Back to Multiple platform build/check report for BioC 3.21:   simplified   long
ABCDEFGHIJKLMNOPQ[R]STUVWXYZ

This page was generated on 2024-12-23 11:47 -0500 (Mon, 23 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" 4372
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 1641/2274HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
raer 1.5.0  (landing page)
Kent Riemondy
Snapshot Date: 2024-12-22 13:40 -0500 (Sun, 22 Dec 2024)
git_url: https://git.bioconductor.org/packages/raer
git_branch: devel
git_last_commit: 438c245
git_last_commit_date: 2024-10-29 11:24:55 -0500 (Tue, 29 Oct 2024)
nebbiolo1Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino7Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  NO, package depends on 'rtracklayer' which is only available as a source package that needs compilation
kjohnson3macOS 13.7.1 Ventura / arm64  OK    OK    OK    OK  NO, package depends on 'rtracklayer' which is only available as a source package that needs compilation
kunpeng2Linux (openEuler 22.03 LTS-SP1) / aarch64  OK    OK    OK  


CHECK results for raer on kunpeng2

To the developers/maintainers of the raer package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/raer.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: raer
Version: 1.5.0
Command: /home/biocbuild/R/R/bin/R CMD check --install=check:raer.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings raer_1.5.0.tar.gz
StartedAt: 2024-12-23 11:05:13 -0000 (Mon, 23 Dec 2024)
EndedAt: 2024-12-23 11:13:47 -0000 (Mon, 23 Dec 2024)
EllapsedTime: 514.6 seconds
RetCode: 0
Status:   OK  
CheckDir: raer.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD check --install=check:raer.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings raer_1.5.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/raer.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 ‘raer/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘raer’ version ‘1.5.0’
* 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 ‘raer’ can be installed ... OK
* used C compiler: ‘aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0’
* 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 ...Warning: program compiled against libxml 212 using older 211
 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 ... 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:
  annot_snps.Rd: GRanges, SummarizedExperiment
  calc_AEI.Rd: GRanges, TxDb, SNPlocs, GPos, BiocParallelParam
  calc_edit_frequency.Rd: RangedSummarizedExperiment
  find_de_sites.Rd: RangedSummarizedExperiment
  find_scde_sites.Rd: SingleCellExperiment, rowData, DataFrame
  make_de_object.Rd: RangedSummarizedExperiment
  pileup_cells.Rd: GRanges, BamFile, BamFileList, SingleCellExperiment,
    rowRanges
  pileup_sites.Rd: RangedSummarizedExperiment, BamFile, BamFileList,
    colData, GRanges, BiocParallel, rowRanges
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 ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... INFO
GNU make is a SystemRequirements.
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking use of PKG_*FLAGS in Makefiles ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
File ‘/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/raer/libs/raer.so’:
  Found ‘abort’, possibly from ‘abort’ (C)
  Found ‘exit’, possibly from ‘exit’ (C)
  Found ‘stderr’, possibly from ‘stderr’ (C)
  Found ‘stdout’, possibly from ‘stdout’ (C)

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs nor [v]sprintf. The detected symbols are linked into
the code but might come from libraries and not actually be called.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                   user system elapsed
annot_snps       18.330  0.721  19.507
get_splice_sites 11.466  0.360  11.847
* 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: 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.21-bioc/meat/raer.Rcheck/00check.log’
for details.


Installation output

raer.Rcheck/00install.out

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


* installing to library ‘/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library’
* installing *source* package ‘raer’ ...
** using staged installation
** libs
using C compiler: ‘aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0’
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -I"/home/biocbuild/R/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/Rhtslib/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -Werror=format-security -c init.c -o init.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -I"/home/biocbuild/R/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/Rhtslib/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -Werror=format-security -c plp.c -o plp.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -I"/home/biocbuild/R/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/Rhtslib/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -Werror=format-security -c plp_data.c -o plp_data.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -I"/home/biocbuild/R/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/Rhtslib/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -Werror=format-security -c plp_utils.c -o plp_utils.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -I"/home/biocbuild/R/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/Rhtslib/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -Werror=format-security -c regfile.c -o regfile.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -I"/home/biocbuild/R/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/Rhtslib/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -Werror=format-security -c sc-plp.c -o sc-plp.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -I"/home/biocbuild/R/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/Rhtslib/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -Werror=format-security -c utils.c -o utils.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -I"/home/biocbuild/R/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/Rhtslib/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -Werror=format-security -c ext/bcftools/bcftools-ext.c -o ext/bcftools/bcftools-ext.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -I"/home/biocbuild/R/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/Rhtslib/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -Werror=format-security -c ext/htsbox/htsbox-ext.c -o ext/htsbox/htsbox-ext.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -I"/home/biocbuild/R/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/Rhtslib/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -Werror=format-security -c ext/samtools/samtools-ext.c -o ext/samtools/samtools-ext.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -shared -L/home/biocbuild/R/R/lib -L/usr/local/lib -o raer.so init.o plp.o plp_data.o plp_utils.o regfile.o sc-plp.o utils.o ext/bcftools/bcftools-ext.o ext/htsbox/htsbox-ext.o ext/samtools/samtools-ext.o /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/Rhtslib/usrlib/libhts.a -lcurl -lbz2 -llzma -lz -L/home/biocbuild/R/R/lib -lR
installing to /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/00LOCK-raer/00new/raer/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
*** copying figures
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (raer)

Tests output

raer.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.

> # This file is part of the standard setup for testthat.
> # It is recommended that you do not modify it.
> #
> # Where should you do additional test configuration?
> # Learn more about the roles of various files in:
> # * https://r-pkgs.org/tests.html
> # * https://testthat.r-lib.org/reference/test_package.html#special-files
> 
> library(testthat)
> library(raer)
> 
> test_check("raer")
Using classic mode.
[raer internal] fail to parse region 'chr1' with /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/raer/extdata/SRR5564269_Aligned.sortedByCoord.out.md.bam
[raer internal] fail to parse region 'chrHello' with /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/raer/extdata/SRR5564269_Aligned.sortedByCoord.out.md.bam
Loading required package: SNPlocs.Hsapiens.dbSNP144.GRCh38
Loading required package: BSgenome
Loading required package: BiocIO

Attaching package: 'BiocIO'

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

    FileForFormat

Loading required package: BSgenome.Hsapiens.NCBI.GRCh38
Warning: program compiled against libxml 212 using older 211
i `filter_clustered_variants()`:  removed 70 sites from 72 (2 remain)
i `filter_clustered_variants()`:  removed 3 sites from 9 (6 remain)
i `filter_clustered_variants()`:  removed 6 sites from 9 (3 remain)
[ FAIL 0 | WARN 3 | SKIP 0 | PASS 262 ]

[ FAIL 0 | WARN 3 | SKIP 0 | PASS 262 ]
> 
> proc.time()
   user  system elapsed 
116.250   3.552 119.744 

Example timings

raer.Rcheck/raer-Ex.timings

nameusersystemelapsed
annot_from_gr1.3230.0281.363
annot_snps18.330 0.72119.507
calc_AEI2.7180.0242.749
calc_confidence0.4180.0160.435
calc_edit_frequency0.7560.0120.770
calc_scAEI1.5740.0161.598
correct_strand0.9120.0000.914
filter_clustered_variants3.1280.0353.171
filter_multiallelic0.4080.0040.414
filter_splice_variants1.7970.0001.802
find_de_sites1.8430.0311.879
find_mispriming_sites0.7810.0040.787
find_scde_sites2.4870.0482.544
get_overlapping_snps3.2650.0163.289
get_splice_sites11.466 0.36011.847
make_de_object0.9250.0080.935
mock_rse0.3310.0000.331
pileup_cells1.4640.0431.512
pileup_sites3.6530.0803.743
raer_example0.0020.0000.001
read_sparray0.9070.0200.929