Qian Liu
| Snapshot Date: 2025-09-28 13:45 -0400 (Sun, 28 Sep 2025) |
| git_url: https://git.bioconductor.org/packages/ReUseData |
| git_branch: devel |
| git_last_commit: c5927b9 |
| git_last_commit_date: 2025-04-15 13:01:44 -0400 (Tue, 15 Apr 2025) |
| Back to Multiple platform build/check report for BioC 3.22: simplified long |
|
This page was generated on 2025-09-29 12:07 -0400 (Mon, 29 Sep 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" | 4833 |
| lconway | macOS 12.7.1 Monterey | x86_64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4621 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4566 |
| taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4563 |
| 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 1752/2334 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| ReUseData 1.9.0 (landing page) Qian Liu
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson3 | macOS 13.7.7 Ventura / arm64 | OK | OK | OK | OK | | ||||||||
| taishan | 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: 1.9.0 |
| 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_1.9.0.tar.gz |
| StartedAt: 2025-09-26 11:13:49 -0000 (Fri, 26 Sep 2025) |
| EndedAt: 2025-09-26 11:16:30 -0000 (Fri, 26 Sep 2025) |
| EllapsedTime: 160.2 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_1.9.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/ReUseData.Rcheck’
* using R version 4.5.0 (2025-04-11)
* 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 ‘ReUseData/DESCRIPTION’ ... OK
* this is package ‘ReUseData’ version ‘1.9.0’
* 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 9.139 0.474 9.866
getCloudData 3.319 0.149 6.255
* 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-3.22-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-4.5.0/site-library’ * installing *source* package ‘ReUseData’ ... ** this is package ‘ReUseData’ version ‘1.9.0’ ** 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 version 4.5.0 (2025-04-11) -- "How About a Twenty-Six"
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...
39fb857ad883c_GRCh38.primary_assembly.genome.fa.1.bt2 added
39fb878f3dc52_GRCh38.primary_assembly.genome.fa.2.bt2 added
39fb8619948c0_GRCh38.primary_assembly.genome.fa.3.bt2 added
39fb858444144_GRCh38.primary_assembly.genome.fa.4.bt2 added
39fb81087fec8_GRCh38.primary_assembly.genome.fa.rev.1.bt2 added
39fb84c821397_GRCh38.primary_assembly.genome.fa.rev.2.bt2 added
39fb831870a37_outfile.txt added
39fb83dde577a_GRCh37_to_GRCh38.chain added
39fb82db66a69_GRCh37_to_NCBI34.chain added
39fb84c6d616b_GRCh37_to_NCBI35.chain added
39fb862a7347d_GRCh37_to_NCBI36.chain added
39fb822aaecdd_GRCh38_to_GRCh37.chain added
39fb86d1f16fe_GRCh38_to_NCBI34.chain added
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39fb8491d8578_GRCh38_to_NCBI36.chain added
39fb8a36f29f_NCBI34_to_GRCh37.chain added
39fb8645f48b_NCBI34_to_GRCh38.chain added
39fb850646650_NCBI35_to_GRCh37.chain added
39fb820da8a69_NCBI35_to_GRCh38.chain added
39fb87703e2ef_NCBI36_to_GRCh37.chain added
39fb833cbea40_NCBI36_to_GRCh38.chain added
39fb87c4ea13a_GRCm38_to_NCBIM36.chain added
39fb86b5d92d3_GRCm38_to_NCBIM37.chain added
39fb845fa0682_NCBIM36_to_GRCm38.chain added
39fb83645c610_NCBIM37_to_GRCm38.chain added
39fb811970fd3_1000G_omni2.5.b37.vcf.gz added
39fb8720da6c7_1000G_omni2.5.b37.vcf.gz.tbi added
39fb85c4d48fb_Mills_and_1000G_gold_standard.indels.b37.vcf.gz added
39fb8b33b69_Mills_and_1000G_gold_standard.indels.b37.vcf.gz.tbi added
39fb8a5959c2_1000G_omni2.5.hg38.vcf.gz added
39fb8418fb29_1000G_omni2.5.hg38.vcf.gz.tbi added
39fb85860c3a5_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz added
39fb834d3614_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz.tbi added
39fb865b243ea_af-only-gnomad.raw.sites.vcf added
39fb830a504e9_af-only-gnomad.raw.sites.vcf.idx added
39fb813d534dc_Mutect2-exome-panel.vcf.idx added
39fb832345781_Mutect2-WGS-panel-b37.vcf added
39fb8622c0f20_Mutect2-WGS-panel-b37.vcf.idx added
39fb851b38c57_small_exac_common_3.vcf added
39fb85feac1ea_small_exac_common_3.vcf.idx added
39fb82e99708c_1000g_pon.hg38.vcf.gz added
39fb8345ac0d4_1000g_pon.hg38.vcf.gz.tbi added
39fb8295aec8_af-only-gnomad.hg38.vcf.gz added
39fb81bb8878a_af-only-gnomad.hg38.vcf.gz.tbi added
39fb875fea4b8_small_exac_common_3.hg38.vcf.gz added
39fb84bb33440_small_exac_common_3.hg38.vcf.gz.tbi added
39fb825ef7a29_gencode.v41.annotation.gtf added
39fb87c449943_gencode.v42.annotation.gtf added
39fb81c179a90_gencode.vM30.annotation.gtf added
39fb846ca0493_gencode.vM31.annotation.gtf added
39fb873487c32_gencode.v41.transcripts.fa added
39fb84fe384d1_gencode.v41.transcripts.fa.fai added
39fb84318a5cd_gencode.v42.transcripts.fa added
39fb85ea60f06_gencode.v42.transcripts.fa.fai added
39fb815dd8b53_gencode.vM30.pc_transcripts.fa added
39fb8795e6bdd_gencode.vM30.pc_transcripts.fa.fai added
39fb8703d1ed9_gencode.vM31.pc_transcripts.fa added
39fb87eb321a_gencode.vM31.pc_transcripts.fa.fai added
39fb855abb4d9_GRCh38.primary_assembly.genome.fa.1.ht2 added
39fb870f05a42_GRCh38.primary_assembly.genome.fa.2.ht2 added
39fb812448bdd_GRCh38.primary_assembly.genome.fa.3.ht2 added
39fb859c4b002_GRCh38.primary_assembly.genome.fa.4.ht2 added
39fb849511de8_GRCh38.primary_assembly.genome.fa.5.ht2 added
39fb81591c1f1_GRCh38.primary_assembly.genome.fa.6.ht2 added
39fb83f76f3ec_GRCh38.primary_assembly.genome.fa.7.ht2 added
39fb879f622d1_GRCh38.primary_assembly.genome.fa.8.ht2 added
39fb82966f6ce_GRCh38_full_analysis_set_plus_decoy_hla.fa.fai added
39fb871ab4b6d_GRCh38_full_analysis_set_plus_decoy_hla.fa.amb added
39fb85c2231f2_GRCh38_full_analysis_set_plus_decoy_hla.fa.ann added
39fb87b1a8325_GRCh38_full_analysis_set_plus_decoy_hla.fa.bwt added
39fb851960d58_GRCh38_full_analysis_set_plus_decoy_hla.fa.pac added
39fb8abba27e_GRCh38_full_analysis_set_plus_decoy_hla.fa.sa added
39fb82f7543f9_GRCh38_full_analysis_set_plus_decoy_hla.fa added
39fb8542bbc20_GRCh38.primary_assembly.genome.fa.fai added
39fb826742a08_GRCh38.primary_assembly.genome.fa.amb added
39fb82573e8b1_GRCh38.primary_assembly.genome.fa.ann added
39fb81fdef060_GRCh38.primary_assembly.genome.fa.bwt added
39fb84c63a431_GRCh38.primary_assembly.genome.fa.pac added
39fb821b881f5_GRCh38.primary_assembly.genome.fa.sa added
39fb83bf68af1_GRCh38.primary_assembly.genome.fa added
39fb8132da8c4_hs37d5.fa.fai added
39fb81500fe27_hs37d5.fa.amb added
39fb8bda0fc2_hs37d5.fa.ann added
39fb856464e91_hs37d5.fa.bwt added
39fb873a70d2d_hs37d5.fa.pac added
39fb821b79b15_hs37d5.fa.sa added
39fb84fa4ba6f_hs37d5.fa added
39fb863e42c07_complete_ref_lens.bin added
39fb829a2cd2f_ctable.bin added
39fb825506f48_ctg_offsets.bin added
39fb854d48649_duplicate_clusters.tsv added
39fb83be7590c_info.json added
39fb87f151f4a_mphf.bin added
39fb81e25a431_pos.bin added
39fb851791afe_pre_indexing.log added
39fb83e8c1337_rank.bin added
39fb8181bc703_ref_indexing.log added
39fb87ae011cc_refAccumLengths.bin added
39fb830375ea4_reflengths.bin added
39fb8743df8f5_refseq.bin added
39fb875fa94f1_seq.bin added
39fb81cd6bfc_versionInfo.json added
39fb87ef99b73_salmon_index added
39fb8256fd8ea_chrLength.txt added
39fb855f9281c_chrName.txt added
39fb8256dc57b_chrNameLength.txt added
39fb84ae3c19b_chrStart.txt added
39fb875d8187d_exonGeTrInfo.tab added
39fb871d169ac_exonInfo.tab added
39fb86c9c4390_geneInfo.tab added
39fb831cea36e_Genome added
39fb84ff1271_genomeParameters.txt added
39fb819d41b8_Log.out added
39fb83da8b330_SA added
39fb85b456102_SAindex added
39fb875444ee5_sjdbInfo.txt added
39fb85f604e45_sjdbList.fromGTF.out.tab added
39fb82aea1b71_sjdbList.out.tab added
39fb859287aec_transcriptInfo.tab added
39fb89031b74_GRCh38.GENCODE.v42_100 added
39fb8503a8ab9_knownGene_hg38.sql added
39fb82dfd0136_knownGene_hg38.txt added
39fb844ea7481_refGene_hg38.sql added
39fb84f4faa04_refGene_hg38.txt added
39fb84c22a567_knownGene_mm39.sql added
39fb816638f7f_knownGene_mm39.txt added
39fb8ddbbd3b_refGene_mm39.sql added
39fb8643e6c6a_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/RtmpDRYsYB/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
25.281 1.694 29.991
ReUseData.Rcheck/ReUseData-Ex.timings
| name | user | system | elapsed | |
| dataHub-class | 9.139 | 0.474 | 9.866 | |
| dataSearch | 1.764 | 0.056 | 1.826 | |
| dataUpdate | 0 | 0 | 0 | |
| getCloudData | 3.319 | 0.149 | 6.255 | |
| getData | 0 | 0 | 0 | |
| meta_data | 0.000 | 0.000 | 0.001 | |
| recipeHub-class | 0.175 | 0.000 | 0.177 | |
| recipeLoad | 1.864 | 0.092 | 2.046 | |
| recipeMake | 0 | 0 | 0 | |
| recipeSearch | 0.786 | 0.007 | 0.796 | |
| recipeUpdate | 0 | 0 | 0 | |