Qian Liu
| Snapshot Date: 2025-10-13 13:40 -0400 (Mon, 13 Oct 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 2025-10-16 11:40 -0400 (Thu, 16 Oct 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" | 4833 |
| merida1 | macOS 12.7.6 Monterey | x86_64 | 4.5.1 RC (2025-06-05 r88288) -- "Great Square Root" | 4614 |
| kjohnson1 | macOS 13.7.5 Ventura | arm64 | 4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" | 4555 |
| kunpeng2 | Linux (openEuler 24.03 LTS) | aarch64 | R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" | 4586 |
| 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 12.7.6 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson1 | macOS 13.7.5 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: 2025-10-15 09:36:34 -0400 (Wed, 15 Oct 2025) |
| EndedAt: 2025-10-15 09:39:04 -0400 (Wed, 15 Oct 2025) |
| EllapsedTime: 150.5 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 7.404 0.912 8.463
getCloudData 2.924 0.167 5.166
* 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...
4daf4cb10231_GRCh38.primary_assembly.genome.fa.1.bt2 added
4daf7907064c_GRCh38.primary_assembly.genome.fa.2.bt2 added
4daf3c2ea5a7_GRCh38.primary_assembly.genome.fa.3.bt2 added
4daf1a7d95cf_GRCh38.primary_assembly.genome.fa.4.bt2 added
4daf2af6569f_GRCh38.primary_assembly.genome.fa.rev.1.bt2 added
4daf12b0f6c2_GRCh38.primary_assembly.genome.fa.rev.2.bt2 added
4daf20184424_outfile.txt added
4daf1921a7f2_GRCh37_to_GRCh38.chain added
4daf70990dc1_GRCh37_to_NCBI34.chain added
4daf505633a7_GRCh37_to_NCBI35.chain added
4daf4b594225_GRCh37_to_NCBI36.chain added
4daf5105b1c8_GRCh38_to_GRCh37.chain added
4daf4cdaeb06_GRCh38_to_NCBI34.chain added
4daf387bfe55_GRCh38_to_NCBI35.chain added
4daf54769b6b_GRCh38_to_NCBI36.chain added
4daf36d5b91f_NCBI34_to_GRCh37.chain added
4daf96cbe59_NCBI34_to_GRCh38.chain added
4daf4244c9e4_NCBI35_to_GRCh37.chain added
4daf3222b9b9_NCBI35_to_GRCh38.chain added
4daf5cf3a66_NCBI36_to_GRCh37.chain added
4daf68030184_NCBI36_to_GRCh38.chain added
4daf1d58b675_GRCm38_to_NCBIM36.chain added
4daf2b32ca60_GRCm38_to_NCBIM37.chain added
4daf13847ac8_NCBIM36_to_GRCm38.chain added
4daf5e98ea7a_NCBIM37_to_GRCm38.chain added
4daf94a201b_1000G_omni2.5.b37.vcf.gz added
4daf6181d160_1000G_omni2.5.b37.vcf.gz.tbi added
4daf11d927a3_Mills_and_1000G_gold_standard.indels.b37.vcf.gz added
4daf47b9477c_Mills_and_1000G_gold_standard.indels.b37.vcf.gz.tbi added
4daf550442ad_1000G_omni2.5.hg38.vcf.gz added
4dafab59776_1000G_omni2.5.hg38.vcf.gz.tbi added
4daf17eac978_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz added
4daf3750f18c_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz.tbi added
4daf23223ab3_af-only-gnomad.raw.sites.vcf added
4daf1c3bcfca_af-only-gnomad.raw.sites.vcf.idx added
4daf1ac6e541_Mutect2-exome-panel.vcf.idx added
4daf77f51c22_Mutect2-WGS-panel-b37.vcf added
4daf7d0a39b4_Mutect2-WGS-panel-b37.vcf.idx added
4daf2a52988e_small_exac_common_3.vcf added
4daf149da857_small_exac_common_3.vcf.idx added
4daf7a96f253_1000g_pon.hg38.vcf.gz added
4daf4bff6605_1000g_pon.hg38.vcf.gz.tbi added
4daf6c82f93d_af-only-gnomad.hg38.vcf.gz added
4dafab94b73_af-only-gnomad.hg38.vcf.gz.tbi added
4dafb087085_small_exac_common_3.hg38.vcf.gz added
4daf5713316b_small_exac_common_3.hg38.vcf.gz.tbi added
4daf2d119476_gencode.v41.annotation.gtf added
4daf5d29e617_gencode.v42.annotation.gtf added
4daf69c11fc9_gencode.vM30.annotation.gtf added
4daf60dfb5d_gencode.vM31.annotation.gtf added
4daf7ff199c5_gencode.v41.transcripts.fa added
4daf4ea69622_gencode.v41.transcripts.fa.fai added
4daf1acaba85_gencode.v42.transcripts.fa added
4daf739b7f80_gencode.v42.transcripts.fa.fai added
4daf65cfe7cb_gencode.vM30.pc_transcripts.fa added
4daf347af4a5_gencode.vM30.pc_transcripts.fa.fai added
4daf7453978d_gencode.vM31.pc_transcripts.fa added
4daf1c02e5a5_gencode.vM31.pc_transcripts.fa.fai added
4daf232c201_GRCh38.primary_assembly.genome.fa.1.ht2 added
4daf525ed0c7_GRCh38.primary_assembly.genome.fa.2.ht2 added
4daf4edce310_GRCh38.primary_assembly.genome.fa.3.ht2 added
4daf7bf57e3_GRCh38.primary_assembly.genome.fa.4.ht2 added
4daf2322fc0e_GRCh38.primary_assembly.genome.fa.5.ht2 added
4daf4dd20d27_GRCh38.primary_assembly.genome.fa.6.ht2 added
4daf195da35b_GRCh38.primary_assembly.genome.fa.7.ht2 added
4daf528fb85f_GRCh38.primary_assembly.genome.fa.8.ht2 added
4daf59918f51_GRCh38_full_analysis_set_plus_decoy_hla.fa.fai added
4daf63583cc7_GRCh38_full_analysis_set_plus_decoy_hla.fa.amb added
4daf35fe5fc5_GRCh38_full_analysis_set_plus_decoy_hla.fa.ann added
4daf4f419a34_GRCh38_full_analysis_set_plus_decoy_hla.fa.bwt added
4daf5bf2f492_GRCh38_full_analysis_set_plus_decoy_hla.fa.pac added
4daf2b96cc67_GRCh38_full_analysis_set_plus_decoy_hla.fa.sa added
4daf3945948c_GRCh38_full_analysis_set_plus_decoy_hla.fa added
4daf71b90b4_GRCh38.primary_assembly.genome.fa.fai added
4daf22b91d11_GRCh38.primary_assembly.genome.fa.amb added
4daf272358e6_GRCh38.primary_assembly.genome.fa.ann added
4daf1a1781d_GRCh38.primary_assembly.genome.fa.bwt added
4daffd4b8c1_GRCh38.primary_assembly.genome.fa.pac added
4daf56ad8f05_GRCh38.primary_assembly.genome.fa.sa added
4daf1c88bdb8_GRCh38.primary_assembly.genome.fa added
4daf555f89aa_hs37d5.fa.fai added
4daf734723af_hs37d5.fa.amb added
4daf4377f149_hs37d5.fa.ann added
4daf77821239_hs37d5.fa.bwt added
4daf7c7a997a_hs37d5.fa.pac added
4daf54f2586e_hs37d5.fa.sa added
4daf728bc953_hs37d5.fa added
4daf374ea2e5_complete_ref_lens.bin added
4dafba884c1_ctable.bin added
4daf64a3a0e1_ctg_offsets.bin added
4daf32974765_duplicate_clusters.tsv added
4daf69d051d5_info.json added
4daf6bacad38_mphf.bin added
4daf15a06ec2_pos.bin added
4daf57c78da5_pre_indexing.log added
4daf6e2478a8_rank.bin added
4daf1c6d9616_ref_indexing.log added
4daf5e988cee_refAccumLengths.bin added
4daf714c8dc6_reflengths.bin added
4daf58effc46_refseq.bin added
4daf739b8547_seq.bin added
4daf674b339c_versionInfo.json added
4daf7a297bbe_salmon_index added
4daf397b359a_chrLength.txt added
4daf47fc2ef1_chrName.txt added
4daf7d6df522_chrNameLength.txt added
4daf3df8cb83_chrStart.txt added
4daf18f9253e_exonGeTrInfo.tab added
4dafcfc1641_exonInfo.tab added
4daf7a190c0f_geneInfo.tab added
4daf266eb69_Genome added
4daf32e93bba_genomeParameters.txt added
4daf6e504a72_Log.out added
4daf5947baf2_SA added
4daf744293a8_SAindex added
4daf3eec3639_sjdbInfo.txt added
4daf5dbf875_sjdbList.fromGTF.out.tab added
4daf2c94cc54_sjdbList.out.tab added
4daf5cf2b5a9_transcriptInfo.tab added
4daf427499eb_GRCh38.GENCODE.v42_100 added
4daf75253562_knownGene_hg38.sql added
4daf5dd3f103_knownGene_hg38.txt added
4daf5742c15_refGene_hg38.sql added
4dafdfa197f_refGene_hg38.txt added
4daf1e9fe804_knownGene_mm39.sql added
4daf14396e51_knownGene_mm39.txt added
4daf46799236_refGene_mm39.sql added
4daf576e3b5f_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/RtmpsakmM6/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
25.006 3.580 30.268
ReUseData.Rcheck/ReUseData-Ex.timings
| name | user | system | elapsed | |
| dataHub-class | 7.404 | 0.912 | 8.463 | |
| dataSearch | 1.253 | 0.057 | 1.333 | |
| dataUpdate | 0 | 0 | 0 | |
| getCloudData | 2.924 | 0.167 | 5.166 | |
| getData | 0.000 | 0.000 | 0.001 | |
| meta_data | 0.002 | 0.001 | 0.002 | |
| recipeHub-class | 0.140 | 0.017 | 0.158 | |
| recipeLoad | 1.484 | 0.101 | 1.614 | |
| recipeMake | 0.001 | 0.000 | 0.001 | |
| recipeSearch | 0.642 | 0.040 | 0.692 | |
| recipeUpdate | 0.000 | 0.000 | 0.001 | |