Qian Liu
| Snapshot Date: 2025-08-31 13:45 -0400 (Sun, 31 Aug 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 2025-09-01 12:04 -0400 (Mon, 01 Sep 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4824 |
| lconway | macOS 12.7.1 Monterey | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4615 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" | 4562 |
| taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4541 |
| 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 1742/2320 | 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: /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:ReUseData.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings ReUseData_1.9.0.tar.gz |
| StartedAt: 2025-09-01 02:16:14 -0400 (Mon, 01 Sep 2025) |
| EndedAt: 2025-09-01 02:19:02 -0400 (Mon, 01 Sep 2025) |
| EllapsedTime: 168.2 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: ReUseData.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:ReUseData.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings ReUseData_1.9.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.22-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 ‘1.9.0’
* 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 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 6.325 0.24 6.567
* 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-3.22-bioc/meat/ReUseData.Rcheck/00check.log’
for details.
ReUseData.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD INSTALL ReUseData ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.22-bioc/R/site-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 (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...
1dbe8d300adf8d_GRCh38.primary_assembly.genome.fa.1.bt2 added
1dbe8d19ab396f_GRCh38.primary_assembly.genome.fa.2.bt2 added
1dbe8d349d530e_GRCh38.primary_assembly.genome.fa.3.bt2 added
1dbe8d5e72c79c_GRCh38.primary_assembly.genome.fa.4.bt2 added
1dbe8d62676848_GRCh38.primary_assembly.genome.fa.rev.1.bt2 added
1dbe8d191b42db_GRCh38.primary_assembly.genome.fa.rev.2.bt2 added
1dbe8d744f0e7c_outfile.txt added
1dbe8d3b90c869_GRCh37_to_GRCh38.chain added
1dbe8d7eb59d47_GRCh37_to_NCBI34.chain added
1dbe8d777b232_GRCh37_to_NCBI35.chain added
1dbe8d2cb7e131_GRCh37_to_NCBI36.chain added
1dbe8d21a86d43_GRCh38_to_GRCh37.chain added
1dbe8d731fa75c_GRCh38_to_NCBI34.chain added
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1dbe8d70d3457_GRCh38_to_NCBI36.chain added
1dbe8d5caec86f_NCBI34_to_GRCh37.chain added
1dbe8d72c66cb4_NCBI34_to_GRCh38.chain added
1dbe8d643c2d2c_NCBI35_to_GRCh37.chain added
1dbe8d274c9d2_NCBI35_to_GRCh38.chain added
1dbe8d1f41a3ed_NCBI36_to_GRCh37.chain added
1dbe8d47a4246b_NCBI36_to_GRCh38.chain added
1dbe8d426ebf2d_GRCm38_to_NCBIM36.chain added
1dbe8d35eee097_GRCm38_to_NCBIM37.chain added
1dbe8d5d866923_NCBIM36_to_GRCm38.chain added
1dbe8d77482c2a_NCBIM37_to_GRCm38.chain added
1dbe8d50a69f1e_1000G_omni2.5.b37.vcf.gz added
1dbe8df9a84f2_1000G_omni2.5.b37.vcf.gz.tbi added
1dbe8d56e25971_Mills_and_1000G_gold_standard.indels.b37.vcf.gz added
1dbe8d6974905a_Mills_and_1000G_gold_standard.indels.b37.vcf.gz.tbi added
1dbe8d6fe95006_1000G_omni2.5.hg38.vcf.gz added
1dbe8d7171590e_1000G_omni2.5.hg38.vcf.gz.tbi added
1dbe8d197f6fe7_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz added
1dbe8d9948975_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz.tbi added
1dbe8d260eac1c_af-only-gnomad.raw.sites.vcf added
1dbe8d77f23783_af-only-gnomad.raw.sites.vcf.idx added
1dbe8d6bfbf1bd_Mutect2-exome-panel.vcf.idx added
1dbe8d3f29eef8_Mutect2-WGS-panel-b37.vcf added
1dbe8d6c414600_Mutect2-WGS-panel-b37.vcf.idx added
1dbe8d278cba26_small_exac_common_3.vcf added
1dbe8d3ddf8c3f_small_exac_common_3.vcf.idx added
1dbe8d73b8f832_1000g_pon.hg38.vcf.gz added
1dbe8d54449b58_1000g_pon.hg38.vcf.gz.tbi added
1dbe8d5f87f982_af-only-gnomad.hg38.vcf.gz added
1dbe8d66d89f8e_af-only-gnomad.hg38.vcf.gz.tbi added
1dbe8d76278d43_small_exac_common_3.hg38.vcf.gz added
1dbe8d66952dd9_small_exac_common_3.hg38.vcf.gz.tbi added
1dbe8d438767fe_gencode.v41.annotation.gtf added
1dbe8d68edf9f8_gencode.v42.annotation.gtf added
1dbe8d4ad15b06_gencode.vM30.annotation.gtf added
1dbe8d45fc31d0_gencode.vM31.annotation.gtf added
1dbe8d82f9de5_gencode.v41.transcripts.fa added
1dbe8d12757f71_gencode.v41.transcripts.fa.fai added
1dbe8d86af0fd_gencode.v42.transcripts.fa added
1dbe8d3e1e7e7c_gencode.v42.transcripts.fa.fai added
1dbe8d6ffbe895_gencode.vM30.pc_transcripts.fa added
1dbe8d7fb31d27_gencode.vM30.pc_transcripts.fa.fai added
1dbe8dec51d9b_gencode.vM31.pc_transcripts.fa added
1dbe8d7f966d87_gencode.vM31.pc_transcripts.fa.fai added
1dbe8d56957698_GRCh38.primary_assembly.genome.fa.1.ht2 added
1dbe8d7839adf5_GRCh38.primary_assembly.genome.fa.2.ht2 added
1dbe8d6f7fbd8d_GRCh38.primary_assembly.genome.fa.3.ht2 added
1dbe8d4806cfa6_GRCh38.primary_assembly.genome.fa.4.ht2 added
1dbe8d11b91ddd_GRCh38.primary_assembly.genome.fa.5.ht2 added
1dbe8d79144702_GRCh38.primary_assembly.genome.fa.6.ht2 added
1dbe8d6e157bc3_GRCh38.primary_assembly.genome.fa.7.ht2 added
1dbe8d9ab5560_GRCh38.primary_assembly.genome.fa.8.ht2 added
1dbe8d651038c0_GRCh38_full_analysis_set_plus_decoy_hla.fa.fai added
1dbe8d2d3f6abb_GRCh38_full_analysis_set_plus_decoy_hla.fa.amb added
1dbe8d75ec9b60_GRCh38_full_analysis_set_plus_decoy_hla.fa.ann added
1dbe8dc9cf2e6_GRCh38_full_analysis_set_plus_decoy_hla.fa.bwt added
1dbe8d6b1ef6fa_GRCh38_full_analysis_set_plus_decoy_hla.fa.pac added
1dbe8d69a59393_GRCh38_full_analysis_set_plus_decoy_hla.fa.sa added
1dbe8d60e18e3e_GRCh38_full_analysis_set_plus_decoy_hla.fa added
1dbe8d4aa6f07c_GRCh38.primary_assembly.genome.fa.fai added
1dbe8d507e3321_GRCh38.primary_assembly.genome.fa.amb added
1dbe8d57091b82_GRCh38.primary_assembly.genome.fa.ann added
1dbe8d313c1e56_GRCh38.primary_assembly.genome.fa.bwt added
1dbe8d14059b1f_GRCh38.primary_assembly.genome.fa.pac added
1dbe8d3ff7157a_GRCh38.primary_assembly.genome.fa.sa added
1dbe8d7c0d795c_GRCh38.primary_assembly.genome.fa added
1dbe8d5a01ccef_hs37d5.fa.fai added
1dbe8d4826b35f_hs37d5.fa.amb added
1dbe8de82f8cd_hs37d5.fa.ann added
1dbe8d626cbded_hs37d5.fa.bwt added
1dbe8d64531dc_hs37d5.fa.pac added
1dbe8d7e7ee162_hs37d5.fa.sa added
1dbe8d621fdb14_hs37d5.fa added
1dbe8d150a4f77_complete_ref_lens.bin added
1dbe8d7e154ee9_ctable.bin added
1dbe8d38b551ad_ctg_offsets.bin added
1dbe8dd43fd6c_duplicate_clusters.tsv added
1dbe8d6d950c76_info.json added
1dbe8dbc2153_mphf.bin added
1dbe8d1efd1b49_pos.bin added
1dbe8d66a95379_pre_indexing.log added
1dbe8d6ed19d16_rank.bin added
1dbe8d28a870aa_ref_indexing.log added
1dbe8d4bb98c39_refAccumLengths.bin added
1dbe8d1c1107d1_reflengths.bin added
1dbe8d1e950c0a_refseq.bin added
1dbe8d58567f1f_seq.bin added
1dbe8d72ffecb_versionInfo.json added
1dbe8d83a9f9d_salmon_index added
1dbe8d39380d5e_chrLength.txt added
1dbe8d51d6ef48_chrName.txt added
1dbe8d58b8d2bf_chrNameLength.txt added
1dbe8d104128e0_chrStart.txt added
1dbe8d3130d9e_exonGeTrInfo.tab added
1dbe8d6cbe6dde_exonInfo.tab added
1dbe8d50383e5a_geneInfo.tab added
1dbe8d7f2086fa_Genome added
1dbe8d46c03ace_genomeParameters.txt added
1dbe8d185ef1b9_Log.out added
1dbe8dda37fc7_SA added
1dbe8d292cf8bb_SAindex added
1dbe8d1ea42395_sjdbInfo.txt added
1dbe8dc22612a_sjdbList.fromGTF.out.tab added
1dbe8db4cd3cf_sjdbList.out.tab added
1dbe8d33ae730c_transcriptInfo.tab added
1dbe8da37b013_GRCh38.GENCODE.v42_100 added
1dbe8d4402257c_knownGene_hg38.sql added
1dbe8d40f27079_knownGene_hg38.txt added
1dbe8d77ccbc8a_refGene_hg38.sql added
1dbe8d44be46d0_refGene_hg38.txt added
1dbe8d5fef8bc2_knownGene_mm39.sql added
1dbe8d5e761003_knownGene_mm39.txt added
1dbe8d338fe3e6_refGene_mm39.sql added
1dbe8d897fc6c_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/RtmpKnLspf/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
18.892 1.490 20.612
ReUseData.Rcheck/ReUseData-Ex.timings
| name | user | system | elapsed | |
| dataHub-class | 6.325 | 0.240 | 6.567 | |
| dataSearch | 1.208 | 0.030 | 1.238 | |
| dataUpdate | 0 | 0 | 0 | |
| getCloudData | 2.690 | 0.065 | 3.604 | |
| getData | 0.001 | 0.000 | 0.001 | |
| meta_data | 0.001 | 0.000 | 0.001 | |
| recipeHub-class | 0.123 | 0.001 | 0.126 | |
| recipeLoad | 1.294 | 0.016 | 1.312 | |
| recipeMake | 0 | 0 | 0 | |
| recipeSearch | 0.530 | 0.005 | 0.535 | |
| recipeUpdate | 0 | 0 | 0 | |