Back to Multiple platform build/check report for BioC 3.20:   simplified   long
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This page was generated on 2024-06-20 12:14 -0400 (Thu, 20 Jun 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 22.04.3 LTS)x86_644.4.0 RC (2024-04-16 r86468) -- "Puppy Cup" 4687
lconwaymacOS 12.7.1 Montereyx86_644.4.1 RC (2024-06-06 r86719) -- "Race for Your Life" 4402
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 1619/2242HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
raer 1.3.0  (landing page)
Kent Riemondy
Snapshot Date: 2024-06-19 14:00 -0400 (Wed, 19 Jun 2024)
git_url: https://git.bioconductor.org/packages/raer
git_branch: devel
git_last_commit: 27290f6
git_last_commit_date: 2024-04-30 11:52:24 -0400 (Tue, 30 Apr 2024)
nebbiolo2Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    ERROR  
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published


CHECK results for raer on nebbiolo2

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.

raw results


Summary

Package: raer
Version: 1.3.0
Command: /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:raer.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings raer_1.3.0.tar.gz
StartedAt: 2024-06-20 02:38:05 -0400 (Thu, 20 Jun 2024)
EndedAt: 2024-06-20 02:50:08 -0400 (Thu, 20 Jun 2024)
EllapsedTime: 723.6 seconds
RetCode: 1
Status:   ERROR  
CheckDir: raer.Rcheck
Warnings: NA

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:raer.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings raer_1.3.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/raer.Rcheck’
* using R version 4.4.0 RC (2024-04-16 r86468)
* using platform: x86_64-pc-linux-gnu
* 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 ‘raer/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘raer’ version ‘1.3.0’
* 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: ‘gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’
* 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 ... 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 ... 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 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 ... NOTE
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/bbs-3.20-bioc/R/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       17.123  1.347  18.479
get_splice_sites  8.313  0.508   8.822
* 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 re-building of vignette outputs ... ERROR
Error(s) in re-building vignettes:
  ...
--- re-building ‘raer.Rmd’ using rmarkdown
The magick package is required to crop "/home/biocbuild/bbs-3.20-bioc/meat/raer.Rcheck/vign_test/raer/vignettes/raer_files/figure-html/unnamed-chunk-4-1.png" but not available.
The magick package is required to crop "/home/biocbuild/bbs-3.20-bioc/meat/raer.Rcheck/vign_test/raer/vignettes/raer_files/figure-html/unnamed-chunk-9-1.png" but not available.
The magick package is required to crop "/home/biocbuild/bbs-3.20-bioc/meat/raer.Rcheck/vign_test/raer/vignettes/raer_files/figure-html/unnamed-chunk-9-2.png" but not available.
The magick package is required to crop "/home/biocbuild/bbs-3.20-bioc/meat/raer.Rcheck/vign_test/raer/vignettes/raer_files/figure-html/unnamed-chunk-9-3.png" but not available.
The magick package is required to crop "/home/biocbuild/bbs-3.20-bioc/meat/raer.Rcheck/vign_test/raer/vignettes/raer_files/figure-html/unnamed-chunk-9-4.png" but not available.
The magick package is required to crop "/home/biocbuild/bbs-3.20-bioc/meat/raer.Rcheck/vign_test/raer/vignettes/raer_files/figure-html/unnamed-chunk-9-5.png" but not available.
The magick package is required to crop "/home/biocbuild/bbs-3.20-bioc/meat/raer.Rcheck/vign_test/raer/vignettes/raer_files/figure-html/unnamed-chunk-10-1.png" but not available.
The magick package is required to crop "/home/biocbuild/bbs-3.20-bioc/meat/raer.Rcheck/vign_test/raer/vignettes/raer_files/figure-html/unnamed-chunk-24-1.png" but not available.

Quitting from lines 497-518 [unnamed-chunk-25] (raer.Rmd)
Error: processing vignette 'raer.Rmd' failed with diagnostics:
failed to load resource
  name: AH99003
  title: UCSC RepeatMasker annotations (Sep2021) for Human (hg38)
  reason: 1 resources failed to download
--- failed re-building ‘raer.Rmd’

SUMMARY: processing the following file failed:
  ‘raer.Rmd’

Error: Vignette re-building failed.
Execution halted

* checking PDF version of manual ... OK
* DONE

Status: 1 ERROR, 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.20-bioc/meat/raer.Rcheck/00check.log’
for details.


Installation output

raer.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD INSTALL raer
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.20-bioc/R/site-library’
* installing *source* package ‘raer’ ...
** using staged installation
** libs
using C compiler: ‘gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’
gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rhtslib/include' -I/usr/local/include    -fpic  -g -O2  -Wall -c init.c -o init.o
gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rhtslib/include' -I/usr/local/include    -fpic  -g -O2  -Wall -c plp.c -o plp.o
gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rhtslib/include' -I/usr/local/include    -fpic  -g -O2  -Wall -c plp_data.c -o plp_data.o
gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rhtslib/include' -I/usr/local/include    -fpic  -g -O2  -Wall -c plp_utils.c -o plp_utils.o
gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rhtslib/include' -I/usr/local/include    -fpic  -g -O2  -Wall -c regfile.c -o regfile.o
gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rhtslib/include' -I/usr/local/include    -fpic  -g -O2  -Wall -c sc-plp.c -o sc-plp.o
gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rhtslib/include' -I/usr/local/include    -fpic  -g -O2  -Wall -c utils.c -o utils.o
gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rhtslib/include' -I/usr/local/include    -fpic  -g -O2  -Wall -c ext/bcftools/bcftools-ext.c -o ext/bcftools/bcftools-ext.o
gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rhtslib/include' -I/usr/local/include    -fpic  -g -O2  -Wall -c ext/htsbox/htsbox-ext.c -o ext/htsbox/htsbox-ext.o
gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rhtslib/include' -I/usr/local/include    -fpic  -g -O2  -Wall -c ext/samtools/samtools-ext.c -o ext/samtools/samtools-ext.o
gcc -shared -L/home/biocbuild/bbs-3.20-bioc/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/bbs-3.20-bioc/R/site-library/Rhtslib/usrlib/libhts.a -lcurl -lbz2 -llzma -lz -L/home/biocbuild/bbs-3.20-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.20-bioc/R/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 version 4.4.0 RC (2024-04-16 r86468) -- "Puppy Cup"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-pc-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/bbs-3.20-bioc/R/site-library/raer/extdata/SRR5564269_Aligned.sortedByCoord.out.md.bam
[raer internal] fail to parse region 'chrHello' with /home/biocbuild/bbs-3.20-bioc/R/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
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 1 | SKIP 0 | PASS 262 ]

[ FAIL 0 | WARN 1 | SKIP 0 | PASS 262 ]
> 
> proc.time()
   user  system elapsed 
 88.187   4.153  92.040 

Example timings

raer.Rcheck/raer-Ex.timings

nameusersystemelapsed
annot_from_gr1.6940.0961.791
annot_snps17.123 1.34718.479
calc_AEI1.7050.2081.913
calc_confidence0.2520.0070.261
calc_edit_frequency0.4470.0030.452
calc_scAEI1.1410.0041.146
correct_strand0.5690.0030.574
filter_clustered_variants2.1570.0152.173
filter_multiallelic0.2540.0030.258
filter_splice_variants1.1320.0041.135
find_de_sites1.2160.0321.248
find_mispriming_sites0.5330.0190.552
find_scde_sites2.0770.1412.217
get_overlapping_snps2.3100.0312.342
get_splice_sites8.3130.5088.822
make_de_object0.5760.0600.637
mock_rse0.2430.0120.255
pileup_cells1.3170.0961.413
pileup_sites2.3820.0202.402
raer_example0.0010.0000.000
read_sparray0.8910.0000.890