Qian Liu
| Snapshot Date: 2025-09-18 13:45 -0400 (Thu, 18 Sep 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 2025-09-19 12:04 -0400 (Fri, 19 Sep 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" | 4808 |
| lconway | macOS 12.7.1 Monterey | x86_64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4597 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4541 |
| taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4553 |
| 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 1750/2330 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| ReUseData 1.9.0 (landing page) Qian Liu
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson3 | macOS 13.7.7 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: /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_1.9.0.tar.gz |
| StartedAt: 2025-09-18 23:23:20 -0400 (Thu, 18 Sep 2025) |
| EndedAt: 2025-09-18 23:25:46 -0400 (Thu, 18 Sep 2025) |
| EllapsedTime: 145.6 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_1.9.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.22-bioc/meat/ReUseData.Rcheck’
* using R version 4.5.1 Patched (2025-09-10 r88807)
* using platform: x86_64-apple-darwin20
* R was compiled by
Apple clang version 14.0.0 (clang-1400.0.29.202)
GNU Fortran (GCC) 14.2.0
* running under: macOS Monterey 12.7.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* 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 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 7.454 0.878 8.436
* 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-x86_64/Resources/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 Patched (2025-09-10 r88807) -- "Great Square Root"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-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...
766b3740d8b4_GRCh38.primary_assembly.genome.fa.1.bt2 added
766b2532dc3_GRCh38.primary_assembly.genome.fa.2.bt2 added
766b22e15e66_GRCh38.primary_assembly.genome.fa.3.bt2 added
766b79fc8c6d_GRCh38.primary_assembly.genome.fa.4.bt2 added
766b336786ac_GRCh38.primary_assembly.genome.fa.rev.1.bt2 added
766b51baa091_GRCh38.primary_assembly.genome.fa.rev.2.bt2 added
766b3383b982_outfile.txt added
766bd08203a_GRCh37_to_GRCh38.chain added
766b107bc685_GRCh37_to_NCBI34.chain added
766b2e264e37_GRCh37_to_NCBI35.chain added
766b54d9148c_GRCh37_to_NCBI36.chain added
766b77d41ed8_GRCh38_to_GRCh37.chain added
766b735345e_GRCh38_to_NCBI34.chain added
766b36010b04_GRCh38_to_NCBI35.chain added
766b7e7a4f4e_GRCh38_to_NCBI36.chain added
766bfeccac1_NCBI34_to_GRCh37.chain added
766b2f34d12_NCBI34_to_GRCh38.chain added
766b3348da41_NCBI35_to_GRCh37.chain added
766b73f0fbb4_NCBI35_to_GRCh38.chain added
766b521d21e3_NCBI36_to_GRCh37.chain added
766b769be832_NCBI36_to_GRCh38.chain added
766b75a96773_GRCm38_to_NCBIM36.chain added
766b44c6eb5e_GRCm38_to_NCBIM37.chain added
766b5f868b98_NCBIM36_to_GRCm38.chain added
766b7a36d926_NCBIM37_to_GRCm38.chain added
766b26ea8c79_1000G_omni2.5.b37.vcf.gz added
766b70ac6fe4_1000G_omni2.5.b37.vcf.gz.tbi added
766b48e61b86_Mills_and_1000G_gold_standard.indels.b37.vcf.gz added
766b7b191fcd_Mills_and_1000G_gold_standard.indels.b37.vcf.gz.tbi added
766b2e770ade_1000G_omni2.5.hg38.vcf.gz added
766b96a8ca7_1000G_omni2.5.hg38.vcf.gz.tbi added
766b32382cc5_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz added
766b6035345_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz.tbi added
766b444fda18_af-only-gnomad.raw.sites.vcf added
766b567780b1_af-only-gnomad.raw.sites.vcf.idx added
766b3fa210d0_Mutect2-exome-panel.vcf.idx added
766b28fde853_Mutect2-WGS-panel-b37.vcf added
766b359fb62b_Mutect2-WGS-panel-b37.vcf.idx added
766b870dc8e_small_exac_common_3.vcf added
766b299ff2f6_small_exac_common_3.vcf.idx added
766b440809d3_1000g_pon.hg38.vcf.gz added
766b6bbd1e89_1000g_pon.hg38.vcf.gz.tbi added
766b4d1feba1_af-only-gnomad.hg38.vcf.gz added
766b6aa6be95_af-only-gnomad.hg38.vcf.gz.tbi added
766b692a5ee6_small_exac_common_3.hg38.vcf.gz added
766b5cbc83fa_small_exac_common_3.hg38.vcf.gz.tbi added
766b5c7cc1a6_gencode.v41.annotation.gtf added
766b28da8ba_gencode.v42.annotation.gtf added
766b22404ca5_gencode.vM30.annotation.gtf added
766b2b67f634_gencode.vM31.annotation.gtf added
766b3654e62f_gencode.v41.transcripts.fa added
766b7fd43386_gencode.v41.transcripts.fa.fai added
766b4482e3fa_gencode.v42.transcripts.fa added
766b6d455539_gencode.v42.transcripts.fa.fai added
766b62de493a_gencode.vM30.pc_transcripts.fa added
766b6f99b18b_gencode.vM30.pc_transcripts.fa.fai added
766b535755ea_gencode.vM31.pc_transcripts.fa added
766bac9a065_gencode.vM31.pc_transcripts.fa.fai added
766b3b414c6b_GRCh38.primary_assembly.genome.fa.1.ht2 added
766b3c002331_GRCh38.primary_assembly.genome.fa.2.ht2 added
766b2d0684bd_GRCh38.primary_assembly.genome.fa.3.ht2 added
766b6f4ab63_GRCh38.primary_assembly.genome.fa.4.ht2 added
766b291ff426_GRCh38.primary_assembly.genome.fa.5.ht2 added
766b70d5ffe1_GRCh38.primary_assembly.genome.fa.6.ht2 added
766b719246a6_GRCh38.primary_assembly.genome.fa.7.ht2 added
766b3a5c768a_GRCh38.primary_assembly.genome.fa.8.ht2 added
766bc6a7bf5_GRCh38_full_analysis_set_plus_decoy_hla.fa.fai added
766b22f01831_GRCh38_full_analysis_set_plus_decoy_hla.fa.amb added
766b40c44ae2_GRCh38_full_analysis_set_plus_decoy_hla.fa.ann added
766b17105ca6_GRCh38_full_analysis_set_plus_decoy_hla.fa.bwt added
766b3332a21e_GRCh38_full_analysis_set_plus_decoy_hla.fa.pac added
766b413179d4_GRCh38_full_analysis_set_plus_decoy_hla.fa.sa added
766b17356ebc_GRCh38_full_analysis_set_plus_decoy_hla.fa added
766b34f9048b_GRCh38.primary_assembly.genome.fa.fai added
766b48995cd8_GRCh38.primary_assembly.genome.fa.amb added
766b4c9e8e24_GRCh38.primary_assembly.genome.fa.ann added
766b3d8604c8_GRCh38.primary_assembly.genome.fa.bwt added
766b29a40606_GRCh38.primary_assembly.genome.fa.pac added
766b4f878945_GRCh38.primary_assembly.genome.fa.sa added
766b4b4539cd_GRCh38.primary_assembly.genome.fa added
766b2dd5e856_hs37d5.fa.fai added
766b36887d9c_hs37d5.fa.amb added
766b3aeea8bc_hs37d5.fa.ann added
766ba87ecde_hs37d5.fa.bwt added
766b61cfe838_hs37d5.fa.pac added
766b1896e6b3_hs37d5.fa.sa added
766b5b03fe61_hs37d5.fa added
766b6331c0f5_complete_ref_lens.bin added
766b577347b3_ctable.bin added
766b5168659f_ctg_offsets.bin added
766b1ce7d37a_duplicate_clusters.tsv added
766b37ecfd69_info.json added
766b27f1152e_mphf.bin added
766b44a5937e_pos.bin added
766b52765867_pre_indexing.log added
766b57a5fc7c_rank.bin added
766b52635dd8_ref_indexing.log added
766b79a63a29_refAccumLengths.bin added
766b10349824_reflengths.bin added
766b6cf06bcb_refseq.bin added
766b1c35144d_seq.bin added
766b60c7d9b2_versionInfo.json added
766b60a566c1_salmon_index added
766bafd3a79_chrLength.txt added
766b7709e391_chrName.txt added
766b2a3b81a5_chrNameLength.txt added
766b28bc8d4c_chrStart.txt added
766b72e08d78_exonGeTrInfo.tab added
766b7467fc33_exonInfo.tab added
766b56deb3f9_geneInfo.tab added
766b36f9ccfd_Genome added
766b4a01123d_genomeParameters.txt added
766bc5488c0_Log.out added
766b1ddfb93_SA added
766b14af70da_SAindex added
766ba1a02d2_sjdbInfo.txt added
766b31af2e2c_sjdbList.fromGTF.out.tab added
766b6400642f_sjdbList.out.tab added
766b55b17cf3_transcriptInfo.tab added
766b77826178_GRCh38.GENCODE.v42_100 added
766b10cd4a94_knownGene_hg38.sql added
766b15db432a_knownGene_hg38.txt added
766b6e16859b_refGene_hg38.sql added
766b89dbb94_refGene_hg38.txt added
766b2b85f5f7_knownGene_mm39.sql added
766b67d74173_knownGene_mm39.txt added
766b650a1a47_refGene_mm39.sql added
766b7a435f23_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/Rtmpu2Zfyb/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
21.698 2.344 25.112
ReUseData.Rcheck/ReUseData-Ex.timings
| name | user | system | elapsed | |
| dataHub-class | 7.454 | 0.878 | 8.436 | |
| dataSearch | 1.363 | 0.056 | 1.427 | |
| dataUpdate | 0.000 | 0.000 | 0.001 | |
| getCloudData | 2.831 | 0.165 | 4.314 | |
| getData | 0 | 0 | 0 | |
| meta_data | 0.001 | 0.000 | 0.001 | |
| recipeHub-class | 0.141 | 0.014 | 0.156 | |
| recipeLoad | 1.559 | 0.099 | 1.669 | |
| recipeMake | 0.001 | 0.000 | 0.000 | |
| recipeSearch | 0.686 | 0.045 | 0.735 | |
| recipeUpdate | 0.000 | 0.000 | 0.001 | |