Qian Liu
| Snapshot Date: 2025-09-18 13:40 -0400 (Thu, 18 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 2025-09-22 11:38 -0400 (Mon, 22 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" | 4581 |
| 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. |
| Package: ReUseData |
| Version: 1.8.0 |
| Command: /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:ReUseData.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings ReUseData_1.8.0.tar.gz |
| StartedAt: 2025-09-22 02:37:46 -0400 (Mon, 22 Sep 2025) |
| EndedAt: 2025-09-22 02:40:43 -0400 (Mon, 22 Sep 2025) |
| EllapsedTime: 177.3 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: ReUseData.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:ReUseData.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings ReUseData_1.8.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.21-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 24.04.3 LTS
* using session charset: UTF-8
* 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 6.043 0.4 6.445
* 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-3.21-bioc/meat/ReUseData.Rcheck/00check.log’
for details.
ReUseData.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD INSTALL ReUseData ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.21-bioc/R/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 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...
22ce2e37111885_GRCh38.primary_assembly.genome.fa.1.bt2 added
22ce2e4c8ce0c0_GRCh38.primary_assembly.genome.fa.2.bt2 added
22ce2e43a80c5d_GRCh38.primary_assembly.genome.fa.3.bt2 added
22ce2e5d12a258_GRCh38.primary_assembly.genome.fa.4.bt2 added
22ce2e113e57cd_GRCh38.primary_assembly.genome.fa.rev.1.bt2 added
22ce2e6e962653_GRCh38.primary_assembly.genome.fa.rev.2.bt2 added
22ce2e6c2ca3d8_outfile.txt added
22ce2e2a23c5a6_GRCh37_to_GRCh38.chain added
22ce2e2c5e4c5f_GRCh37_to_NCBI34.chain added
22ce2e8ea9381_GRCh37_to_NCBI35.chain added
22ce2e51cb6ad4_GRCh37_to_NCBI36.chain added
22ce2e5effe75e_GRCh38_to_GRCh37.chain added
22ce2e11b00841_GRCh38_to_NCBI34.chain added
22ce2e992e2e4_GRCh38_to_NCBI35.chain added
22ce2e3053c661_GRCh38_to_NCBI36.chain added
22ce2e48280075_NCBI34_to_GRCh37.chain added
22ce2eec09727_NCBI34_to_GRCh38.chain added
22ce2efa57c16_NCBI35_to_GRCh37.chain added
22ce2e36832932_NCBI35_to_GRCh38.chain added
22ce2e31abb22f_NCBI36_to_GRCh37.chain added
22ce2e9d6e034_NCBI36_to_GRCh38.chain added
22ce2e37aced38_GRCm38_to_NCBIM36.chain added
22ce2e7fe41dc3_GRCm38_to_NCBIM37.chain added
22ce2e29aa4914_NCBIM36_to_GRCm38.chain added
22ce2e5b80f98d_NCBIM37_to_GRCm38.chain added
22ce2e24cdc2da_1000G_omni2.5.b37.vcf.gz added
22ce2e28473486_1000G_omni2.5.b37.vcf.gz.tbi added
22ce2e3183f532_Mills_and_1000G_gold_standard.indels.b37.vcf.gz added
22ce2e4decc0a6_Mills_and_1000G_gold_standard.indels.b37.vcf.gz.tbi added
22ce2e2a7b0819_1000G_omni2.5.hg38.vcf.gz added
22ce2e51ba0c87_1000G_omni2.5.hg38.vcf.gz.tbi added
22ce2e4fdd92b_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz added
22ce2e7707e8d9_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz.tbi added
22ce2e156218e4_af-only-gnomad.raw.sites.vcf added
22ce2e62107b83_af-only-gnomad.raw.sites.vcf.idx added
22ce2e84640a7_Mutect2-exome-panel.vcf.idx added
22ce2e3f83f37_Mutect2-WGS-panel-b37.vcf added
22ce2e4e3d1f5b_Mutect2-WGS-panel-b37.vcf.idx added
22ce2e326a064d_small_exac_common_3.vcf added
22ce2e30568b96_small_exac_common_3.vcf.idx added
22ce2e5727b2dc_1000g_pon.hg38.vcf.gz added
22ce2e4357121_1000g_pon.hg38.vcf.gz.tbi added
22ce2ef5672f4_af-only-gnomad.hg38.vcf.gz added
22ce2e68d7bb1d_af-only-gnomad.hg38.vcf.gz.tbi added
22ce2edc85405_small_exac_common_3.hg38.vcf.gz added
22ce2e3faa3956_small_exac_common_3.hg38.vcf.gz.tbi added
22ce2e30ffbb92_gencode.v41.annotation.gtf added
22ce2e1c88eb2d_gencode.v42.annotation.gtf added
22ce2e4f4fb56c_gencode.vM30.annotation.gtf added
22ce2e6782e4c5_gencode.vM31.annotation.gtf added
22ce2e4e349d5c_gencode.v41.transcripts.fa added
22ce2e592695a1_gencode.v41.transcripts.fa.fai added
22ce2e1f2fd1fd_gencode.v42.transcripts.fa added
22ce2e4e18bb1f_gencode.v42.transcripts.fa.fai added
22ce2e2d0deb5_gencode.vM30.pc_transcripts.fa added
22ce2e7ab0cb8a_gencode.vM30.pc_transcripts.fa.fai added
22ce2e72e67df9_gencode.vM31.pc_transcripts.fa added
22ce2e2b18133b_gencode.vM31.pc_transcripts.fa.fai added
22ce2e2c34c0bd_GRCh38.primary_assembly.genome.fa.1.ht2 added
22ce2e40d33e9f_GRCh38.primary_assembly.genome.fa.2.ht2 added
22ce2e55931b54_GRCh38.primary_assembly.genome.fa.3.ht2 added
22ce2e7deecd44_GRCh38.primary_assembly.genome.fa.4.ht2 added
22ce2e45d117ca_GRCh38.primary_assembly.genome.fa.5.ht2 added
22ce2e4c9b042e_GRCh38.primary_assembly.genome.fa.6.ht2 added
22ce2e1350e628_GRCh38.primary_assembly.genome.fa.7.ht2 added
22ce2e27e1934d_GRCh38.primary_assembly.genome.fa.8.ht2 added
22ce2e54e144d5_GRCh38_full_analysis_set_plus_decoy_hla.fa.fai added
22ce2e1749255f_GRCh38_full_analysis_set_plus_decoy_hla.fa.amb added
22ce2e761eb2a9_GRCh38_full_analysis_set_plus_decoy_hla.fa.ann added
22ce2e74b4b22_GRCh38_full_analysis_set_plus_decoy_hla.fa.bwt added
22ce2e479fb0f6_GRCh38_full_analysis_set_plus_decoy_hla.fa.pac added
22ce2e4d466585_GRCh38_full_analysis_set_plus_decoy_hla.fa.sa added
22ce2eb80bc43_GRCh38_full_analysis_set_plus_decoy_hla.fa added
22ce2e56f623ea_GRCh38.primary_assembly.genome.fa.fai added
22ce2e361e20a3_GRCh38.primary_assembly.genome.fa.amb added
22ce2e19491048_GRCh38.primary_assembly.genome.fa.ann added
22ce2e16a05d40_GRCh38.primary_assembly.genome.fa.bwt added
22ce2e671ddc35_GRCh38.primary_assembly.genome.fa.pac added
22ce2e35d1fb75_GRCh38.primary_assembly.genome.fa.sa added
22ce2e65f012ad_GRCh38.primary_assembly.genome.fa added
22ce2e4ea0c0fa_hs37d5.fa.fai added
22ce2e40698d2_hs37d5.fa.amb added
22ce2e3f16a84e_hs37d5.fa.ann added
22ce2e6dd092f8_hs37d5.fa.bwt added
22ce2e521f53f1_hs37d5.fa.pac added
22ce2e41e78703_hs37d5.fa.sa added
22ce2e68815e82_hs37d5.fa added
22ce2e4505d1eb_complete_ref_lens.bin added
22ce2e6cff9a3e_ctable.bin added
22ce2e14b61f3f_ctg_offsets.bin added
22ce2e5d9108a_duplicate_clusters.tsv added
22ce2e4292b592_info.json added
22ce2e12a4ec83_mphf.bin added
22ce2e4baa2855_pos.bin added
22ce2ef2db9c0_pre_indexing.log added
22ce2e25f5d2ab_rank.bin added
22ce2e738bbba2_ref_indexing.log added
22ce2e640efe95_refAccumLengths.bin added
22ce2e3d3ef80b_reflengths.bin added
22ce2e69aa6e4b_refseq.bin added
22ce2e6b5a49b7_seq.bin added
22ce2e4dea901_versionInfo.json added
22ce2e36f0d3d1_salmon_index added
22ce2e76db05fa_chrLength.txt added
22ce2e5bd4cceb_chrName.txt added
22ce2e6d0ef474_chrNameLength.txt added
22ce2e10241643_chrStart.txt added
22ce2e72752a2c_exonGeTrInfo.tab added
22ce2e542cd0a9_exonInfo.tab added
22ce2e45f611b8_geneInfo.tab added
22ce2e58653cd9_Genome added
22ce2e22cd91a4_genomeParameters.txt added
22ce2e49fcaa8a_Log.out added
22ce2e177be527_SA added
22ce2e109e249c_SAindex added
22ce2e1c1bfe7c_sjdbInfo.txt added
22ce2e59636c2a_sjdbList.fromGTF.out.tab added
22ce2e791f831e_sjdbList.out.tab added
22ce2e6121d067_transcriptInfo.tab added
22ce2e46630668_GRCh38.GENCODE.v42_100 added
22ce2edd5a25e_knownGene_hg38.sql added
22ce2e66fae0f1_knownGene_hg38.txt added
22ce2e8f5bbfa_refGene_hg38.sql added
22ce2e207a8ee1_refGene_hg38.txt added
22ce2e32a50946_knownGene_mm39.sql added
22ce2e182375bb_knownGene_mm39.txt added
22ce2e4670618d_refGene_mm39.sql added
22ce2e2630c4e9_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/RtmpiUlFqe/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
20.636 2.030 23.168
ReUseData.Rcheck/ReUseData-Ex.timings
| name | user | system | elapsed | |
| dataHub-class | 6.043 | 0.400 | 6.445 | |
| dataSearch | 1.169 | 0.042 | 1.211 | |
| dataUpdate | 0 | 0 | 0 | |
| getCloudData | 2.686 | 0.128 | 3.999 | |
| getData | 0.000 | 0.000 | 0.001 | |
| meta_data | 0.000 | 0.000 | 0.001 | |
| recipeHub-class | 0.127 | 0.001 | 0.128 | |
| recipeLoad | 1.248 | 0.018 | 1.271 | |
| recipeMake | 0.000 | 0.000 | 0.001 | |
| recipeSearch | 0.526 | 0.011 | 0.537 | |
| recipeUpdate | 0 | 0 | 0 | |