Qian Liu
| Snapshot Date: 2025-12-15 13:45 -0500 (Mon, 15 Dec 2025) |
| git_url: https://git.bioconductor.org/packages/ReUseData |
| git_branch: RELEASE_3_22 |
| git_last_commit: 2d4066b |
| git_last_commit_date: 2025-10-29 11:20:44 -0500 (Wed, 29 Oct 2025) |
| Back to Multiple platform build/check report for BioC 3.22: simplified long |
|
This page was generated on 2025-12-18 12:07 -0500 (Thu, 18 Dec 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble" | 4882 |
| merida1 | macOS 12.7.6 Monterey | x86_64 | 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble" | 4673 |
| kjohnson1 | macOS 13.7.5 Ventura | arm64 | 4.5.2 Patched (2025-11-04 r88984) -- "[Not] Part in a Rumble" | 4607 |
| taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4671 |
| 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 1773/2361 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| ReUseData 1.10.0 (landing page) Qian Liu
| nebbiolo2 | 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 | | ||||||||
| 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: 1.10.0 |
| 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_1.10.0.tar.gz |
| StartedAt: 2025-12-17 19:09:25 -0500 (Wed, 17 Dec 2025) |
| EndedAt: 2025-12-17 19:12:56 -0500 (Wed, 17 Dec 2025) |
| EllapsedTime: 210.3 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_1.10.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.22-bioc/meat/ReUseData.Rcheck’
* using R version 4.5.2 Patched (2025-11-04 r88984)
* 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 13.7.8
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘ReUseData/DESCRIPTION’ ... OK
* this is package ‘ReUseData’ version ‘1.10.0’
* 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 8.177 0.958 12.724
getCloudData 3.067 0.181 6.550
* 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-3.22-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 ‘1.10.0’ ** 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 4.5.2 Patched (2025-11-04 r88984) -- "[Not] Part in a Rumble"
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...
a11661459402_GRCh38.primary_assembly.genome.fa.1.bt2 added
a1161ef84132_GRCh38.primary_assembly.genome.fa.2.bt2 added
a1163c804980_GRCh38.primary_assembly.genome.fa.3.bt2 added
a116a599188_GRCh38.primary_assembly.genome.fa.4.bt2 added
a1167e617d06_GRCh38.primary_assembly.genome.fa.rev.1.bt2 added
a116325755bc_GRCh38.primary_assembly.genome.fa.rev.2.bt2 added
a1163bdc376_outfile.txt added
a1161f6b79e5_GRCh37_to_GRCh38.chain added
a116490fb980_GRCh37_to_NCBI34.chain added
a116275ba7f9_GRCh37_to_NCBI35.chain added
a1167270e09e_GRCh37_to_NCBI36.chain added
a11650aadfc4_GRCh38_to_GRCh37.chain added
a116248e63c_GRCh38_to_NCBI34.chain added
a11636e50_GRCh38_to_NCBI35.chain added
a116613f4631_GRCh38_to_NCBI36.chain added
a1161196cd8_NCBI34_to_GRCh37.chain added
a1162c38d978_NCBI34_to_GRCh38.chain added
a116484d6bf6_NCBI35_to_GRCh37.chain added
a11652eb088f_NCBI35_to_GRCh38.chain added
a116447f0ed0_NCBI36_to_GRCh37.chain added
a11671a59cd1_NCBI36_to_GRCh38.chain added
a1162fda97a1_GRCm38_to_NCBIM36.chain added
a1163818e392_GRCm38_to_NCBIM37.chain added
a1166a04a303_NCBIM36_to_GRCm38.chain added
a116566a5055_NCBIM37_to_GRCm38.chain added
a1165dc028c5_1000G_omni2.5.b37.vcf.gz added
a11672b4cd98_1000G_omni2.5.b37.vcf.gz.tbi added
a1163c25f0fd_Mills_and_1000G_gold_standard.indels.b37.vcf.gz added
a1165ef090e4_Mills_and_1000G_gold_standard.indels.b37.vcf.gz.tbi added
a1163b8996e_1000G_omni2.5.hg38.vcf.gz added
a1164c6106aa_1000G_omni2.5.hg38.vcf.gz.tbi added
a11675fcaa12_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz added
a1161f01c042_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz.tbi added
a1162bf53cf5_af-only-gnomad.raw.sites.vcf added
a11671750f5e_af-only-gnomad.raw.sites.vcf.idx added
a1163c441e83_Mutect2-exome-panel.vcf.idx added
a1161c2f495e_Mutect2-WGS-panel-b37.vcf added
a1166479c8c6_Mutect2-WGS-panel-b37.vcf.idx added
a116776c72b2_small_exac_common_3.vcf added
a11670de415e_small_exac_common_3.vcf.idx added
a116f95bc36_1000g_pon.hg38.vcf.gz added
a1162f778538_1000g_pon.hg38.vcf.gz.tbi added
a1164fcb37e0_af-only-gnomad.hg38.vcf.gz added
a11626c17c0d_af-only-gnomad.hg38.vcf.gz.tbi added
a11668b74d5b_small_exac_common_3.hg38.vcf.gz added
a1165a37c712_small_exac_common_3.hg38.vcf.gz.tbi added
a1163ee9d04_gencode.v41.annotation.gtf added
a116268673a0_gencode.v42.annotation.gtf added
a11645112122_gencode.vM30.annotation.gtf added
a1166796629a_gencode.vM31.annotation.gtf added
a1164223a197_gencode.v41.transcripts.fa added
a1163145e26d_gencode.v41.transcripts.fa.fai added
a11663147b60_gencode.v42.transcripts.fa added
a11655b00e71_gencode.v42.transcripts.fa.fai added
a116198448aa_gencode.vM30.pc_transcripts.fa added
a1163bbe9dfc_gencode.vM30.pc_transcripts.fa.fai added
a1165f762a08_gencode.vM31.pc_transcripts.fa added
a11646c1a42e_gencode.vM31.pc_transcripts.fa.fai added
a1165301ec4c_GRCh38.primary_assembly.genome.fa.1.ht2 added
a11623409c27_GRCh38.primary_assembly.genome.fa.2.ht2 added
a11666cbd685_GRCh38.primary_assembly.genome.fa.3.ht2 added
a1165070ea7c_GRCh38.primary_assembly.genome.fa.4.ht2 added
a11625329c26_GRCh38.primary_assembly.genome.fa.5.ht2 added
a1161da995de_GRCh38.primary_assembly.genome.fa.6.ht2 added
a11668ae3108_GRCh38.primary_assembly.genome.fa.7.ht2 added
a11641539e9_GRCh38.primary_assembly.genome.fa.8.ht2 added
a116d8cf217_GRCh38_full_analysis_set_plus_decoy_hla.fa.fai added
a1162069caf4_GRCh38_full_analysis_set_plus_decoy_hla.fa.amb added
a11618b69cc_GRCh38_full_analysis_set_plus_decoy_hla.fa.ann added
a11667ced0de_GRCh38_full_analysis_set_plus_decoy_hla.fa.bwt added
a1163af2d410_GRCh38_full_analysis_set_plus_decoy_hla.fa.pac added
a1161c4084ac_GRCh38_full_analysis_set_plus_decoy_hla.fa.sa added
a1164fc646b1_GRCh38_full_analysis_set_plus_decoy_hla.fa added
a116624b3761_GRCh38.primary_assembly.genome.fa.fai added
a1163820f3b1_GRCh38.primary_assembly.genome.fa.amb added
a1167b5f0640_GRCh38.primary_assembly.genome.fa.ann added
a1161b939307_GRCh38.primary_assembly.genome.fa.bwt added
a1167599beb5_GRCh38.primary_assembly.genome.fa.pac added
a11640b79964_GRCh38.primary_assembly.genome.fa.sa added
a11655b7956d_GRCh38.primary_assembly.genome.fa added
a1167b35312_hs37d5.fa.fai added
a116e12c6b1_hs37d5.fa.amb added
a11672b295ae_hs37d5.fa.ann added
a1162a810d56_hs37d5.fa.bwt added
a1167e929ee6_hs37d5.fa.pac added
a1164bfe4ef5_hs37d5.fa.sa added
a11624f1ddcd_hs37d5.fa added
a116318d0ae_complete_ref_lens.bin added
a116522c5118_ctable.bin added
a1165b8028cd_ctg_offsets.bin added
a1163af6d9a9_duplicate_clusters.tsv added
a116244c047d_info.json added
a1167ababd28_mphf.bin added
a11679d8cc0a_pos.bin added
a11683be305_pre_indexing.log added
a11613b5617c_rank.bin added
a11669131dff_ref_indexing.log added
a1166616863d_refAccumLengths.bin added
a11650c74327_reflengths.bin added
a1164a09dedf_refseq.bin added
a1164e072872_seq.bin added
a11637f07c63_versionInfo.json added
a116d766446_salmon_index added
a11657b13691_chrLength.txt added
a11633759691_chrName.txt added
a1166cf023fb_chrNameLength.txt added
a1169ca6b9d_chrStart.txt added
a116485f1570_exonGeTrInfo.tab added
a1165a78912e_exonInfo.tab added
a11621839169_geneInfo.tab added
a11644bf95af_Genome added
a1167dfc376b_genomeParameters.txt added
a116399a926b_Log.out added
a1165302cc58_SA added
a1165cb5cffb_SAindex added
a1162469974a_sjdbInfo.txt added
a116104b8df3_sjdbList.fromGTF.out.tab added
a116505454e0_sjdbList.out.tab added
a11650906753_transcriptInfo.tab added
a116386fa377_GRCh38.GENCODE.v42_100 added
a1162954f693_knownGene_hg38.sql added
a1169084218_knownGene_hg38.txt added
a1167d2b3a49_refGene_hg38.sql added
a11620ffced2_refGene_hg38.txt added
a1167a634dea_knownGene_mm39.sql added
a116d907c6c_knownGene_mm39.txt added
a1168d89d69_refGene_mm39.sql added
a11645465d08_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/Rtmp1Hcc9i/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
25.258 2.582 38.562
ReUseData.Rcheck/ReUseData-Ex.timings
| name | user | system | elapsed | |
| dataHub-class | 8.177 | 0.958 | 12.724 | |
| dataSearch | 1.380 | 0.067 | 2.045 | |
| dataUpdate | 0.000 | 0.001 | 0.000 | |
| getCloudData | 3.067 | 0.181 | 6.550 | |
| getData | 0 | 0 | 0 | |
| meta_data | 0.001 | 0.000 | 0.002 | |
| recipeHub-class | 0.159 | 0.016 | 0.213 | |
| recipeLoad | 1.713 | 0.121 | 2.488 | |
| recipeMake | 0.000 | 0.000 | 0.001 | |
| recipeSearch | 0.693 | 0.048 | 1.114 | |
| recipeUpdate | 0 | 0 | 0 | |