Qian Liu
| Snapshot Date: 2025-08-29 13:45 -0400 (Fri, 29 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 2025-08-30 12:09 -0400 (Sat, 30 Aug 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. - See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host. |
| Package: ReUseData |
| Version: 1.9.0 |
| Command: /home/biocbuild/R/R/bin/R CMD check --install=check:ReUseData.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings ReUseData_1.9.0.tar.gz |
| StartedAt: 2025-08-29 10:44:07 -0000 (Fri, 29 Aug 2025) |
| EndedAt: 2025-08-29 10:46:43 -0000 (Fri, 29 Aug 2025) |
| EllapsedTime: 156.1 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: ReUseData.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/R/R/bin/R CMD check --install=check:ReUseData.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings ReUseData_1.9.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/ReUseData.Rcheck’
* using R version 4.5.0 (2025-04-11)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0
GNU Fortran (GCC) 14.2.0
* running under: openEuler 24.03 (LTS)
* 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 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 8.815 0.355 9.210
getCloudData 3.373 0.339 6.619
* 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
‘/home/biocbuild/bbs-3.22-bioc/meat/ReUseData.Rcheck/00check.log’
for details.
ReUseData.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R/bin/R CMD INSTALL ReUseData ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/R/R-4.5.0/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 4.5.0 (2025-04-11) -- "How About a Twenty-Six"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: aarch64-unknown-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...
b20f3756eb23e_GRCh38.primary_assembly.genome.fa.1.bt2 added
b20f3263883c2_GRCh38.primary_assembly.genome.fa.2.bt2 added
b20f34e01cb9b_GRCh38.primary_assembly.genome.fa.3.bt2 added
b20f31a06a437_GRCh38.primary_assembly.genome.fa.4.bt2 added
b20f363379b3f_GRCh38.primary_assembly.genome.fa.rev.1.bt2 added
b20f37b52319c_GRCh38.primary_assembly.genome.fa.rev.2.bt2 added
b20f3706f43ba_outfile.txt added
b20f31e08e08e_GRCh37_to_GRCh38.chain added
b20f3279ecda1_GRCh37_to_NCBI34.chain added
b20f325480741_GRCh37_to_NCBI35.chain added
b20f34336725a_GRCh37_to_NCBI36.chain added
b20f36ae6ca9f_GRCh38_to_GRCh37.chain added
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b20f37a8f6a2b_GRCh38_to_NCBI35.chain added
b20f358a35d1c_GRCh38_to_NCBI36.chain added
b20f344a2f575_NCBI34_to_GRCh37.chain added
b20f3482054e3_NCBI34_to_GRCh38.chain added
b20f37315ae01_NCBI35_to_GRCh37.chain added
b20f33ae0a607_NCBI35_to_GRCh38.chain added
b20f367ca4fb4_NCBI36_to_GRCh37.chain added
b20f35ce98e95_NCBI36_to_GRCh38.chain added
b20f3f710587_GRCm38_to_NCBIM36.chain added
b20f355149bf6_GRCm38_to_NCBIM37.chain added
b20f33e7c4794_NCBIM36_to_GRCm38.chain added
b20f31fb33e4a_NCBIM37_to_GRCm38.chain added
b20f3658a497a_1000G_omni2.5.b37.vcf.gz added
b20f34a34d41f_1000G_omni2.5.b37.vcf.gz.tbi added
b20f32426782c_Mills_and_1000G_gold_standard.indels.b37.vcf.gz added
b20f33975bac9_Mills_and_1000G_gold_standard.indels.b37.vcf.gz.tbi added
b20f310e566f2_1000G_omni2.5.hg38.vcf.gz added
b20f36a9e2b_1000G_omni2.5.hg38.vcf.gz.tbi added
b20f32ee46d07_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz added
b20f3371deab5_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz.tbi added
b20f34e6c69c6_af-only-gnomad.raw.sites.vcf added
b20f348eb113e_af-only-gnomad.raw.sites.vcf.idx added
b20f31a5585f4_Mutect2-exome-panel.vcf.idx added
b20f349be9b63_Mutect2-WGS-panel-b37.vcf added
b20f3395a54f8_Mutect2-WGS-panel-b37.vcf.idx added
b20f3385e6682_small_exac_common_3.vcf added
b20f3715d6904_small_exac_common_3.vcf.idx added
b20f35ea25c39_1000g_pon.hg38.vcf.gz added
b20f37b94d8dc_1000g_pon.hg38.vcf.gz.tbi added
b20f35c4433a3_af-only-gnomad.hg38.vcf.gz added
b20f323d650f6_af-only-gnomad.hg38.vcf.gz.tbi added
b20f376244307_small_exac_common_3.hg38.vcf.gz added
b20f334e790bf_small_exac_common_3.hg38.vcf.gz.tbi added
b20f36879466b_gencode.v41.annotation.gtf added
b20f33e4497ea_gencode.v42.annotation.gtf added
b20f327fd3ec0_gencode.vM30.annotation.gtf added
b20f32359ec73_gencode.vM31.annotation.gtf added
b20f3260ee79e_gencode.v41.transcripts.fa added
b20f34e6cd55_gencode.v41.transcripts.fa.fai added
b20f332caf1fa_gencode.v42.transcripts.fa added
b20f37b238394_gencode.v42.transcripts.fa.fai added
b20f3436314e9_gencode.vM30.pc_transcripts.fa added
b20f3527e3044_gencode.vM30.pc_transcripts.fa.fai added
b20f360adcd0f_gencode.vM31.pc_transcripts.fa added
b20f3d97e908_gencode.vM31.pc_transcripts.fa.fai added
b20f376a4a870_GRCh38.primary_assembly.genome.fa.1.ht2 added
b20f31a2387d8_GRCh38.primary_assembly.genome.fa.2.ht2 added
b20f31e7d4ffb_GRCh38.primary_assembly.genome.fa.3.ht2 added
b20f3770f469b_GRCh38.primary_assembly.genome.fa.4.ht2 added
b20f34907f4df_GRCh38.primary_assembly.genome.fa.5.ht2 added
b20f3559b3ab0_GRCh38.primary_assembly.genome.fa.6.ht2 added
b20f3457bb062_GRCh38.primary_assembly.genome.fa.7.ht2 added
b20f311f3061d_GRCh38.primary_assembly.genome.fa.8.ht2 added
b20f36ff0c0a4_GRCh38_full_analysis_set_plus_decoy_hla.fa.fai added
b20f3f3a4bc5_GRCh38_full_analysis_set_plus_decoy_hla.fa.amb added
b20f34b4d5b15_GRCh38_full_analysis_set_plus_decoy_hla.fa.ann added
b20f3284f2726_GRCh38_full_analysis_set_plus_decoy_hla.fa.bwt added
b20f397b4c9_GRCh38_full_analysis_set_plus_decoy_hla.fa.pac added
b20f329efb74f_GRCh38_full_analysis_set_plus_decoy_hla.fa.sa added
b20f323e40002_GRCh38_full_analysis_set_plus_decoy_hla.fa added
b20f35cdbe86d_GRCh38.primary_assembly.genome.fa.fai added
b20f34dc60845_GRCh38.primary_assembly.genome.fa.amb added
b20f31a084309_GRCh38.primary_assembly.genome.fa.ann added
b20f311c3792c_GRCh38.primary_assembly.genome.fa.bwt added
b20f3363f4eb1_GRCh38.primary_assembly.genome.fa.pac added
b20f3584cdaf3_GRCh38.primary_assembly.genome.fa.sa added
b20f339c0b7ed_GRCh38.primary_assembly.genome.fa added
b20f359993b24_hs37d5.fa.fai added
b20f37e5bc291_hs37d5.fa.amb added
b20f33ea78542_hs37d5.fa.ann added
b20f3c642d1e_hs37d5.fa.bwt added
b20f3797f4626_hs37d5.fa.pac added
b20f320a9a2c_hs37d5.fa.sa added
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b20f35a2d1335_complete_ref_lens.bin added
b20f3fa28334_ctable.bin added
b20f3558705d2_ctg_offsets.bin added
b20f374509b0d_duplicate_clusters.tsv added
b20f32e1fd32f_info.json added
b20f34c964c6d_mphf.bin added
b20f33d588fec_pos.bin added
b20f33bb0ddf_pre_indexing.log added
b20f31211fccf_rank.bin added
b20f34f4b9609_ref_indexing.log added
b20f373abce83_refAccumLengths.bin added
b20f3214c4894_reflengths.bin added
b20f31a98f11e_refseq.bin added
b20f31bfaf5a9_seq.bin added
b20f321e3fd5e_versionInfo.json added
b20f34488a86d_salmon_index added
b20f33fdef5ab_chrLength.txt added
b20f37ebfe5cb_chrName.txt added
b20f3124eb0b3_chrNameLength.txt added
b20f359e738b4_chrStart.txt added
b20f310835ef7_exonGeTrInfo.tab added
b20f3488dff64_exonInfo.tab added
b20f3323413a7_geneInfo.tab added
b20f34a4416e4_Genome added
b20f322273a88_genomeParameters.txt added
b20f3308fd639_Log.out added
b20f38eb9c27_SA added
b20f32e8b67a6_SAindex added
b20f32a0f1c5f_sjdbInfo.txt added
b20f3af63653_sjdbList.fromGTF.out.tab added
b20f3d6dc508_sjdbList.out.tab added
b20f343c2f94_transcriptInfo.tab added
b20f31a98b987_GRCh38.GENCODE.v42_100 added
b20f362f4cada_knownGene_hg38.sql added
b20f3788ccaa1_knownGene_hg38.txt added
b20f348b88cb7_refGene_hg38.sql added
b20f32f8b1747_refGene_hg38.txt added
b20f335e55a8d_knownGene_mm39.sql added
b20f34c739a96_knownGene_mm39.txt added
b20f3419d1417_refGene_mm39.sql added
b20f3530f096_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:
/home/biocbuild/tmp/RtmpWVp7tm/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
24.426 1.684 28.148
ReUseData.Rcheck/ReUseData-Ex.timings
| name | user | system | elapsed | |
| dataHub-class | 8.815 | 0.355 | 9.210 | |
| dataSearch | 1.736 | 0.036 | 1.777 | |
| dataUpdate | 0 | 0 | 0 | |
| getCloudData | 3.373 | 0.339 | 6.619 | |
| getData | 0.001 | 0.000 | 0.000 | |
| meta_data | 0.001 | 0.000 | 0.001 | |
| recipeHub-class | 0.188 | 0.004 | 0.195 | |
| recipeLoad | 1.981 | 0.129 | 2.121 | |
| recipeMake | 0.001 | 0.000 | 0.000 | |
| recipeSearch | 0.789 | 0.063 | 0.855 | |
| recipeUpdate | 0 | 0 | 0 | |