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This page was generated on 2024-12-24 11:46 -0500 (Tue, 24 Dec 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.1 LTS)x86_64R Under development (unstable) (2024-10-21 r87258) -- "Unsuffered Consequences" 4754
palomino7Windows Server 2022 Datacenterx64R Under development (unstable) (2024-10-26 r87273 ucrt) -- "Unsuffered Consequences" 4472
lconwaymacOS 12.7.1 Montereyx86_64R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" 4426
kjohnson3macOS 13.7.1 Venturaarm64R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" 4381
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch64R Under development (unstable) (2024-11-24 r87369) -- "Unsuffered Consequences" 4373
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 599/2274HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
DRIMSeq 1.35.0  (landing page)
Malgorzata Nowicka
Snapshot Date: 2024-12-23 13:40 -0500 (Mon, 23 Dec 2024)
git_url: https://git.bioconductor.org/packages/DRIMSeq
git_branch: devel
git_last_commit: bffc717
git_last_commit_date: 2024-10-29 10:08:39 -0500 (Tue, 29 Oct 2024)
nebbiolo1Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
palomino7Windows Server 2022 Datacenter / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
kjohnson3macOS 13.7.1 Ventura / arm64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
kunpeng2Linux (openEuler 22.03 LTS-SP1) / aarch64  OK    OK    WARNINGS  


CHECK results for DRIMSeq on kunpeng2

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.
- See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host.

raw results


Summary

Package: DRIMSeq
Version: 1.35.0
Command: /home/biocbuild/R/R/bin/R CMD check --install=check:DRIMSeq.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings DRIMSeq_1.35.0.tar.gz
StartedAt: 2024-12-24 06:18:13 -0000 (Tue, 24 Dec 2024)
EndedAt: 2024-12-24 06:23:05 -0000 (Tue, 24 Dec 2024)
EllapsedTime: 292.3 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: DRIMSeq.Rcheck
Warnings: 1

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD check --install=check:DRIMSeq.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings DRIMSeq_1.35.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/DRIMSeq.Rcheck’
* using R Under development (unstable) (2024-11-24 r87369)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
    aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0
    GNU Fortran (GCC) 14.2.0
* running under: openEuler 24.03 (LTS)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘DRIMSeq/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘DRIMSeq’ version ‘1.35.0’
* 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 code 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 ... NOTE
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  dmFit.Rd: edgeR
  dmPrecision.Rd: edgeR
  dmSQTLdata.Rd: GRanges-class
  dmTest.Rd: edgeR
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... WARNING
Documented arguments not in \usage in Rd file 'dmSQTLtest-class.Rd':
  ‘...’

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 149.523  1.243 151.235
dmDStest-class    10.165  0.108  10.321
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 1 WARNING, 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.21-bioc/meat/DRIMSeq.Rcheck/00check.log’
for details.


Installation output

DRIMSeq.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD INSTALL DRIMSeq
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/R/R-4.5.0-devel_2024-11-24/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 Under development (unstable) (2024-11-24 r87369) -- "Unsuffered Consequences"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: aarch64-unknown-linux-gnu

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 
  9.990   0.317  10.316 

Example timings

DRIMSeq.Rcheck/DRIMSeq-Ex.timings

nameusersystemelapsed
dmDSdata-class0.0110.0000.012
dmDSdata0.010.000.01
dmDSfit-class0.0090.0000.009
dmDSprecision-class0.0090.0000.009
dmDStest-class10.165 0.10810.321
dmFilter0.0250.0000.033
dmFit0.0110.0000.010
dmPrecision0.0100.0000.011
dmSQTLdata-class0.0100.0000.011
dmSQTLdata0.0110.0000.011
dmSQTLfit-class0.0120.0000.012
dmSQTLprecision-class0.0110.0000.011
dmSQTLtest-class149.523 1.243151.235
dmTest0.0090.0000.010
plotData0.0180.0000.017
plotPValues0.0080.0000.009
plotPrecision0.0080.0000.008
plotProportions0.0080.0000.009