64
inertia           5.55   0.07    5.63
plot.RCM          5.06   0.00    5.07
liks              5.00   0.02    5.01
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
  Running 'testthat.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: 1 NOTE
See
  'D:/biocbuild/bbs-3.15-bioc/meat/RCM.Rcheck/00check.log'
for details.



Installation output

RCM.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL RCM
###
##############################################################################
##############################################################################


* installing to library 'D:/biocbuild/bbs-3.15-bioc/R/library'
* installing *source* package 'RCM' ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'RCM'
    finding HTML links ... done
    JacCol_constr                           html  
    JacCol_constr_noLab                     html  
    LR_nb                                   html  
    LR_nb_Jac                               html  
    NBalphaInfl                             html  
    NBcolInfl                               html  
    NBjacobianAbunds                        html  
    NBjacobianCol                           html  
    NBjacobianColNP                         html  
    NBjacobianLibSizes                      html  
    NBjacobianPsi                           html  
    NBjacobianRow                           html  
    NBpsiInfl                               html  
    NBrowInfl                               html  
    RCM                                     html  
    RCM_NB                                  html  
    Zeller                                  html  
    addOrthProjection                       html  
    arrayprod                               html  
    buildCentMat                            html  
    buildConfMat                            html  
    buildConfMat.character                  html  
    buildConfMat.data.frame                 html  
    buildCovMat                             html  
    buildDesign                             html  
    checkAlias                              html  
    constrCorresp                           html  
    correctXMissingness                     html  
    dLR_nb                                  html  
    dNBabunds                               html  
    dNBlibSizes                             html  
    dNBllcol                                html  
    dNBllcolNP                              html  
    dNBllcol_constr                         html  
    dNBllcol_constr_noLab                   html  
    dNBllrow                                html  
    dNBpsis                                 html  
    deviances                               html  
    ellipseCoord                            html  
    estDisp                                 html  
    estNBparams                             html  
    estNBparamsNoLab                        html  
    estNPresp                               html  
    extractCoord                            html  
    extractE                                html  
    filterConfounders                       html  
    getDevMat                               html  
    getDevianceRes                          html  
    getInflCol                              html  
    getInflRow                              html  
    getInt                                  html  
    getLogLik                               html  
    getModelMat                             html  
    getRowMat                               html  
    heq_nb                                  html  
    heq_nb_jac                              html  
    indentPlot                              html  
    inertia                                 html  
    liks                                    html  
    plot.RCM                                html  
    plotRespFun                             html  
    residualPlot                            html  
    respFunJacMat                           html  
    respFunScoreMat                         html  
    rowMultiply                             html  
    seq_k                                   html  
    trimOnConfounders                       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
* DONE (RCM)
Making 'packages.html' ...Warning in packageDescription(i, lib.loc = lib, fields = "Title", encoding = "UTF-8") :
  DESCRIPTION file of package 'HiCcompare' is missing or broken
Warning in packageDescription(i, lib.loc = lib, fields = "Title", encoding = "UTF-8") :
  DESCRIPTION file of package 'semisup' is missing or broken
 done

Tests output

RCM.Rcheck/tests/testthat.Rout


R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences"
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.

> library(testthat)
> library(RCM)
Loading required package: DBI
> 
> test_check("RCM")
[ FAIL 0 | WARN 10 | SKIP 0 | PASS 37 ]

[ FAIL 0 | WARN 10 | SKIP 0 | PASS 37 ]
> 
> proc.time()
   user  system elapsed 
  92.70    4.31   97.42 

Example timings

RCM.Rcheck/RCM-Ex.timings

nameusersystemelapsed
RCM6.250.616.86
RCM_NB4.980.665.64
addOrthProjection5.510.666.17
checkAlias000
extractCoord5.600.325.92
getDevianceRes7.310.047.34
inertia5.550.075.63
liks5.000.025.01
plot.RCM5.060.005.07
plotRespFun6.450.116.56
residualPlot2.240.002.23