Qian Liu
| Snapshot Date: 2025-09-22 13:40 -0400 (Mon, 22 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 2025-09-25 11:41 -0400 (Thu, 25 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: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:ReUseData.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings ReUseData_1.8.0.tar.gz |
| StartedAt: 2025-09-24 08:45:43 -0400 (Wed, 24 Sep 2025) |
| EndedAt: 2025-09-24 08:48:14 -0400 (Wed, 24 Sep 2025) |
| EllapsedTime: 151.3 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: ReUseData.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:ReUseData.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings ReUseData_1.8.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/ReUseData.Rcheck’
* using R version 4.5.1 Patched (2025-06-14 r88325)
* using platform: aarch64-apple-darwin20
* R was compiled by
Apple clang version 16.0.0 (clang-1600.0.26.6)
GNU Fortran (GCC) 14.2.0
* running under: macOS Ventura 13.7.5
* 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 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 7.224 0.841 8.145
getCloudData 2.857 0.155 5.058
* 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
‘/Users/biocbuild/bbs-3.21-bioc/meat/ReUseData.Rcheck/00check.log’
for details.
ReUseData.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL ReUseData ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/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 Patched (2025-06-14 r88325) -- "Great Square Root"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin20
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...
c35b392a8b78_GRCh38.primary_assembly.genome.fa.1.bt2 added
c35b182a909a_GRCh38.primary_assembly.genome.fa.2.bt2 added
c35b127b7adb_GRCh38.primary_assembly.genome.fa.3.bt2 added
c35b68bec957_GRCh38.primary_assembly.genome.fa.4.bt2 added
c35b4594a47a_GRCh38.primary_assembly.genome.fa.rev.1.bt2 added
c35b21ba6946_GRCh38.primary_assembly.genome.fa.rev.2.bt2 added
c35b555583f6_outfile.txt added
c35b614ab73e_GRCh37_to_GRCh38.chain added
c35b70447958_GRCh37_to_NCBI34.chain added
c35b1f7ab9fd_GRCh37_to_NCBI35.chain added
c35b3248a130_GRCh37_to_NCBI36.chain added
c35b3e4e701a_GRCh38_to_GRCh37.chain added
c35bfa1daeb_GRCh38_to_NCBI34.chain added
c35b4b2b8251_GRCh38_to_NCBI35.chain added
c35b1578ba65_GRCh38_to_NCBI36.chain added
c35b291547e6_NCBI34_to_GRCh37.chain added
c35b3423621c_NCBI34_to_GRCh38.chain added
c35b7efe3701_NCBI35_to_GRCh37.chain added
c35b63cd63c9_NCBI35_to_GRCh38.chain added
c35b4152544f_NCBI36_to_GRCh37.chain added
c35b41d300a_NCBI36_to_GRCh38.chain added
c35b183ce2a2_GRCm38_to_NCBIM36.chain added
c35b4543061c_GRCm38_to_NCBIM37.chain added
c35b33463bca_NCBIM36_to_GRCm38.chain added
c35b47ff6512_NCBIM37_to_GRCm38.chain added
c35b5044a5ab_1000G_omni2.5.b37.vcf.gz added
c35b4ad8a6b8_1000G_omni2.5.b37.vcf.gz.tbi added
c35b55a9a06b_Mills_and_1000G_gold_standard.indels.b37.vcf.gz added
c35b7362fcbc_Mills_and_1000G_gold_standard.indels.b37.vcf.gz.tbi added
c35b67bed5d2_1000G_omni2.5.hg38.vcf.gz added
c35b21c80334_1000G_omni2.5.hg38.vcf.gz.tbi added
c35b524a5c3f_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz added
c35bfee564e_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz.tbi added
c35b6864230d_af-only-gnomad.raw.sites.vcf added
c35b6396006_af-only-gnomad.raw.sites.vcf.idx added
c35b20cf2d1b_Mutect2-exome-panel.vcf.idx added
c35b19a5871_Mutect2-WGS-panel-b37.vcf added
c35b3c246389_Mutect2-WGS-panel-b37.vcf.idx added
c35b7902d637_small_exac_common_3.vcf added
c35b293df2f2_small_exac_common_3.vcf.idx added
c35b22190305_1000g_pon.hg38.vcf.gz added
c35b18154ec0_1000g_pon.hg38.vcf.gz.tbi added
c35b1ee52b9a_af-only-gnomad.hg38.vcf.gz added
c35b57919b4e_af-only-gnomad.hg38.vcf.gz.tbi added
c35b186b4acc_small_exac_common_3.hg38.vcf.gz added
c35b2bfba39a_small_exac_common_3.hg38.vcf.gz.tbi added
c35b15b1ea05_gencode.v41.annotation.gtf added
c35b537af963_gencode.v42.annotation.gtf added
c35b2e8afd66_gencode.vM30.annotation.gtf added
c35b27024b69_gencode.vM31.annotation.gtf added
c35b7a4ee81_gencode.v41.transcripts.fa added
c35b5d265b12_gencode.v41.transcripts.fa.fai added
c35b1252a85_gencode.v42.transcripts.fa added
c35b2f0a8259_gencode.v42.transcripts.fa.fai added
c35b5af3b92f_gencode.vM30.pc_transcripts.fa added
c35b3702eb4f_gencode.vM30.pc_transcripts.fa.fai added
c35b20a6abc0_gencode.vM31.pc_transcripts.fa added
c35b1e55daff_gencode.vM31.pc_transcripts.fa.fai added
c35b169caae8_GRCh38.primary_assembly.genome.fa.1.ht2 added
c35b79870f1_GRCh38.primary_assembly.genome.fa.2.ht2 added
c35b291ee21c_GRCh38.primary_assembly.genome.fa.3.ht2 added
c35b2a8eb15b_GRCh38.primary_assembly.genome.fa.4.ht2 added
c35b7e1de330_GRCh38.primary_assembly.genome.fa.5.ht2 added
c35b5c2ea4ff_GRCh38.primary_assembly.genome.fa.6.ht2 added
c35b7a5290a0_GRCh38.primary_assembly.genome.fa.7.ht2 added
c35b4295371d_GRCh38.primary_assembly.genome.fa.8.ht2 added
c35b52557311_GRCh38_full_analysis_set_plus_decoy_hla.fa.fai added
c35b67f58b51_GRCh38_full_analysis_set_plus_decoy_hla.fa.amb added
c35b298da829_GRCh38_full_analysis_set_plus_decoy_hla.fa.ann added
c35b131b310f_GRCh38_full_analysis_set_plus_decoy_hla.fa.bwt added
c35b5e31d995_GRCh38_full_analysis_set_plus_decoy_hla.fa.pac added
c35b1ac3f583_GRCh38_full_analysis_set_plus_decoy_hla.fa.sa added
c35b372b792f_GRCh38_full_analysis_set_plus_decoy_hla.fa added
c35b72118f5_GRCh38.primary_assembly.genome.fa.fai added
c35bded807b_GRCh38.primary_assembly.genome.fa.amb added
c35b638e1261_GRCh38.primary_assembly.genome.fa.ann added
c35b458d157_GRCh38.primary_assembly.genome.fa.bwt added
c35b6317a8fb_GRCh38.primary_assembly.genome.fa.pac added
c35b26572990_GRCh38.primary_assembly.genome.fa.sa added
c35b2469c09a_GRCh38.primary_assembly.genome.fa added
c35b1ae3d123_hs37d5.fa.fai added
c35b62b75e9f_hs37d5.fa.amb added
c35b74a54b5a_hs37d5.fa.ann added
c35bff63d8a_hs37d5.fa.bwt added
c35b6f423735_hs37d5.fa.pac added
c35b6436b1a3_hs37d5.fa.sa added
c35b42c877bb_hs37d5.fa added
c35b772cb83d_complete_ref_lens.bin added
c35b18f3e9eb_ctable.bin added
c35b35825019_ctg_offsets.bin added
c35b7e58b4c0_duplicate_clusters.tsv added
c35b71c2ea0d_info.json added
c35b339435d4_mphf.bin added
c35b475a0bc0_pos.bin added
c35b68b98ed8_pre_indexing.log added
c35b6e513c9e_rank.bin added
c35b1762e1a7_ref_indexing.log added
c35b5ccca6ef_refAccumLengths.bin added
c35b7fe3c481_reflengths.bin added
c35b427a32bf_refseq.bin added
c35b6499bbb1_seq.bin added
c35b28f19510_versionInfo.json added
c35bc716270_salmon_index added
c35b67f5ad71_chrLength.txt added
c35b324e0b09_chrName.txt added
c35b21b695ac_chrNameLength.txt added
c35b5a1c607e_chrStart.txt added
c35b7d031e69_exonGeTrInfo.tab added
c35b57c1bf9d_exonInfo.tab added
c35b710b096d_geneInfo.tab added
c35bb980d16_Genome added
c35b2b83254c_genomeParameters.txt added
c35b2f05b6e5_Log.out added
c35b202a8c81_SA added
c35b496e79a6_SAindex added
c35b73f4a6f3_sjdbInfo.txt added
c35b42fcd6fe_sjdbList.fromGTF.out.tab added
c35b6586e00d_sjdbList.out.tab added
c35b79dfa98d_transcriptInfo.tab added
c35b4af4a67d_GRCh38.GENCODE.v42_100 added
c35b3de7efd_knownGene_hg38.sql added
c35b4631607_knownGene_hg38.txt added
c35b53b27d1_refGene_hg38.sql added
c35b6eb30d05_refGene_hg38.txt added
c35b2d1bfc0a_knownGene_mm39.sql added
c35b8400ba9_knownGene_mm39.txt added
c35b24bd887a_refGene_mm39.sql added
c35b174b146e_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/RtmpQWXxTZ/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
26.017 3.827 32.026
ReUseData.Rcheck/ReUseData-Ex.timings
| name | user | system | elapsed | |
| dataHub-class | 7.224 | 0.841 | 8.145 | |
| dataSearch | 1.195 | 0.053 | 1.256 | |
| dataUpdate | 0.000 | 0.000 | 0.001 | |
| getCloudData | 2.857 | 0.155 | 5.058 | |
| getData | 0.001 | 0.000 | 0.000 | |
| meta_data | 0.001 | 0.000 | 0.001 | |
| recipeHub-class | 0.147 | 0.013 | 0.162 | |
| recipeLoad | 1.461 | 0.093 | 1.561 | |
| recipeMake | 0.000 | 0.001 | 0.001 | |
| recipeSearch | 0.600 | 0.038 | 0.639 | |
| recipeUpdate | 0 | 0 | 0 | |