Qian Liu
| Snapshot Date: 2025-07-27 13:25 -0400 (Sun, 27 Jul 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 2025-07-28 12:06 -0400 (Mon, 28 Jul 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.2 LTS) | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4796 |
| palomino8 | Windows Server 2022 Datacenter | x64 | 4.5.1 (2025-06-13 ucrt) -- "Great Square Root" | 4536 |
| lconway | macOS 12.7.1 Monterey | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4578 |
| kjohnson3 | macOS 13.7.1 Ventura | arm64 | 4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" | 4519 |
| taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4512 |
| 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 1737/2313 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| ReUseData 1.9.0 (landing page) Qian Liu
| nebbiolo2 | Linux (Ubuntu 24.04.2 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino8 | Windows Server 2022 Datacenter / x64 | ... NOT SUPPORTED ... | ||||||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson3 | macOS 13.7.1 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. |
| Package: ReUseData |
| Version: 1.9.0 |
| Command: /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:ReUseData.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings ReUseData_1.9.0.tar.gz |
| StartedAt: 2025-07-28 01:40:43 -0400 (Mon, 28 Jul 2025) |
| EndedAt: 2025-07-28 01:43:27 -0400 (Mon, 28 Jul 2025) |
| EllapsedTime: 164.2 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: ReUseData.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:ReUseData.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings ReUseData_1.9.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/ReUseData.Rcheck’
* using R version 4.5.1 (2025-06-13)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.2 LTS
* using session charset: UTF-8
* 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 6.127 0.245 6.374
* 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 ... OK
* 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/bbs-3.22-bioc/R/bin/R CMD INSTALL ReUseData ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.22-bioc/R/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 4.5.1 (2025-06-13) -- "Great Square Root"
Copyright (C) 2025 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.
> 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...
3afd7c3b07605_GRCh38.primary_assembly.genome.fa.1.bt2 added
3afd7ceb99448_GRCh38.primary_assembly.genome.fa.2.bt2 added
3afd7c7fd9eadb_GRCh38.primary_assembly.genome.fa.3.bt2 added
3afd7c78177566_GRCh38.primary_assembly.genome.fa.4.bt2 added
3afd7c6161011f_GRCh38.primary_assembly.genome.fa.rev.1.bt2 added
3afd7c4068fad_GRCh38.primary_assembly.genome.fa.rev.2.bt2 added
3afd7c6d2c54ca_outfile.txt added
3afd7c77911702_GRCh37_to_GRCh38.chain added
3afd7c18770b59_GRCh37_to_NCBI34.chain added
3afd7c57739997_GRCh37_to_NCBI35.chain added
3afd7c74b420fc_GRCh37_to_NCBI36.chain added
3afd7c397b6244_GRCh38_to_GRCh37.chain added
3afd7c4413ac7_GRCh38_to_NCBI34.chain added
3afd7c509c530c_GRCh38_to_NCBI35.chain added
3afd7c738b49a_GRCh38_to_NCBI36.chain added
3afd7c79876a6f_NCBI34_to_GRCh37.chain added
3afd7c77fb29cc_NCBI34_to_GRCh38.chain added
3afd7c6c633a32_NCBI35_to_GRCh37.chain added
3afd7c1722a1c7_NCBI35_to_GRCh38.chain added
3afd7c7bade397_NCBI36_to_GRCh37.chain added
3afd7c450096a9_NCBI36_to_GRCh38.chain added
3afd7c7b153080_GRCm38_to_NCBIM36.chain added
3afd7c7e7c4ce7_GRCm38_to_NCBIM37.chain added
3afd7c3baec9d5_NCBIM36_to_GRCm38.chain added
3afd7c1ae7be2_NCBIM37_to_GRCm38.chain added
3afd7c450801f9_1000G_omni2.5.b37.vcf.gz added
3afd7c1d44e572_1000G_omni2.5.b37.vcf.gz.tbi added
3afd7c41f9d4e9_Mills_and_1000G_gold_standard.indels.b37.vcf.gz added
3afd7c52f9f0a_Mills_and_1000G_gold_standard.indels.b37.vcf.gz.tbi added
3afd7c6b1f5dbf_1000G_omni2.5.hg38.vcf.gz added
3afd7c60cc081a_1000G_omni2.5.hg38.vcf.gz.tbi added
3afd7c8e01510_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz added
3afd7c79d8f208_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz.tbi added
3afd7c60a5f2f5_af-only-gnomad.raw.sites.vcf added
3afd7cf78a76_af-only-gnomad.raw.sites.vcf.idx added
3afd7c5b39f327_Mutect2-exome-panel.vcf.idx added
3afd7c64ac82a2_Mutect2-WGS-panel-b37.vcf added
3afd7c6e23df41_Mutect2-WGS-panel-b37.vcf.idx added
3afd7c52cb0a29_small_exac_common_3.vcf added
3afd7c7d238dfb_small_exac_common_3.vcf.idx added
3afd7c459778d8_1000g_pon.hg38.vcf.gz added
3afd7c477f2b26_1000g_pon.hg38.vcf.gz.tbi added
3afd7c369ef03f_af-only-gnomad.hg38.vcf.gz added
3afd7c49d8b39f_af-only-gnomad.hg38.vcf.gz.tbi added
3afd7c181b7e32_small_exac_common_3.hg38.vcf.gz added
3afd7c3dd7a4da_small_exac_common_3.hg38.vcf.gz.tbi added
3afd7c43601e0e_gencode.v41.annotation.gtf added
3afd7c1016a7fe_gencode.v42.annotation.gtf added
3afd7c2a3adf0c_gencode.vM30.annotation.gtf added
3afd7c5a82bfd6_gencode.vM31.annotation.gtf added
3afd7cbc48b95_gencode.v41.transcripts.fa added
3afd7c6f3b75b5_gencode.v41.transcripts.fa.fai added
3afd7c5597f056_gencode.v42.transcripts.fa added
3afd7ca40d87d_gencode.v42.transcripts.fa.fai added
3afd7c2aea3f8a_gencode.vM30.pc_transcripts.fa added
3afd7c57466c38_gencode.vM30.pc_transcripts.fa.fai added
3afd7c4f48da76_gencode.vM31.pc_transcripts.fa added
3afd7c482f24fc_gencode.vM31.pc_transcripts.fa.fai added
3afd7c19404121_GRCh38.primary_assembly.genome.fa.1.ht2 added
3afd7c54787981_GRCh38.primary_assembly.genome.fa.2.ht2 added
3afd7c334e82bc_GRCh38.primary_assembly.genome.fa.3.ht2 added
3afd7c7a0c493b_GRCh38.primary_assembly.genome.fa.4.ht2 added
3afd7c5d588e91_GRCh38.primary_assembly.genome.fa.5.ht2 added
3afd7c2d2774c4_GRCh38.primary_assembly.genome.fa.6.ht2 added
3afd7c5ab23c31_GRCh38.primary_assembly.genome.fa.7.ht2 added
3afd7c5e501907_GRCh38.primary_assembly.genome.fa.8.ht2 added
3afd7c86167eb_GRCh38_full_analysis_set_plus_decoy_hla.fa.fai added
3afd7c3f5ebed3_GRCh38_full_analysis_set_plus_decoy_hla.fa.amb added
3afd7c4c73f848_GRCh38_full_analysis_set_plus_decoy_hla.fa.ann added
3afd7c5b2c7215_GRCh38_full_analysis_set_plus_decoy_hla.fa.bwt added
3afd7c3c824ccf_GRCh38_full_analysis_set_plus_decoy_hla.fa.pac added
3afd7c120b7120_GRCh38_full_analysis_set_plus_decoy_hla.fa.sa added
3afd7c22ab9d3b_GRCh38_full_analysis_set_plus_decoy_hla.fa added
3afd7c73213d0e_GRCh38.primary_assembly.genome.fa.fai added
3afd7c5be424bf_GRCh38.primary_assembly.genome.fa.amb added
3afd7c3ac71b6d_GRCh38.primary_assembly.genome.fa.ann added
3afd7c30f8e1e8_GRCh38.primary_assembly.genome.fa.bwt added
3afd7c1f4442ce_GRCh38.primary_assembly.genome.fa.pac added
3afd7c4addc36b_GRCh38.primary_assembly.genome.fa.sa added
3afd7c5b33c0f5_GRCh38.primary_assembly.genome.fa added
3afd7c79c702a4_hs37d5.fa.fai added
3afd7c56a24f00_hs37d5.fa.amb added
3afd7c4a6f36aa_hs37d5.fa.ann added
3afd7c4f5ef2fa_hs37d5.fa.bwt added
3afd7c60e3277d_hs37d5.fa.pac added
3afd7c75597635_hs37d5.fa.sa added
3afd7c26a55f32_hs37d5.fa added
3afd7c302c01f4_complete_ref_lens.bin added
3afd7c3d889b31_ctable.bin added
3afd7c3fe5a053_ctg_offsets.bin added
3afd7c4a47b75_duplicate_clusters.tsv added
3afd7c70d71ded_info.json added
3afd7c39f1e98e_mphf.bin added
3afd7c61fd0a06_pos.bin added
3afd7c1dfe92b1_pre_indexing.log added
3afd7c14a425bf_rank.bin added
3afd7c404d230d_ref_indexing.log added
3afd7c265ffa9d_refAccumLengths.bin added
3afd7c5402e493_reflengths.bin added
3afd7ccc11b56_refseq.bin added
3afd7c18c6cb2_seq.bin added
3afd7c10853162_versionInfo.json added
3afd7c1ecc8c76_salmon_index added
3afd7c243809ed_chrLength.txt added
3afd7c3a66e70_chrName.txt added
3afd7c7ab0b136_chrNameLength.txt added
3afd7c5eff255a_chrStart.txt added
3afd7c349f5059_exonGeTrInfo.tab added
3afd7c19f4f404_exonInfo.tab added
3afd7c29dce8c5_geneInfo.tab added
3afd7cfd3114e_Genome added
3afd7c13bbf6a8_genomeParameters.txt added
3afd7c7f37c5_Log.out added
3afd7c5a4247f8_SA added
3afd7c631ae9a2_SAindex added
3afd7c61625f43_sjdbInfo.txt added
3afd7c4f9bbe2d_sjdbList.fromGTF.out.tab added
3afd7c9c048d4_sjdbList.out.tab added
3afd7c118e6137_transcriptInfo.tab added
3afd7cd24595f_GRCh38.GENCODE.v42_100 added
3afd7c49a5e927_knownGene_hg38.sql added
3afd7c1632dcac_knownGene_hg38.txt added
3afd7c7dfb774c_refGene_hg38.sql added
3afd7c397d2b5_refGene_hg38.txt added
3afd7c782fe6b2_knownGene_mm39.sql added
3afd7c1bfa09fe_knownGene_mm39.txt added
3afd7c183bf875_refGene_mm39.sql added
3afd7c387d09bf_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:
/tmp/RtmpAaKwZk/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
18.954 1.402 20.697
ReUseData.Rcheck/ReUseData-Ex.timings
| name | user | system | elapsed | |
| dataHub-class | 6.127 | 0.245 | 6.374 | |
| dataSearch | 1.191 | 0.013 | 1.205 | |
| dataUpdate | 0.001 | 0.001 | 0.000 | |
| getCloudData | 2.739 | 0.073 | 3.776 | |
| getData | 0.001 | 0.000 | 0.000 | |
| meta_data | 0.000 | 0.000 | 0.001 | |
| recipeHub-class | 0.125 | 0.001 | 0.127 | |
| recipeLoad | 1.263 | 0.020 | 1.284 | |
| recipeMake | 0.001 | 0.000 | 0.000 | |
| recipeSearch | 0.594 | 0.010 | 0.604 | |
| recipeUpdate | 0 | 0 | 0 | |