Qian Liu
| Snapshot Date: 2025-08-14 13:40 -0400 (Thu, 14 Aug 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 2025-08-18 11:44 -0400 (Mon, 18 Aug 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" | 4824 |
| palomino7 | Windows Server 2022 Datacenter | x64 | 4.5.1 (2025-06-13 ucrt) -- "Great Square Root" | 4566 |
| merida1 | macOS 12.7.5 Monterey | x86_64 | 4.5.1 RC (2025-06-05 r88288) -- "Great Square Root" | 4604 |
| kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" | 4545 |
| kunpeng2 | Linux (openEuler 24.03 LTS) | aarch64 | R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" | 4579 |
| 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 | | ||||||||
| palomino7 | Windows Server 2022 Datacenter / x64 | ... NOT SUPPORTED ... | ||||||||||||
| 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: 2025-08-15 08:42:24 -0400 (Fri, 15 Aug 2025) |
| EndedAt: 2025-08-15 08:46:59 -0400 (Fri, 15 Aug 2025) |
| EllapsedTime: 275.2 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 RC (2025-06-05 r88288)
* 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 ‘1.8.0’
* 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 12.518 1.324 16.906
getCloudData 4.808 0.226 12.469
* 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-x86_64/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 RC (2025-06-05 r88288) -- "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...
140ec1c999bad_GRCh38.primary_assembly.genome.fa.1.bt2 added
140ec28bb8986_GRCh38.primary_assembly.genome.fa.2.bt2 added
140ec3041d14e_GRCh38.primary_assembly.genome.fa.3.bt2 added
140ec311470a2_GRCh38.primary_assembly.genome.fa.4.bt2 added
140ec34eeb4da_GRCh38.primary_assembly.genome.fa.rev.1.bt2 added
140ec23a36f5c_GRCh38.primary_assembly.genome.fa.rev.2.bt2 added
140ec3ee4134b_outfile.txt added
140ec6faec12e_GRCh37_to_GRCh38.chain added
140ec3a0cec4a_GRCh37_to_NCBI34.chain added
140ec266d0c0c_GRCh37_to_NCBI35.chain added
140ec4131fb89_GRCh37_to_NCBI36.chain added
140ec387900cf_GRCh38_to_GRCh37.chain added
140ec10243300_GRCh38_to_NCBI34.chain added
140ec38904d47_GRCh38_to_NCBI35.chain added
140ec9c18d54_GRCh38_to_NCBI36.chain added
140ec2258acd_NCBI34_to_GRCh37.chain added
140ec6ebb99d4_NCBI34_to_GRCh38.chain added
140ec5e706617_NCBI35_to_GRCh37.chain added
140ec253ea071_NCBI35_to_GRCh38.chain added
140ec32976dd1_NCBI36_to_GRCh37.chain added
140ec73aace49_NCBI36_to_GRCh38.chain added
140ec52cd55f2_GRCm38_to_NCBIM36.chain added
140ec26c5ad56_GRCm38_to_NCBIM37.chain added
140ec7bf6fcfc_NCBIM36_to_GRCm38.chain added
140ec145b43f9_NCBIM37_to_GRCm38.chain added
140ec73cb9adf_1000G_omni2.5.b37.vcf.gz added
140ec3c24e1dd_1000G_omni2.5.b37.vcf.gz.tbi added
140ec19689304_Mills_and_1000G_gold_standard.indels.b37.vcf.gz added
140ec208bf8a4_Mills_and_1000G_gold_standard.indels.b37.vcf.gz.tbi added
140ec4570e7ad_1000G_omni2.5.hg38.vcf.gz added
140ec777a3278_1000G_omni2.5.hg38.vcf.gz.tbi added
140ec7787a18f_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz added
140ec697ff097_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz.tbi added
140ec4e8c7f9d_af-only-gnomad.raw.sites.vcf added
140ec6a0e44b4_af-only-gnomad.raw.sites.vcf.idx added
140ec4ec0bbd1_Mutect2-exome-panel.vcf.idx added
140ec4f6abebb_Mutect2-WGS-panel-b37.vcf added
140ec69100fb8_Mutect2-WGS-panel-b37.vcf.idx added
140ec1d782eeb_small_exac_common_3.vcf added
140ec3d50556a_small_exac_common_3.vcf.idx added
140ec6517c198_1000g_pon.hg38.vcf.gz added
140ec7aa71601_1000g_pon.hg38.vcf.gz.tbi added
140ec6f95da8f_af-only-gnomad.hg38.vcf.gz added
140ec57401b84_af-only-gnomad.hg38.vcf.gz.tbi added
140ec31cea3dc_small_exac_common_3.hg38.vcf.gz added
140ec7567da0f_small_exac_common_3.hg38.vcf.gz.tbi added
140ec751d4b00_gencode.v41.annotation.gtf added
140ec56272911_gencode.v42.annotation.gtf added
140ec24f94747_gencode.vM30.annotation.gtf added
140ec69b69947_gencode.vM31.annotation.gtf added
140ec53093a89_gencode.v41.transcripts.fa added
140ec2e222f6_gencode.v41.transcripts.fa.fai added
140ec4c6545f4_gencode.v42.transcripts.fa added
140eccd3bd5b_gencode.v42.transcripts.fa.fai added
140ec2134a7f1_gencode.vM30.pc_transcripts.fa added
140ec7fdd03f_gencode.vM30.pc_transcripts.fa.fai added
140ec2872dc32_gencode.vM31.pc_transcripts.fa added
140eccd66b5d_gencode.vM31.pc_transcripts.fa.fai added
140ec5122ad40_GRCh38.primary_assembly.genome.fa.1.ht2 added
140ec3b9c6e5d_GRCh38.primary_assembly.genome.fa.2.ht2 added
140ec1b11ba3e_GRCh38.primary_assembly.genome.fa.3.ht2 added
140ec28da4a54_GRCh38.primary_assembly.genome.fa.4.ht2 added
140ec1345e5c0_GRCh38.primary_assembly.genome.fa.5.ht2 added
140ec51eeaa22_GRCh38.primary_assembly.genome.fa.6.ht2 added
140ecbe3c834_GRCh38.primary_assembly.genome.fa.7.ht2 added
140ec176cd405_GRCh38.primary_assembly.genome.fa.8.ht2 added
140ec69d3a046_GRCh38_full_analysis_set_plus_decoy_hla.fa.fai added
140ec44bf89f1_GRCh38_full_analysis_set_plus_decoy_hla.fa.amb added
140ec7af95079_GRCh38_full_analysis_set_plus_decoy_hla.fa.ann added
140ec6127702_GRCh38_full_analysis_set_plus_decoy_hla.fa.bwt added
140ec2643276b_GRCh38_full_analysis_set_plus_decoy_hla.fa.pac added
140ec2d0f56d_GRCh38_full_analysis_set_plus_decoy_hla.fa.sa added
140ec64a0c88c_GRCh38_full_analysis_set_plus_decoy_hla.fa added
140ec77ce92f0_GRCh38.primary_assembly.genome.fa.fai added
140ec1b110803_GRCh38.primary_assembly.genome.fa.amb added
140ec7b250ad6_GRCh38.primary_assembly.genome.fa.ann added
140ec3ceaa6c3_GRCh38.primary_assembly.genome.fa.bwt added
140ec516a6b73_GRCh38.primary_assembly.genome.fa.pac added
140ec21b474c7_GRCh38.primary_assembly.genome.fa.sa added
140ec4e5ec61a_GRCh38.primary_assembly.genome.fa added
140ec301ffd28_hs37d5.fa.fai added
140ec42565c7_hs37d5.fa.amb added
140ec333cedf1_hs37d5.fa.ann added
140ec6529837e_hs37d5.fa.bwt added
140ec877f915_hs37d5.fa.pac added
140ec7c81d60a_hs37d5.fa.sa added
140ec300b6a62_hs37d5.fa added
140ec3d756092_complete_ref_lens.bin added
140ec651730c3_ctable.bin added
140ec5582860e_ctg_offsets.bin added
140ec6c2f2cfd_duplicate_clusters.tsv added
140ecd32cd88_info.json added
140ec253a27d_mphf.bin added
140ec40d0bdbc_pos.bin added
140ec4858a2e2_pre_indexing.log added
140ec332dc889_rank.bin added
140ec2c8b49f_ref_indexing.log added
140ec46ca3426_refAccumLengths.bin added
140ec525cf19_reflengths.bin added
140ec753f74f2_refseq.bin added
140ec1916f801_seq.bin added
140ec32f41685_versionInfo.json added
140ec36f28fe5_salmon_index added
140ec6ec51f91_chrLength.txt added
140ec4f9ba167_chrName.txt added
140ec72819a05_chrNameLength.txt added
140ec1aa6f8fe_chrStart.txt added
140ec4824f95d_exonGeTrInfo.tab added
140ec736f6dab_exonInfo.tab added
140ec188930c2_geneInfo.tab added
140ec56e01d23_Genome added
140ec13991164_genomeParameters.txt added
140ec2644c649_Log.out added
140ec6d35f63f_SA added
140ec71b9da1c_SAindex added
140ec609e9e98_sjdbInfo.txt added
140ec4dbe3eb6_sjdbList.fromGTF.out.tab added
140ec507469a_sjdbList.out.tab added
140ec20ac2b0a_transcriptInfo.tab added
140ec73dae48_GRCh38.GENCODE.v42_100 added
140ec627cfcae_knownGene_hg38.sql added
140ec7bb13605_knownGene_hg38.txt added
140ec2f51c1b4_refGene_hg38.sql added
140ec208428b1_refGene_hg38.txt added
140ec448b8d24_knownGene_mm39.sql added
140ec25df59a4_knownGene_mm39.txt added
140ec6a763168_refGene_mm39.sql added
140ec75a5d972_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/RtmprnkAgh/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
42.946 5.336 53.796
ReUseData.Rcheck/ReUseData-Ex.timings
| name | user | system | elapsed | |
| dataHub-class | 12.518 | 1.324 | 16.906 | |
| dataSearch | 2.636 | 0.090 | 2.941 | |
| dataUpdate | 0.000 | 0.001 | 0.001 | |
| getCloudData | 4.808 | 0.226 | 12.469 | |
| getData | 0.001 | 0.002 | 0.002 | |
| meta_data | 0.001 | 0.001 | 0.002 | |
| recipeHub-class | 0.269 | 0.018 | 0.289 | |
| recipeLoad | 2.710 | 0.137 | 2.914 | |
| recipeMake | 0.000 | 0.001 | 0.002 | |
| recipeSearch | 1.165 | 0.055 | 1.229 | |
| recipeUpdate | 0.001 | 0.000 | 0.001 | |