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This page was generated on 2024-03-29 11:35:55 -0400 (Fri, 29 Mar 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 22.04.3 LTS)x86_644.3.3 (2024-02-29) -- "Angel Food Cake" 4669
palomino4Windows Server 2022 Datacenterx644.3.3 (2024-02-29 ucrt) -- "Angel Food Cake" 4404
merida1macOS 12.7.1 Montereyx86_644.3.3 (2024-02-29) -- "Angel Food Cake" 4427
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

Package 599/2266HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
DRIMSeq 1.30.0  (landing page)
Malgorzata Nowicka
Snapshot Date: 2024-03-27 14:05:05 -0400 (Wed, 27 Mar 2024)
git_url: https://git.bioconductor.org/packages/DRIMSeq
git_branch: RELEASE_3_18
git_last_commit: dca4fea
git_last_commit_date: 2023-10-24 10:48:39 -0400 (Tue, 24 Oct 2023)
nebbiolo2Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
palomino4Windows Server 2022 Datacenter / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
merida1macOS 12.7.1 Monterey / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.1 Ventura / arm64see weekly results here

CHECK results for DRIMSeq on nebbiolo2


To the developers/maintainers of the DRIMSeq package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/DRIMSeq.git to reflect on this report. See Troubleshooting Build Report for more information.
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results


Summary

Package: DRIMSeq
Version: 1.30.0
Command: /home/biocbuild/bbs-3.18-bioc/R/bin/R CMD check --install=check:DRIMSeq.install-out.txt --library=/home/biocbuild/bbs-3.18-bioc/R/site-library --timings DRIMSeq_1.30.0.tar.gz
StartedAt: 2024-03-27 22:05:54 -0400 (Wed, 27 Mar 2024)
EndedAt: 2024-03-27 22:11:15 -0400 (Wed, 27 Mar 2024)
EllapsedTime: 321.0 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: DRIMSeq.Rcheck
Warnings: 1

Command output

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.18-bioc/R/bin/R CMD check --install=check:DRIMSeq.install-out.txt --library=/home/biocbuild/bbs-3.18-bioc/R/site-library --timings DRIMSeq_1.30.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.18-bioc/meat/DRIMSeq.Rcheck’
* using R version 4.3.3 (2024-02-29)
* using platform: x86_64-pc-linux-gnu (64-bit)
* R was compiled by
    gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
    GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
* running under: Ubuntu 22.04.4 LTS
* using session charset: UTF-8
* checking for file ‘DRIMSeq/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘DRIMSeq’ 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 for sufficient/correct file permissions ... OK
* checking whether package ‘DRIMSeq’ 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 ... NOTE
Problems with news in ‘NEWS’:
  Cannot process chunk/lines:
    v0.99.0: - Bioconductor submission.
  Cannot process chunk/lines:
    v1.1.2: - Bioconductor accepted devel version.
  Cannot process chunk/lines:
    v1.1.3: - New features: 
    	i) The level of moderation is calculated automatically. 
    	ii) Permutation approach to adjust p-values in sQTL analyses.
  Cannot process chunk/lines:
    v1.1.4: - Use data frames with counts and genotypes when creating the dmDSdata and dmSQTLdata objects.
  Cannot process chunk/lines:
    v1.3.1: - Equals to v1.1.4.
  Cannot process chunk/lines:
    v1.3.2: - Implementation of the two-stage test dmTwoStageTest().
  Cannot process chunk/lines:
    Additionally:
    	i) Removing max_features argument from dmFilter.
    	ii) Keeping only the grid approach for estimating tagwise dispersion. 
    	iii) Allow to use only a subset of genes (disp_subset parameter) in common dispersion estimation to speed up the calculations; if disp_subset < 1, use set.seed() to make the analysis reproducible.
    	iv) Always use tagwise dispersion for fitting full and null models.
    	v) In one group fitting, return NA for tags having the last feature with zero counts in all samples. We always use the q-th feature as a denominator in logit calculation. In such a case all the logits are anyways Inf.
    	vi) Use plotPValues instead of plotTest
    	vii) Use 'prop' instead of 'pi' and 'disp' instead of 'gamma0'.
    	viii) Use only 'constrOptim' (old 'constrOptimG') to estimate proportions and 'optim' to estimate coefficients in the regression model. 
    	ix) Use plotProportions instead of plotFit.
    	x) No 'out_dir' parameter in plotting functions. All plotting functions return a ggplot object.
    	xi) Use term "precision" instead of "dispersion" as in DRIMSeq we directly estimate the precision parameter. Dispersion can be calculated with formula: dispersion = 1 / (1 + precision).
* 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 loading without being on the library search path ... 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 ... WARNING
Documented arguments not in \usage in documentation object 'dmSQTLtest-class':
  ‘...’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                   user system elapsed
dmSQTLtest-class 88.492  0.939  89.433
dmDStest-class    6.961  0.108   7.069
* 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 ...
  ‘DRIMSeq.Rnw’ using ‘UTF-8’... OK
 NONE
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 1 WARNING, 1 NOTE
See
  ‘/home/biocbuild/bbs-3.18-bioc/meat/DRIMSeq.Rcheck/00check.log’
for details.



Installation output

DRIMSeq.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.18-bioc/R/bin/R CMD INSTALL DRIMSeq
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.18-bioc/R/site-library’
* installing *source* package ‘DRIMSeq’ ...
** using staged installation
** R
** inst
** preparing package for lazy loading
Creating a new generic function for ‘proportions’ in package ‘DRIMSeq’
** help
*** installing help indices
** 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 (DRIMSeq)

Tests output

DRIMSeq.Rcheck/tests/testthat.Rout


R version 4.3.3 (2024-02-29) -- "Angel Food Cake"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (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(DRIMSeq)

Attaching package: 'DRIMSeq'

The following object is masked from 'package:base':

    proportions

> 
> test_check("DRIMSeq")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 21 ]
> 
> proc.time()
   user  system elapsed 
  7.069   0.285   7.342 

Example timings

DRIMSeq.Rcheck/DRIMSeq-Ex.timings

nameusersystemelapsed
dmDSdata-class0.0120.0000.012
dmDSdata0.0090.0000.010
dmDSfit-class0.0080.0000.008
dmDSprecision-class0.0040.0000.005
dmDStest-class6.9610.1087.069
dmFilter0.0210.0000.022
dmFit0.0050.0000.005
dmPrecision0.0050.0000.005
dmSQTLdata-class0.0060.0000.006
dmSQTLdata0.0060.0000.005
dmSQTLfit-class0.0050.0000.005
dmSQTLprecision-class0.0050.0000.005
dmSQTLtest-class88.492 0.93989.433
dmTest0.0080.0000.007
plotData0.010.000.01
plotPValues0.0050.0000.005
plotPrecision0.0050.0000.004
plotProportions0.0040.0000.005