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) |
| Back to Multiple platform build/check report for BioC 3.15 |
|
This page was generated on 2022-03-18 11:08:26 -0400 (Fri, 18 Mar 2022).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 20.04.4 LTS) | x86_64 | R Under development (unstable) (2022-02-17 r81757) -- "Unsuffered Consequences" | 4334 |
| riesling1 | Windows Server 2019 Standard | x64 | R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences" | 4097 |
| palomino3 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2022-02-17 r81757 ucrt) -- "Unsuffered Consequences" | 4083 |
| merida1 | macOS 10.14.6 Mojave | x86_64 | R 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 | ||||
|
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. |
| Package 1553/2090 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| RCM 1.11.2 (landing page) Stijn Hawinkel
| nebbiolo1 | Linux (Ubuntu 20.04.4 LTS) / x86_64 | OK | OK | OK | | ||||||||
| riesling1 | Windows Server 2019 Standard / x64 | OK | OK | OK | OK | |||||||||
| palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| merida1 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | | ||||||||
| 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 |
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### 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
###
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* 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.
RCM.Rcheck/00install.out
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###
### Running command:
###
### D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL RCM
###
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* 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
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
RCM.Rcheck/RCM-Ex.timings
| name | user | system | elapsed | |
| RCM | 6.25 | 0.61 | 6.86 | |
| RCM_NB | 4.98 | 0.66 | 5.64 | |
| addOrthProjection | 5.51 | 0.66 | 6.17 | |
| checkAlias | 0 | 0 | 0 | |
| extractCoord | 5.60 | 0.32 | 5.92 | |
| getDevianceRes | 7.31 | 0.04 | 7.34 | |
| inertia | 5.55 | 0.07 | 5.63 | |
| liks | 5.00 | 0.02 | 5.01 | |
| plot.RCM | 5.06 | 0.00 | 5.07 | |
| plotRespFun | 6.45 | 0.11 | 6.56 | |
| residualPlot | 2.24 | 0.00 | 2.23 | |