Qian Liu
| Snapshot Date: 2025-09-25 13:40 -0400 (Thu, 25 Sep 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) |
| Back to Multiple platform build/check report for BioC 3.21: simplified long |
|
This page was generated on 2025-09-29 11:41 -0400 (Mon, 29 Sep 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4827 |
| merida1 | macOS 12.7.5 Monterey | x86_64 | 4.5.1 RC (2025-06-05 r88288) -- "Great Square Root" | 4608 |
| kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" | 4549 |
| kunpeng2 | Linux (openEuler 24.03 LTS) | aarch64 | R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" | 4580 |
| 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 1758/2341 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| ReUseData 1.8.0 (landing page) Qian Liu
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| merida1 | macOS 12.7.5 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | OK | OK | OK | | ||||||||
| kunpeng2 | Linux (openEuler 24.03 LTS) / aarch64 | OK | OK | OK | ||||||||||
|
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. |
| 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: 2025-09-26 14:30:22 -0000 (Fri, 26 Sep 2025) |
| EndedAt: 2025-09-26 14:33:10 -0000 (Fri, 26 Sep 2025) |
| EllapsedTime: 168.1 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: ReUseData.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### 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 9.311 0.343 9.687
getCloudData 3.472 0.259 6.993
* 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.
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)
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.)
}[1;30mINFO[0m Final process status is success
Updating data record...
outfile.txt added
Updating data record...
2536b302dbedc_GRCh38.primary_assembly.genome.fa.1.bt2 added
2536b18fbabe_GRCh38.primary_assembly.genome.fa.2.bt2 added
2536b1432b574_GRCh38.primary_assembly.genome.fa.3.bt2 added
2536b1efba8df_GRCh38.primary_assembly.genome.fa.4.bt2 added
2536b2cb279a9_GRCh38.primary_assembly.genome.fa.rev.1.bt2 added
2536bc9b603a_GRCh38.primary_assembly.genome.fa.rev.2.bt2 added
2536b40b745f8_outfile.txt added
2536b621208cf_GRCh37_to_GRCh38.chain added
2536b13237a86_GRCh37_to_NCBI34.chain added
2536bb9cf3b6_GRCh37_to_NCBI35.chain added
2536b61ee75fa_GRCh37_to_NCBI36.chain added
2536b6be4bfeb_GRCh38_to_GRCh37.chain added
2536b47545b15_GRCh38_to_NCBI34.chain added
2536b12f4fe49_GRCh38_to_NCBI35.chain added
2536b15ccd976_GRCh38_to_NCBI36.chain added
2536b2b380cca_NCBI34_to_GRCh37.chain added
2536b11326754_NCBI34_to_GRCh38.chain added
2536b11f1b52e_NCBI35_to_GRCh37.chain added
2536b2c0cfe6d_NCBI35_to_GRCh38.chain added
2536bc206b8e_NCBI36_to_GRCh37.chain added
2536b3ddb4c97_NCBI36_to_GRCh38.chain added
2536b6489f690_GRCm38_to_NCBIM36.chain added
2536b626afa16_GRCm38_to_NCBIM37.chain added
2536b396be075_NCBIM36_to_GRCm38.chain added
2536b3e0215a5_NCBIM37_to_GRCm38.chain added
2536b17cddc4a_1000G_omni2.5.b37.vcf.gz added
2536b66fffe0b_1000G_omni2.5.b37.vcf.gz.tbi added
2536b24793dc8_Mills_and_1000G_gold_standard.indels.b37.vcf.gz added
2536b73529b4d_Mills_and_1000G_gold_standard.indels.b37.vcf.gz.tbi added
2536b781986f0_1000G_omni2.5.hg38.vcf.gz added
2536b37c80242_1000G_omni2.5.hg38.vcf.gz.tbi added
2536b23805a2a_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz added
2536b79a941af_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz.tbi added
2536b4bfab7b6_af-only-gnomad.raw.sites.vcf added
2536b427c0309_af-only-gnomad.raw.sites.vcf.idx added
2536b265bbb58_Mutect2-exome-panel.vcf.idx added
2536b589617f0_Mutect2-WGS-panel-b37.vcf added
2536b3334901_Mutect2-WGS-panel-b37.vcf.idx added
2536b86dc427_small_exac_common_3.vcf added
2536b6bb99277_small_exac_common_3.vcf.idx added
2536bed03cb7_1000g_pon.hg38.vcf.gz added
2536b6a5c3a21_1000g_pon.hg38.vcf.gz.tbi added
2536b579e5262_af-only-gnomad.hg38.vcf.gz added
2536b562497cd_af-only-gnomad.hg38.vcf.gz.tbi added
2536b7d51386b_small_exac_common_3.hg38.vcf.gz added
2536b6d6b2bd8_small_exac_common_3.hg38.vcf.gz.tbi added
2536b15ca497_gencode.v41.annotation.gtf added
2536be839fbf_gencode.v42.annotation.gtf added
2536b7f5ce106_gencode.vM30.annotation.gtf added
2536b2d69a304_gencode.vM31.annotation.gtf added
2536b1aa40b4d_gencode.v41.transcripts.fa added
2536b3d382d9d_gencode.v41.transcripts.fa.fai added
2536b11f39994_gencode.v42.transcripts.fa added
2536b7d0f0563_gencode.v42.transcripts.fa.fai added
2536b76a40e12_gencode.vM30.pc_transcripts.fa added
2536b4ff5af3a_gencode.vM30.pc_transcripts.fa.fai added
2536b14dce1ae_gencode.vM31.pc_transcripts.fa added
2536b5da40c1d_gencode.vM31.pc_transcripts.fa.fai added
2536b746eed02_GRCh38.primary_assembly.genome.fa.1.ht2 added
2536b82f7cfb_GRCh38.primary_assembly.genome.fa.2.ht2 added
2536b55bd930e_GRCh38.primary_assembly.genome.fa.3.ht2 added
2536b2c36ef44_GRCh38.primary_assembly.genome.fa.4.ht2 added
2536b2bafd725_GRCh38.primary_assembly.genome.fa.5.ht2 added
2536b4f66d4bd_GRCh38.primary_assembly.genome.fa.6.ht2 added
2536b7831a6fb_GRCh38.primary_assembly.genome.fa.7.ht2 added
2536b6e2bda2f_GRCh38.primary_assembly.genome.fa.8.ht2 added
2536b75c29015_GRCh38_full_analysis_set_plus_decoy_hla.fa.fai added
2536b50c7beeb_GRCh38_full_analysis_set_plus_decoy_hla.fa.amb added
2536b715f2330_GRCh38_full_analysis_set_plus_decoy_hla.fa.ann added
2536b7e30543c_GRCh38_full_analysis_set_plus_decoy_hla.fa.bwt added
2536b3c815162_GRCh38_full_analysis_set_plus_decoy_hla.fa.pac added
2536b2f5fe8_GRCh38_full_analysis_set_plus_decoy_hla.fa.sa added
2536b688c8e5e_GRCh38_full_analysis_set_plus_decoy_hla.fa added
2536b141fa3c4_GRCh38.primary_assembly.genome.fa.fai added
2536b5653f7b5_GRCh38.primary_assembly.genome.fa.amb added
2536b65ddc6c9_GRCh38.primary_assembly.genome.fa.ann added
2536b18acf9d_GRCh38.primary_assembly.genome.fa.bwt added
2536b57b09c4c_GRCh38.primary_assembly.genome.fa.pac added
2536b74616688_GRCh38.primary_assembly.genome.fa.sa added
2536be7b0a3_GRCh38.primary_assembly.genome.fa added
2536b51a3f51_hs37d5.fa.fai added
2536bf0571d5_hs37d5.fa.amb added
2536b3e1fde41_hs37d5.fa.ann added
2536b170dd8e5_hs37d5.fa.bwt added
2536bc147739_hs37d5.fa.pac added
2536b34c3ec53_hs37d5.fa.sa added
2536b6703881f_hs37d5.fa added
2536b20f158e7_complete_ref_lens.bin added
2536b1267f871_ctable.bin added
2536b5b727522_ctg_offsets.bin added
2536b2920d5e2_duplicate_clusters.tsv added
2536b68258b7f_info.json added
2536b7a96466_mphf.bin added
2536b54d0ad08_pos.bin added
2536b378c603c_pre_indexing.log added
2536b7fdb0b61_rank.bin added
2536b42fc8737_ref_indexing.log added
2536b2d4ef051_refAccumLengths.bin added
2536b50a2ca4d_reflengths.bin added
2536b345baa67_refseq.bin added
2536b2b7f448d_seq.bin added
2536bd241baf_versionInfo.json added
2536b348b0a4f_salmon_index added
2536b140bd2eb_chrLength.txt added
2536b2143bf74_chrName.txt added
2536badf0204_chrNameLength.txt added
2536b79e999b4_chrStart.txt added
2536b22ce8f11_exonGeTrInfo.tab added
2536b628f9e51_exonInfo.tab added
2536b6e4b003c_geneInfo.tab added
2536b23b63fb4_Genome added
2536b67a9dda2_genomeParameters.txt added
2536b7d507212_Log.out added
2536b61d61df5_SA added
2536b7eb7b687_SAindex added
2536b964e94b_sjdbInfo.txt added
2536b169a0a49_sjdbList.fromGTF.out.tab added
2536b65bb3ea7_sjdbList.out.tab added
2536b2a564232_transcriptInfo.tab added
2536b290202ba_GRCh38.GENCODE.v42_100 added
2536b412db3c9_knownGene_hg38.sql added
2536b53771814_knownGene_hg38.txt added
2536b11278e39_refGene_hg38.sql added
2536b48d7182f_refGene_hg38.txt added
2536b2847c51c_knownGene_mm39.sql added
2536b48b3ee75_knownGene_mm39.txt added
2536b48b22391_refGene_mm39.sql added
2536b6b444c53_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/RtmpNOjaxF/test_gcpData/outfile.txt
}[1;30mINFO[0m 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
30.253 2.086 34.123
ReUseData.Rcheck/ReUseData-Ex.timings
| name | user | system | elapsed | |
| dataHub-class | 9.311 | 0.343 | 9.687 | |
| dataSearch | 1.599 | 0.004 | 1.609 | |
| dataUpdate | 0.000 | 0.001 | 0.000 | |
| getCloudData | 3.472 | 0.259 | 6.993 | |
| getData | 0.001 | 0.000 | 0.000 | |
| meta_data | 0.001 | 0.000 | 0.001 | |
| recipeHub-class | 0.196 | 0.004 | 0.203 | |
| recipeLoad | 1.983 | 0.076 | 2.067 | |
| recipeMake | 0 | 0 | 0 | |
| recipeSearch | 0.765 | 0.031 | 0.799 | |
| recipeUpdate | 0.000 | 0.000 | 0.001 | |