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This page was generated on 2025-08-28 11:43 -0400 (Thu, 28 Aug 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 (2025-06-13) -- "Great Square Root" 4824
merida1macOS 12.7.5 Montereyx86_644.5.1 RC (2025-06-05 r88288) -- "Great Square Root" 4604
kjohnson1macOS 13.6.6 Venturaarm644.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" 4545
kunpeng2Linux (openEuler 24.03 LTS)aarch64R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" 4579
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 1758/2341HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ReUseData 1.8.0  (landing page)
Qian Liu
Snapshot Date: 2025-08-25 13:40 -0400 (Mon, 25 Aug 2025)
git_url: https://git.bioconductor.org/packages/ReUseData
git_branch: RELEASE_3_21
git_last_commit: 601a107
git_last_commit_date: 2025-04-15 13:01:44 -0400 (Tue, 15 Apr 2025)
nebbiolo1Linux (Ubuntu 24.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 12.7.5 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.6 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published
kunpeng2Linux (openEuler 24.03 LTS) / aarch64  OK    OK    OK  


CHECK results for ReUseData on kunpeng2

To the developers/maintainers of the ReUseData package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/ReUseData.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: ReUseData
Version: 1.8.0
Command: /home/biocbuild/R/R/bin/R CMD check --install=check:ReUseData.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings ReUseData_1.8.0.tar.gz
StartedAt: 2025-08-26 13:50:38 -0000 (Tue, 26 Aug 2025)
EndedAt: 2025-08-26 13:53:34 -0000 (Tue, 26 Aug 2025)
EllapsedTime: 176.1 seconds
RetCode: 0
Status:   OK  
CheckDir: ReUseData.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD check --install=check:ReUseData.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings ReUseData_1.8.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/ReUseData.Rcheck’
* using R Under development (unstable) (2025-02-19 r87757)
* 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-SP1)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘ReUseData/DESCRIPTION’ ... OK
* this is package ‘ReUseData’ version ‘1.8.0’
* 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 ... NOTE
Found the following hidden files and directories:
  .BBSoptions
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘ReUseData’ 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 ... 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
               user system elapsed
dataHub-class 9.161  0.427   9.628
getCloudData  3.452  0.291   5.422
* 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 NOTE
See
  ‘/home/biocbuild/bbs-3.21-bioc/meat/ReUseData.Rcheck/00check.log’
for details.


Installation output

ReUseData.Rcheck/00install.out

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


* installing to library ‘/home/biocbuild/R/R-devel_2025-02-19/site-library’
* installing *source* package ‘ReUseData’ ...
** this is package ‘ReUseData’ version ‘1.8.0’
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** 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 (ReUseData)

Tests output

ReUseData.Rcheck/tests/testthat.Rout


R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences"
Copyright (C) 2025 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(ReUseData)
> 
> test_check("ReUseData")
Note: you need to assign a name for the recipe: rcpName <- recipeLoad('xx')
Data recipe loaded!
Use inputs() to check required input parameters before evaluation.
Check here: https://rcwl.org/dataRecipes/echo_out.html
for user instructions (e.g., eligible input values, data source, etc.)

}INFO Final process status is success

Updating data record...
outfile.txt added

Updating data record...
1da830654e99b4_GRCh38.primary_assembly.genome.fa.1.bt2 added
1da830598e10ad_GRCh38.primary_assembly.genome.fa.2.bt2 added
1da8304dc39ac6_GRCh38.primary_assembly.genome.fa.3.bt2 added
1da8302919cb8_GRCh38.primary_assembly.genome.fa.4.bt2 added
1da8301c1944af_GRCh38.primary_assembly.genome.fa.rev.1.bt2 added
1da83067e56284_GRCh38.primary_assembly.genome.fa.rev.2.bt2 added
1da830507fae6a_outfile.txt added
1da83022e235af_GRCh37_to_GRCh38.chain added
1da8302c22fb31_GRCh37_to_NCBI34.chain added
1da8308e36aad_GRCh37_to_NCBI35.chain added
1da8307d70bf78_GRCh37_to_NCBI36.chain added
1da83033f33a3d_GRCh38_to_GRCh37.chain added
1da83036958834_GRCh38_to_NCBI34.chain added
1da8302a5cc8dc_GRCh38_to_NCBI35.chain added
1da8301b5c7b59_GRCh38_to_NCBI36.chain added
1da830367ef62_NCBI34_to_GRCh37.chain added
1da83065b68b39_NCBI34_to_GRCh38.chain added
1da83051f2740a_NCBI35_to_GRCh37.chain added
1da8301a6258d9_NCBI35_to_GRCh38.chain added
1da83060643265_NCBI36_to_GRCh37.chain added
1da83039f986a8_NCBI36_to_GRCh38.chain added
1da83077b1f2e7_GRCm38_to_NCBIM36.chain added
1da830f8c76bb_GRCm38_to_NCBIM37.chain added
1da83013b5d74d_NCBIM36_to_GRCm38.chain added
1da830715bfcae_NCBIM37_to_GRCm38.chain added
1da83035685f10_1000G_omni2.5.b37.vcf.gz added
1da8301ec218ae_1000G_omni2.5.b37.vcf.gz.tbi added
1da8303cab02b9_Mills_and_1000G_gold_standard.indels.b37.vcf.gz added
1da8304ccb531b_Mills_and_1000G_gold_standard.indels.b37.vcf.gz.tbi added
1da83057162b0b_1000G_omni2.5.hg38.vcf.gz added
1da8304bb78dad_1000G_omni2.5.hg38.vcf.gz.tbi added
1da8303219eccf_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz added
1da83030a43bb8_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz.tbi added
1da830197b2874_af-only-gnomad.raw.sites.vcf added
1da83034ab8987_af-only-gnomad.raw.sites.vcf.idx added
1da8304cbd8067_Mutect2-exome-panel.vcf.idx added
1da8301608af8_Mutect2-WGS-panel-b37.vcf added
1da83052b37f1_Mutect2-WGS-panel-b37.vcf.idx added
1da8306f9fb616_small_exac_common_3.vcf added
1da8302d838629_small_exac_common_3.vcf.idx added
1da830e0ea29e_1000g_pon.hg38.vcf.gz added
1da8306d10758f_1000g_pon.hg38.vcf.gz.tbi added
1da8306176c066_af-only-gnomad.hg38.vcf.gz added
1da83044a42ad3_af-only-gnomad.hg38.vcf.gz.tbi added
1da830176d3e6b_small_exac_common_3.hg38.vcf.gz added
1da8307cd33bbf_small_exac_common_3.hg38.vcf.gz.tbi added
1da830480c1a35_gencode.v41.annotation.gtf added
1da8307d23c9a4_gencode.v42.annotation.gtf added
1da8304ec5afc9_gencode.vM30.annotation.gtf added
1da830626e730e_gencode.vM31.annotation.gtf added
1da8305d87fc0a_gencode.v41.transcripts.fa added
1da8308bf3671_gencode.v41.transcripts.fa.fai added
1da8305a2065f5_gencode.v42.transcripts.fa added
1da8306d1472c5_gencode.v42.transcripts.fa.fai added
1da8301c750dbe_gencode.vM30.pc_transcripts.fa added
1da8304b7c62a3_gencode.vM30.pc_transcripts.fa.fai added
1da830227cd1d5_gencode.vM31.pc_transcripts.fa added
1da8303b37266d_gencode.vM31.pc_transcripts.fa.fai added
1da830827655c_GRCh38.primary_assembly.genome.fa.1.ht2 added
1da8306f4824f0_GRCh38.primary_assembly.genome.fa.2.ht2 added
1da830124d5178_GRCh38.primary_assembly.genome.fa.3.ht2 added
1da83053def30a_GRCh38.primary_assembly.genome.fa.4.ht2 added
1da830216211bf_GRCh38.primary_assembly.genome.fa.5.ht2 added
1da83042f18d30_GRCh38.primary_assembly.genome.fa.6.ht2 added
1da8306d5a1b7e_GRCh38.primary_assembly.genome.fa.7.ht2 added
1da830560d9b46_GRCh38.primary_assembly.genome.fa.8.ht2 added
1da830faf0d98_GRCh38_full_analysis_set_plus_decoy_hla.fa.fai added
1da8306ebaa676_GRCh38_full_analysis_set_plus_decoy_hla.fa.amb added
1da8305b38d338_GRCh38_full_analysis_set_plus_decoy_hla.fa.ann added
1da8307f4ec3ae_GRCh38_full_analysis_set_plus_decoy_hla.fa.bwt added
1da8301c3e2c9f_GRCh38_full_analysis_set_plus_decoy_hla.fa.pac added
1da830694775d6_GRCh38_full_analysis_set_plus_decoy_hla.fa.sa added
1da8306c5f393d_GRCh38_full_analysis_set_plus_decoy_hla.fa added
1da8307db4ed06_GRCh38.primary_assembly.genome.fa.fai added
1da8302deba0a9_GRCh38.primary_assembly.genome.fa.amb added
1da8303cc77a8_GRCh38.primary_assembly.genome.fa.ann added
1da8307a8828c5_GRCh38.primary_assembly.genome.fa.bwt added
1da83075f7bade_GRCh38.primary_assembly.genome.fa.pac added
1da830f0414d_GRCh38.primary_assembly.genome.fa.sa added
1da830494dd88f_GRCh38.primary_assembly.genome.fa added
1da83058662ded_hs37d5.fa.fai added
1da8305e783d57_hs37d5.fa.amb added
1da830520d0f00_hs37d5.fa.ann added
1da830328693e2_hs37d5.fa.bwt added
1da8304b8cb01c_hs37d5.fa.pac added
1da8306e821cbf_hs37d5.fa.sa added
1da8307e02f686_hs37d5.fa added
1da8306e0981f1_complete_ref_lens.bin added
1da83029b9432c_ctable.bin added
1da83062a5be2_ctg_offsets.bin added
1da8305d51a6e1_duplicate_clusters.tsv added
1da8303c0694a4_info.json added
1da8305a094eec_mphf.bin added
1da8307eb3b8a0_pos.bin added
1da8307ef821d4_pre_indexing.log added
1da83047636a6a_rank.bin added
1da83054c153e6_ref_indexing.log added
1da830ea72f6c_refAccumLengths.bin added
1da830361e10e0_reflengths.bin added
1da8302ffa271e_refseq.bin added
1da830df5f31b_seq.bin added
1da830525c3d80_versionInfo.json added
1da83019419cf5_salmon_index added
1da8307a552c58_chrLength.txt added
1da83050112a86_chrName.txt added
1da830472d3d9e_chrNameLength.txt added
1da8307e21a401_chrStart.txt added
1da8304a99534b_exonGeTrInfo.tab added
1da8303d24f87d_exonInfo.tab added
1da8307f11e54e_geneInfo.tab added
1da83013e72bda_Genome added
1da830158b266a_genomeParameters.txt added
1da8305d8a22a5_Log.out added
1da83065f43adb_SA added
1da8304811ba4c_SAindex added
1da8302916d2c1_sjdbInfo.txt added
1da8305476579a_sjdbList.fromGTF.out.tab added
1da8304614b0d2_sjdbList.out.tab added
1da830172054b2_transcriptInfo.tab added
1da8307e2f9ac6_GRCh38.GENCODE.v42_100 added
1da8304c3f0cb5_knownGene_hg38.sql added
1da8307471fb93_knownGene_hg38.txt added
1da8303a362f6a_refGene_hg38.sql added
1da83026485ba1_refGene_hg38.txt added
1da8307325b433_knownGene_mm39.sql added
1da830392e513e_knownGene_mm39.txt added
1da8306dabc60c_refGene_mm39.sql added
1da83047e70819_refGene_mm39.txt added
trying URL 'https://storage.googleapis.com/reusedata/echo/outfile.txt'
Content type 'text/plain' length 30 bytes
==================================================
downloaded 30 bytes

trying URL 'https://storage.googleapis.com/reusedata/echo/echo_out_Hello_World!_outfile.yml'
Content type 'application/x-yaml' length 151 bytes
==================================================
downloaded 151 bytes

trying URL 'https://storage.googleapis.com/reusedata/echo/echo_out_Hello_World!_outfile.cwl'
Content type 'application/octet-stream' length 1152 bytes
==================================================
downloaded 1152 bytes

trying URL 'https://storage.googleapis.com/reusedata/echo/echo_out_Hello_World!_outfile.md5'
Content type 'application/octet-stream' length 45 bytes
==================================================
downloaded 45 bytes

trying URL 'https://storage.googleapis.com/reusedata/echo/echo_out_Hello_World!_outfile.sh'
Content type 'application/x-shellscript' length 68 bytes
==================================================
downloaded 68 bytes

Data is downloaded: 
/home/biocbuild/tmp/RtmpJrn8q0/test_gcpData/outfile.txt
}INFO Final process status is success
NOTE: existing caches will be removed and regenerated!
Updating recipes...
STAR_index.R added
bowtie2_index.R added
echo_out.R added
ensembl_liftover.R added
gcp_broad_gatk_hg19.R added
gcp_broad_gatk_hg38.R added
gcp_gatk_mutect2_b37.R added
gcp_gatk_mutect2_hg38.R added
gencode_annotation.R added
gencode_genome_grch38.R added
gencode_transcripts.R added
hisat2_index.R added
reference_genome.R added
salmon_index.R added
ucsc_database.R added

Data recipe loaded!
Use inputs(ensembl_liftover) to check required input parameters before evaluation.
Check here: https://rcwl.org/dataRecipes/ensembl_liftover.html
for user instructions (e.g., eligible input values, data source, etc.)

[ FAIL 0 | WARN 0 | SKIP 0 | PASS 44 ]
> Sys.setenv(cachePath = file.path(tempdir(), "cache"))
> 
> 
> 
> proc.time()
   user  system elapsed 
 31.041   1.990  35.655 

Example timings

ReUseData.Rcheck/ReUseData-Ex.timings

nameusersystemelapsed
dataHub-class9.1610.4279.628
dataSearch1.6410.0031.649
dataUpdate000
getCloudData3.4520.2915.422
getData000
meta_data0.0000.0010.001
recipeHub-class0.1800.0060.187
recipeLoad1.9220.1202.049
recipeMake000
recipeSearch0.8270.0230.853
recipeUpdate000