Multiple platform build/check report for BioC 3.21 - CHECK results for RNAmodR on kunpeng2

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo1	Linux (Ubuntu 24.04.1 LTS)	x86_64	R Under development (unstable) (2024-10-21 r87258) -- "Unsuffered Consequences"	4754
palomino7	Windows Server 2022 Datacenter	x64	R Under development (unstable) (2024-10-26 r87273 ucrt) -- "Unsuffered Consequences"	4472
lconway	macOS 12.7.1 Monterey	x86_64	R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences"	4426
kjohnson3	macOS 13.7.1 Ventura	arm64	R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences"	4381
kunpeng2	Linux (openEuler 22.03 LTS-SP1)	aarch64	R 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*

CHECK results for RNAmodR on kunpeng2

To the developers/maintainers of the RNAmodR package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/RNAmodR.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: RNAmodR

Version: 1.21.0

Command: /home/biocbuild/R/R/bin/R CMD check --install=check:RNAmodR.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings RNAmodR_1.21.0.tar.gz

StartedAt: 2024-12-24 10:30:39 -0000 (Tue, 24 Dec 2024)

EndedAt: 2024-12-24 10:43:32 -0000 (Tue, 24 Dec 2024)

EllapsedTime: 772.9 seconds

RetCode: 0

Status: WARNINGS

CheckDir: RNAmodR.Rcheck

Warnings: 6

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD check --install=check:RNAmodR.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings RNAmodR_1.21.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/RNAmodR.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 ‘RNAmodR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘RNAmodR’ version ‘1.21.0’
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘RNAmodR’ can be installed ... WARNING
Found the following significant warnings:
  Warning: program compiled against libxml 212 using older 211
See ‘/home/biocbuild/bbs-3.21-bioc/meat/RNAmodR.Rcheck/00install.out’ for details.
* 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 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 ... NOTE
Warning: program compiled against libxml 212 using older 211

A namespace must be able to be loaded with just the base namespace
loaded: otherwise if the namespace gets loaded by a saved object, the
session will be unable to start.

Probably some imports need to be declared in the NAMESPACE file.
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking dependencies in R code ... NOTE
Warning: program compiled against libxml 212 using older 211
Unexported objects imported by ':::' calls:
  'BiocGenerics:::replaceSlots' 'Biostrings:::XString'
  'IRanges:::.valid.CompressedList' 'IRanges:::coerceToCompressedList'
  'S4Vectors:::.valid.DataFrame' 'S4Vectors:::labeledLine'
  'S4Vectors:::make_zero_col_DataFrame'
  'S4Vectors:::prepare_objects_to_bind'
  See the note in ?`:::` about the use of this operator.
There are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
  '.get_inosine_score'
* checking S3 generic/method consistency ... WARNING
Warning: program compiled against libxml 212 using older 211
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
* checking replacement functions ... WARNING
Warning: program compiled against libxml 212 using older 211
The argument of a replacement function which corresponds to the right
hand side must be named ‘value’.
* checking foreign function calls ... NOTE
Warning: program compiled against libxml 212 using older 211
See chapter ‘System and foreign language interfaces’ in the ‘Writing R
Extensions’ manual.
* checking R code for possible problems ... NOTE
Warning: program compiled against libxml 212 using older 211
* checking Rd files ... NOTE
checkRd: (-1) ModInosine-functions.Rd:64-66: Lost braces in \itemize; meant \describe ?
checkRd: (-1) ModInosine-functions.Rd:44: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) ModInosine-functions.Rd:45: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) ModInosine-functions.Rd:46: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) ModInosine-functions.Rd:47-49: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) ModInosine-functions.Rd:50: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) ModInosine-functions.Rd:51: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) ModInosine.Rd:39-40: Lost braces in \itemize; meant \describe ?
checkRd: (-1) ModInosine.Rd:41-42: Lost braces in \itemize; meant \describe ?
checkRd: (-1) ModInosine.Rd:43-44: Lost braces in \itemize; meant \describe ?
checkRd: (-1) Modifier-class.Rd:124-126: Lost braces in \itemize; meant \describe ?
checkRd: (-1) Modifier-class.Rd:127-128: Lost braces in \itemize; meant \describe ?
checkRd: (-1) Modifier-class.Rd:129-130: Lost braces in \itemize; meant \describe ?
checkRd: (-1) Modifier-class.Rd:78-81: Lost braces in \itemize; meant \describe ?
checkRd: (-1) Modifier-class.Rd:82: Lost braces in \itemize; meant \describe ?
checkRd: (-1) Modifier-class.Rd:83-85: Lost braces in \itemize; meant \describe ?
checkRd: (-1) Modifier-class.Rd:103-105: Lost braces in \itemize; meant \describe ?
checkRd: (-1) Modifier-class.Rd:194-195: Lost braces in \itemize; meant \describe ?
checkRd: (-1) Modifier-class.Rd:196-197: Lost braces in \itemize; meant \describe ?
checkRd: (-1) Modifier-class.Rd:198-199: Lost braces in \itemize; meant \describe ?
checkRd: (-1) Modifier-functions.Rd:138-139: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) Modifier-functions.Rd:140-141: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) Modifier-functions.Rd:142-143: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) Modifier-functions.Rd:144: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) Modifier-functions.Rd:145: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) Modifier-functions.Rd:146-147: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) Modifier-functions.Rd:148: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) Modifier-functions.Rd:149: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) Modifier-functions.Rd:150-151: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) Modifier-functions.Rd:152: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) Modifier-functions.Rd:153-154: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) Modifier-functions.Rd:155-156: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) ModifierSet-class.Rd:49-51: Lost braces in \itemize; meant \describe ?
checkRd: (-1) ModifierSet-class.Rd:52-53: Lost braces in \itemize; meant \describe ?
checkRd: (-1) ModifierSet-class.Rd:54-57: Lost braces in \itemize; meant \describe ?
checkRd: (-1) ModifierSet-class.Rd:74-80: Lost braces in \itemize; meant \describe ?
checkRd: (-1) RNAmodR-datasets.Rd:20: Lost braces in \itemize; meant \describe ?
checkRd: (-1) RNAmodR-datasets.Rd:21: Lost braces in \itemize; meant \describe ?
checkRd: (-1) RNAmodR-datasets.Rd:22: Lost braces in \itemize; meant \describe ?
checkRd: (-1) RNAmodR-datasets.Rd:23: Lost braces in \itemize; meant \describe ?
checkRd: (-1) RNAmodR-datasets.Rd:24: Lost braces in \itemize; meant \describe ?
checkRd: (-1) RNAmodR-datasets.Rd:25: Lost braces in \itemize; meant \describe ?
checkRd: (-1) RNAmodR-datasets.Rd:26: Lost braces in \itemize; meant \describe ?
checkRd: (-1) RNAmodR-datasets.Rd:27: Lost braces in \itemize; meant \describe ?
checkRd: (-1) RNAmodR-datasets.Rd:28: Lost braces in \itemize; meant \describe ?
checkRd: (-1) RNAmodR-datasets.Rd:29: Lost braces in \itemize; meant \describe ?
checkRd: (-1) RNAmodR-datasets.Rd:30: Lost braces in \itemize; meant \describe ?
checkRd: (-1) RNAmodR-development.Rd:49-55: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) RNAmodR-development.Rd:56-57: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) SequenceData-class.Rd:56-57: Lost braces in \itemize; meant \describe ?
checkRd: (-1) SequenceData-class.Rd:58-59: Lost braces in \itemize; meant \describe ?
checkRd: (-1) SequenceData-class.Rd:60-62: Lost braces in \itemize; meant \describe ?
checkRd: (-1) SequenceData-class.Rd:63-64: Lost braces in \itemize; meant \describe ?
checkRd: (-1) SequenceData-class.Rd:75: Lost braces in \itemize; meant \describe ?
checkRd: (-1) SequenceData-class.Rd:76-78: Lost braces in \itemize; meant \describe ?
checkRd: (-1) SequenceData-functions.Rd:159: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) SequenceData-functions.Rd:160-161: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) SequenceData-functions.Rd:162-163: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) SequenceData-functions.Rd:164-165: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) aggregate.Rd:64-68: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) aggregate.Rd:69-72: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) aggregate.Rd:73-74: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) aggregate.Rd:79-80: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) aggregate.Rd:82-83: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) aggregate.Rd:85-86: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) compareByCoord.Rd:45-46: Lost braces in \itemize; meant \describe ?
checkRd: (-1) compareByCoord.Rd:47: Lost braces in \itemize; meant \describe ?
checkRd: (-1) compareByCoord.Rd:48-50: Lost braces in \itemize; meant \describe ?
checkRd: (-1) compareByCoord.Rd:51-54: Lost braces in \itemize; meant \describe ?
checkRd: (-1) compareByCoord.Rd:55-56: Lost braces in \itemize; meant \describe ?
checkRd: (-1) compareByCoord.Rd:57: Lost braces in \itemize; meant \describe ?
checkRd: (-1) modify.Rd:41: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) modify.Rd:42-43: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) plotData.Rd:122-124: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plotData.Rd:125-127: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plotData.Rd:128-129: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plotData.Rd:130-131: Lost braces in \itemize; meant \describe ?
checkRd: (-1) subsetByCoord.Rd:99-105: Lost braces in \itemize; meant \describe ?
checkRd: (-1) subsetByCoord.Rd:106-107: Lost braces in \itemize; meant \describe ?
checkRd: (-1) subsetByCoord.Rd:108-110: Lost braces in \itemize; meant \describe ?
checkRd: (-1) subsetByCoord.Rd:111-113: Lost braces in \itemize; meant \describe ?
checkRd: (-1) subsetByCoord.Rd:124-125: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) subsetByCoord.Rd:128-129: Lost braces in \itemize; \value handles \item{}{} directly
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... WARNING
Warning: program compiled against libxml 212 using older 211
All user-level objects in a package should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* checking for code/documentation mismatches ... WARNING
Warning: program compiled against libxml 212 using older 211
Warning: program compiled against libxml 212 using older 211
Warning: program compiled against libxml 212 using older 211
* checking Rd \usage sections ... NOTE
Documented arguments not in \usage in Rd file 'RNAmodR-internals.Rd':
  ‘object’ ‘range’ ‘data’ ‘modType’ ‘scoreFun’ ‘source’ ‘type’ ‘j’
  ‘value’

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.
Warning: program compiled against libxml 212 using older 211
The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... WARNING
  Warning: program compiled against libxml 212 using older 211
* 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
stats                          67.354  5.395  72.483
CoverageSequenceData-class     12.898  1.697  22.158
ModInosine                     10.185  0.120  15.624
EndSequenceData-class           8.027  0.240  13.507
ProtectedEndSequenceData-class  7.560  0.220  12.501
PileupSequenceData-class        7.270  0.172  12.622
* 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: 6 WARNINGs, 6 NOTEs
See
  ‘/home/biocbuild/bbs-3.21-bioc/meat/RNAmodR.Rcheck/00check.log’
for details.

Installation output

RNAmodR.Rcheck/00install.out

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


* installing to library ‘/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library’
* installing *source* package ‘RNAmodR’ ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
Warning: program compiled against libxml 212 using older 211
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
Warning: program compiled against libxml 212 using older 211
** testing if installed package can be loaded from final location
Warning: program compiled against libxml 212 using older 211
** testing if installed package keeps a record of temporary installation path
* DONE (RNAmodR)

Tests output

RNAmodR.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(RNAmodR)
Loading required package: S4Vectors
Loading required package: stats4
Loading required package: BiocGenerics
Loading required package: generics

Attaching package: 'generics'

The following objects are masked from 'package:base':

    as.difftime, as.factor, as.ordered, intersect, is.element, setdiff,
    setequal, union


Attaching package: 'BiocGenerics'

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, aperm, append,
    as.data.frame, basename, cbind, colnames, dirname, do.call,
    duplicated, eval, evalq, get, grep, grepl, is.unsorted, lapply,
    mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int,
    rank, rbind, rownames, sapply, saveRDS, table, tapply, unique,
    unsplit, which.max, which.min


Attaching package: 'S4Vectors'

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

    findMatches

The following objects are masked from 'package:base':

    I, expand.grid, unname

Loading required package: IRanges
Loading required package: GenomicRanges
Loading required package: GenomeInfoDb
Loading required package: Modstrings
Loading required package: Biostrings
Loading required package: XVector

Attaching package: 'Biostrings'

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

    strsplit

Warning: program compiled against libxml 212 using older 211

Attaching package: 'RNAmodR'

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

    compare

> 
> test_check("RNAmodR")
[E::idx_find_and_load] Could not retrieve index file for '/home/biocbuild/.cache/R/ExperimentHub/233c5a3e5bac1c_2547'
[E::idx_find_and_load] Could not retrieve index file for '/home/biocbuild/.cache/R/ExperimentHub/233c5a3e5bac1c_2547'
[E::idx_find_and_load] Could not retrieve index file for '/home/biocbuild/.cache/R/ExperimentHub/233c5a3e5bac1c_2547'
[E::idx_find_and_load] Could not retrieve index file for '/home/biocbuild/.cache/R/ExperimentHub/233c5a3e5bac1c_2547'
[E::idx_find_and_load] Could not retrieve index file for '/home/biocbuild/.cache/R/ExperimentHub/233c5a3e5bac1c_2547'
[E::idx_find_and_load] Could not retrieve index file for '/home/biocbuild/.cache/R/ExperimentHub/233c5a3e5bac1c_2547'
[ FAIL 0 | WARN 2 | SKIP 9 | PASS 192 ]

══ Skipped tests (9) ═══════════════════════════════════════════════════════════
• On Bioconductor (9): 'test-0SequenceData.R:53:3',
  'test-0SequenceDataFrame.R:23:3', 'test-1SequenceDataSet.R:57:3',
  'test-2Modifier.R:85:3', 'test-3normalization.R:3:3', 'test-3subset.R:4:3',
  'test-3zcomparison.R:4:3', 'test-4roc.R:3:3', 'test-8visualization.R:158:3'

[ FAIL 0 | WARN 2 | SKIP 9 | PASS 192 ]
> 
> proc.time()
   user  system elapsed 
 65.777   3.220  76.764

Example timings

RNAmodR.Rcheck/RNAmodR-Ex.timings

name	user	system	elapsed
CoverageSequenceData-class	12.898	1.697	22.158
EndSequenceData-class	8.027	0.240	13.507
ModInosine-functions	2.286	0.882	3.174
ModInosine	10.185	0.120	15.624
Modifier-functions	0.276	0.004	0.280
NormEndSequenceData-class	0.001	0.000	0.000
PileupSequenceData-class	7.270	0.172	12.622
ProtectedEndSequenceData-class	7.560	0.220	12.501
RNAmodR-development	0.095	0.000	0.095
SequenceData-functions	0.073	0.004	0.078
SequenceDataFrame-class	0.072	0.000	0.072
SequenceDataList-class	0.143	0.000	0.143
SequenceDataSet-class	0.096	0.000	0.097
SequenceModDNAStringSetTrack-class	1.788	0.108	1.899
SequenceModRNAStringSetTrack-class	0.174	0.000	0.174
aggregate	0.663	0.000	0.665
compareByCoord	2.654	0.007	2.668
modify	0.650	0.000	0.651
plotData	2.570	0.004	2.579
plotROC	1.905	0.080	1.988
settings	0.097	0.008	0.105
stats	67.354	5.395	72.483
subsetByCoord	0.794	0.004	0.800