Qian Liu
| Snapshot Date: 2025-08-11 13:40 -0400 (Mon, 11 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 2025-08-14 11:41 -0400 (Thu, 14 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: /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:ReUseData.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings ReUseData_1.8.0.tar.gz |
| StartedAt: 2025-08-14 01:54:59 -0400 (Thu, 14 Aug 2025) |
| EndedAt: 2025-08-14 01:57:57 -0400 (Thu, 14 Aug 2025) |
| EllapsedTime: 178.3 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: ReUseData.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:ReUseData.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings ReUseData_1.8.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/ReUseData.Rcheck’
* using R version 4.5.1 (2025-06-13)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.3 LTS
* using session charset: UTF-8
* 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 loading without being on the library search path ... 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 6.199 0.396 6.596
* 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 re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE
Status: 1 NOTE
See
‘/home/biocbuild/bbs-3.21-bioc/meat/ReUseData.Rcheck/00check.log’
for details.
ReUseData.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD INSTALL ReUseData ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.21-bioc/R/site-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 (2025-06-13) -- "Great Square Root"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu
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...
3aa6d8390b8267_GRCh38.primary_assembly.genome.fa.1.bt2 added
3aa6d8315ee58b_GRCh38.primary_assembly.genome.fa.2.bt2 added
3aa6d872eed0b2_GRCh38.primary_assembly.genome.fa.3.bt2 added
3aa6d86def54e1_GRCh38.primary_assembly.genome.fa.4.bt2 added
3aa6d837aa3ce8_GRCh38.primary_assembly.genome.fa.rev.1.bt2 added
3aa6d85a55efd8_GRCh38.primary_assembly.genome.fa.rev.2.bt2 added
3aa6d82ac45fba_outfile.txt added
3aa6d870c8ab59_GRCh37_to_GRCh38.chain added
3aa6d87f3e9371_GRCh37_to_NCBI34.chain added
3aa6d86fc840f_GRCh37_to_NCBI35.chain added
3aa6d88450bbe_GRCh37_to_NCBI36.chain added
3aa6d872742db9_GRCh38_to_GRCh37.chain added
3aa6d8357e3088_GRCh38_to_NCBI34.chain added
3aa6d83e40bfb4_GRCh38_to_NCBI35.chain added
3aa6d8494754ff_GRCh38_to_NCBI36.chain added
3aa6d810c42f12_NCBI34_to_GRCh37.chain added
3aa6d87f75b72_NCBI34_to_GRCh38.chain added
3aa6d849dabf2_NCBI35_to_GRCh37.chain added
3aa6d843e5ea7f_NCBI35_to_GRCh38.chain added
3aa6d8614ee6e_NCBI36_to_GRCh37.chain added
3aa6d81d24c59_NCBI36_to_GRCh38.chain added
3aa6d83a9bac3f_GRCm38_to_NCBIM36.chain added
3aa6d842b07e1c_GRCm38_to_NCBIM37.chain added
3aa6d83e0cbc81_NCBIM36_to_GRCm38.chain added
3aa6d817583d89_NCBIM37_to_GRCm38.chain added
3aa6d819894240_1000G_omni2.5.b37.vcf.gz added
3aa6d86ed50fb3_1000G_omni2.5.b37.vcf.gz.tbi added
3aa6d81a732036_Mills_and_1000G_gold_standard.indels.b37.vcf.gz added
3aa6d860cf2d2_Mills_and_1000G_gold_standard.indels.b37.vcf.gz.tbi added
3aa6d833555a51_1000G_omni2.5.hg38.vcf.gz added
3aa6d8677ebe4e_1000G_omni2.5.hg38.vcf.gz.tbi added
3aa6d83f18753a_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz added
3aa6d864b43fdc_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz.tbi added
3aa6d85a6d8f01_af-only-gnomad.raw.sites.vcf added
3aa6d82d07ca1b_af-only-gnomad.raw.sites.vcf.idx added
3aa6d81c5e7cc4_Mutect2-exome-panel.vcf.idx added
3aa6d834c37ed9_Mutect2-WGS-panel-b37.vcf added
3aa6d857cc29d5_Mutect2-WGS-panel-b37.vcf.idx added
3aa6d8d27281e_small_exac_common_3.vcf added
3aa6d83402124a_small_exac_common_3.vcf.idx added
3aa6d85ec8ade4_1000g_pon.hg38.vcf.gz added
3aa6d8156c33dc_1000g_pon.hg38.vcf.gz.tbi added
3aa6d826764003_af-only-gnomad.hg38.vcf.gz added
3aa6d81446de6c_af-only-gnomad.hg38.vcf.gz.tbi added
3aa6d853acf390_small_exac_common_3.hg38.vcf.gz added
3aa6d86fbd9502_small_exac_common_3.hg38.vcf.gz.tbi added
3aa6d8250b0d7f_gencode.v41.annotation.gtf added
3aa6d85ba44f02_gencode.v42.annotation.gtf added
3aa6d8745b40f4_gencode.vM30.annotation.gtf added
3aa6d868f0f7fe_gencode.vM31.annotation.gtf added
3aa6d861b93d71_gencode.v41.transcripts.fa added
3aa6d8762d8d4d_gencode.v41.transcripts.fa.fai added
3aa6d8238ca43d_gencode.v42.transcripts.fa added
3aa6d82469bb8d_gencode.v42.transcripts.fa.fai added
3aa6d8343a49ce_gencode.vM30.pc_transcripts.fa added
3aa6d83ae4e1c7_gencode.vM30.pc_transcripts.fa.fai added
3aa6d83df2fdcd_gencode.vM31.pc_transcripts.fa added
3aa6d8230f5981_gencode.vM31.pc_transcripts.fa.fai added
3aa6d8555801fd_GRCh38.primary_assembly.genome.fa.1.ht2 added
3aa6d843fff09f_GRCh38.primary_assembly.genome.fa.2.ht2 added
3aa6d85664b3d3_GRCh38.primary_assembly.genome.fa.3.ht2 added
3aa6d83cd6c04c_GRCh38.primary_assembly.genome.fa.4.ht2 added
3aa6d831865d9_GRCh38.primary_assembly.genome.fa.5.ht2 added
3aa6d83b18f3af_GRCh38.primary_assembly.genome.fa.6.ht2 added
3aa6d817444f4d_GRCh38.primary_assembly.genome.fa.7.ht2 added
3aa6d830202ff4_GRCh38.primary_assembly.genome.fa.8.ht2 added
3aa6d857777074_GRCh38_full_analysis_set_plus_decoy_hla.fa.fai added
3aa6d84c07ce26_GRCh38_full_analysis_set_plus_decoy_hla.fa.amb added
3aa6d87ec59ca_GRCh38_full_analysis_set_plus_decoy_hla.fa.ann added
3aa6d8649e9892_GRCh38_full_analysis_set_plus_decoy_hla.fa.bwt added
3aa6d89e071_GRCh38_full_analysis_set_plus_decoy_hla.fa.pac added
3aa6d866b507ae_GRCh38_full_analysis_set_plus_decoy_hla.fa.sa added
3aa6d87a0acc6e_GRCh38_full_analysis_set_plus_decoy_hla.fa added
3aa6d826802074_GRCh38.primary_assembly.genome.fa.fai added
3aa6d87afbe61b_GRCh38.primary_assembly.genome.fa.amb added
3aa6d84db7bffe_GRCh38.primary_assembly.genome.fa.ann added
3aa6d8163db577_GRCh38.primary_assembly.genome.fa.bwt added
3aa6d82006f39a_GRCh38.primary_assembly.genome.fa.pac added
3aa6d8295c0f00_GRCh38.primary_assembly.genome.fa.sa added
3aa6d8a98f66b_GRCh38.primary_assembly.genome.fa added
3aa6d88f7eb98_hs37d5.fa.fai added
3aa6d8b154c71_hs37d5.fa.amb added
3aa6d8c683b9_hs37d5.fa.ann added
3aa6d82c848fd6_hs37d5.fa.bwt added
3aa6d82f7f07fe_hs37d5.fa.pac added
3aa6d83500cd87_hs37d5.fa.sa added
3aa6d86769719d_hs37d5.fa added
3aa6d86d7205cb_complete_ref_lens.bin added
3aa6d858102709_ctable.bin added
3aa6d83cc1739a_ctg_offsets.bin added
3aa6d83171f66b_duplicate_clusters.tsv added
3aa6d82e74dadc_info.json added
3aa6d8799833e6_mphf.bin added
3aa6d8348a5c44_pos.bin added
3aa6d8698dce8b_pre_indexing.log added
3aa6d810dc8333_rank.bin added
3aa6d864aa8c39_ref_indexing.log added
3aa6d841053eff_refAccumLengths.bin added
3aa6d85ce4515a_reflengths.bin added
3aa6d86c96e603_refseq.bin added
3aa6d825a3d791_seq.bin added
3aa6d85cee31cb_versionInfo.json added
3aa6d8534bedb1_salmon_index added
3aa6d81faea3ff_chrLength.txt added
3aa6d836e523f_chrName.txt added
3aa6d84e47d3cc_chrNameLength.txt added
3aa6d86d6663fd_chrStart.txt added
3aa6d819ac07b6_exonGeTrInfo.tab added
3aa6d86e4ec766_exonInfo.tab added
3aa6d816c272fe_geneInfo.tab added
3aa6d82444fe22_Genome added
3aa6d87746b2ff_genomeParameters.txt added
3aa6d821d7bf6f_Log.out added
3aa6d8250b81db_SA added
3aa6d823cb42d5_SAindex added
3aa6d85156c76e_sjdbInfo.txt added
3aa6d85a0c4f62_sjdbList.fromGTF.out.tab added
3aa6d8b34b472_sjdbList.out.tab added
3aa6d83ec8cd39_transcriptInfo.tab added
3aa6d8321c766b_GRCh38.GENCODE.v42_100 added
3aa6d847f6280c_knownGene_hg38.sql added
3aa6d8703ac3a4_knownGene_hg38.txt added
3aa6d860915147_refGene_hg38.sql added
3aa6d8418e5bf3_refGene_hg38.txt added
3aa6d824c51fe9_knownGene_mm39.sql added
3aa6d84a1f1fd3_knownGene_mm39.txt added
3aa6d8526adf26_refGene_mm39.sql added
3aa6d896fac22_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/RtmpKDMoDK/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
20.164 1.904 22.600
ReUseData.Rcheck/ReUseData-Ex.timings
| name | user | system | elapsed | |
| dataHub-class | 6.199 | 0.396 | 6.596 | |
| dataSearch | 1.184 | 0.030 | 1.214 | |
| dataUpdate | 0.001 | 0.000 | 0.000 | |
| getCloudData | 2.882 | 0.100 | 3.890 | |
| getData | 0 | 0 | 0 | |
| meta_data | 0.001 | 0.000 | 0.001 | |
| recipeHub-class | 0.125 | 0.004 | 0.130 | |
| recipeLoad | 1.342 | 0.031 | 1.373 | |
| recipeMake | 0.000 | 0.001 | 0.001 | |
| recipeSearch | 0.556 | 0.014 | 0.569 | |
| recipeUpdate | 0 | 0 | 0 | |