Qian Liu
| Snapshot Date: 2025-08-03 13:25 -0400 (Sun, 03 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 2025-08-04 12:09 -0400 (Mon, 04 Aug 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.2 LTS) | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4796 |
| palomino8 | Windows Server 2022 Datacenter | x64 | 4.5.1 (2025-06-13 ucrt) -- "Great Square Root" | 4536 |
| lconway | macOS 12.7.1 Monterey | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4578 |
| kjohnson3 | macOS 13.7.1 Ventura | arm64 | 4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" | 4519 |
| taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4517 |
| 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 1737/2313 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| ReUseData 1.9.0 (landing page) Qian Liu
| nebbiolo2 | Linux (Ubuntu 24.04.2 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino8 | Windows Server 2022 Datacenter / x64 | ... NOT SUPPORTED ... | ||||||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson3 | macOS 13.7.1 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: 2025-08-03 23:33:59 -0400 (Sun, 03 Aug 2025) |
| EndedAt: 2025-08-03 23:36:24 -0400 (Sun, 03 Aug 2025) |
| EllapsedTime: 145.5 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 (2025-06-13)
* 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 7.607 0.907 8.62
* 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 (2025-06-13) -- "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...
251f18d6fe87_GRCh38.primary_assembly.genome.fa.1.bt2 added
251f4ae05dce_GRCh38.primary_assembly.genome.fa.2.bt2 added
251f502ea5c9_GRCh38.primary_assembly.genome.fa.3.bt2 added
251f2686583f_GRCh38.primary_assembly.genome.fa.4.bt2 added
251f3e0ba3db_GRCh38.primary_assembly.genome.fa.rev.1.bt2 added
251f6e329eaf_GRCh38.primary_assembly.genome.fa.rev.2.bt2 added
251f3d502bae_outfile.txt added
251f5a63cbf4_GRCh37_to_GRCh38.chain added
251f4de32e88_GRCh37_to_NCBI34.chain added
251f7e040aaa_GRCh37_to_NCBI35.chain added
251f3b585f88_GRCh37_to_NCBI36.chain added
251f26e7f828_GRCh38_to_GRCh37.chain added
251f47551e0c_GRCh38_to_NCBI34.chain added
251f2527ca6a_GRCh38_to_NCBI35.chain added
251f575a0834_GRCh38_to_NCBI36.chain added
251f57d0bab9_NCBI34_to_GRCh37.chain added
251f4892f4b9_NCBI34_to_GRCh38.chain added
251f2800c2e8_NCBI35_to_GRCh37.chain added
251f49fc21dc_NCBI35_to_GRCh38.chain added
251f48131876_NCBI36_to_GRCh37.chain added
251f5dab0ff1_NCBI36_to_GRCh38.chain added
251f9a3c742_GRCm38_to_NCBIM36.chain added
251f5f6ec2ff_GRCm38_to_NCBIM37.chain added
251f60c4244b_NCBIM36_to_GRCm38.chain added
251f6d2ae98e_NCBIM37_to_GRCm38.chain added
251f1c4ba1a0_1000G_omni2.5.b37.vcf.gz added
251f29601de3_1000G_omni2.5.b37.vcf.gz.tbi added
251f654a374d_Mills_and_1000G_gold_standard.indels.b37.vcf.gz added
251f6b74d42e_Mills_and_1000G_gold_standard.indels.b37.vcf.gz.tbi added
251f43164f1f_1000G_omni2.5.hg38.vcf.gz added
251f6da49ea1_1000G_omni2.5.hg38.vcf.gz.tbi added
251f52aa9443_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz added
251f3cebe51b_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz.tbi added
251f230e6edc_af-only-gnomad.raw.sites.vcf added
251f8903f7f_af-only-gnomad.raw.sites.vcf.idx added
251f3638af3d_Mutect2-exome-panel.vcf.idx added
251f4378e99a_Mutect2-WGS-panel-b37.vcf added
251f3730a011_Mutect2-WGS-panel-b37.vcf.idx added
251f595cd865_small_exac_common_3.vcf added
251f5e82fcb8_small_exac_common_3.vcf.idx added
251f699dc481_1000g_pon.hg38.vcf.gz added
251f74d02752_1000g_pon.hg38.vcf.gz.tbi added
251fdc5b468_af-only-gnomad.hg38.vcf.gz added
251f2ec71ee8_af-only-gnomad.hg38.vcf.gz.tbi added
251f12be2956_small_exac_common_3.hg38.vcf.gz added
251f28bd6b7_small_exac_common_3.hg38.vcf.gz.tbi added
251f2abd89af_gencode.v41.annotation.gtf added
251f19a5615_gencode.v42.annotation.gtf added
251f3b897d85_gencode.vM30.annotation.gtf added
251f3f8fc54c_gencode.vM31.annotation.gtf added
251f77e2212d_gencode.v41.transcripts.fa added
251f1ef04ed8_gencode.v41.transcripts.fa.fai added
251f32c856c6_gencode.v42.transcripts.fa added
251f7eb8fb35_gencode.v42.transcripts.fa.fai added
251f22749592_gencode.vM30.pc_transcripts.fa added
251f1407b5ea_gencode.vM30.pc_transcripts.fa.fai added
251f6381fec_gencode.vM31.pc_transcripts.fa added
251f4eb7c224_gencode.vM31.pc_transcripts.fa.fai added
251f22af1dc_GRCh38.primary_assembly.genome.fa.1.ht2 added
251f516ca3a0_GRCh38.primary_assembly.genome.fa.2.ht2 added
251f336a8723_GRCh38.primary_assembly.genome.fa.3.ht2 added
251f16ce2534_GRCh38.primary_assembly.genome.fa.4.ht2 added
251f37ec849e_GRCh38.primary_assembly.genome.fa.5.ht2 added
251f8f6bdc1_GRCh38.primary_assembly.genome.fa.6.ht2 added
251f7f23ce7f_GRCh38.primary_assembly.genome.fa.7.ht2 added
251f7ca350f_GRCh38.primary_assembly.genome.fa.8.ht2 added
251f6c616fc7_GRCh38_full_analysis_set_plus_decoy_hla.fa.fai added
251f70f1a967_GRCh38_full_analysis_set_plus_decoy_hla.fa.amb added
251f9a8e31f_GRCh38_full_analysis_set_plus_decoy_hla.fa.ann added
251f2ed70d2d_GRCh38_full_analysis_set_plus_decoy_hla.fa.bwt added
251f28a21d61_GRCh38_full_analysis_set_plus_decoy_hla.fa.pac added
251f2b36e01e_GRCh38_full_analysis_set_plus_decoy_hla.fa.sa added
251f1fb3e7bc_GRCh38_full_analysis_set_plus_decoy_hla.fa added
251f5c32f7e6_GRCh38.primary_assembly.genome.fa.fai added
251f16314c54_GRCh38.primary_assembly.genome.fa.amb added
251f7e8a2a2d_GRCh38.primary_assembly.genome.fa.ann added
251f20d73142_GRCh38.primary_assembly.genome.fa.bwt added
251ffe2f4e6_GRCh38.primary_assembly.genome.fa.pac added
251f7d3c302f_GRCh38.primary_assembly.genome.fa.sa added
251f7a7f9de4_GRCh38.primary_assembly.genome.fa added
251f50572290_hs37d5.fa.fai added
251f89e4525_hs37d5.fa.amb added
251f4ecd848e_hs37d5.fa.ann added
251f16b9af0d_hs37d5.fa.bwt added
251f78938a22_hs37d5.fa.pac added
251f1e51fc06_hs37d5.fa.sa added
251f1878fd77_hs37d5.fa added
251f2f489c2e_complete_ref_lens.bin added
251f4805a842_ctable.bin added
251f6b69a9fe_ctg_offsets.bin added
251f661799c9_duplicate_clusters.tsv added
251f17718f7c_info.json added
251f208321ea_mphf.bin added
251f1279a53_pos.bin added
251f4f04bfbc_pre_indexing.log added
251f40c7f82b_rank.bin added
251f875f047_ref_indexing.log added
251f76f1c9a7_refAccumLengths.bin added
251f7bee2ff2_reflengths.bin added
251f528df86e_refseq.bin added
251f66b12819_seq.bin added
251f78bfb5fa_versionInfo.json added
251f72446e04_salmon_index added
251f6a930337_chrLength.txt added
251f59b8468a_chrName.txt added
251f511f3c0a_chrNameLength.txt added
251f599ede21_chrStart.txt added
251f4d09767e_exonGeTrInfo.tab added
251f284271b5_exonInfo.tab added
251f223736b9_geneInfo.tab added
251f56e9bd3b_Genome added
251fb869911_genomeParameters.txt added
251f31ab3100_Log.out added
251f5e1e1079_SA added
251f7cba835_SAindex added
251f4b903392_sjdbInfo.txt added
251f6829dcff_sjdbList.fromGTF.out.tab added
251f146c1ec6_sjdbList.out.tab added
251f465863a3_transcriptInfo.tab added
251f54f58669_GRCh38.GENCODE.v42_100 added
251f434b8312_knownGene_hg38.sql added
251f128a3542_knownGene_hg38.txt added
251f2fae8990_refGene_hg38.sql added
251f6bc96564_refGene_hg38.txt added
251f731fbf84_knownGene_mm39.sql added
251f2956ae28_knownGene_mm39.txt added
251f79c3d94b_refGene_mm39.sql added
251f28ef0961_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/Rtmp3vzPoD/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
21.646 2.397 25.037
ReUseData.Rcheck/ReUseData-Ex.timings
| name | user | system | elapsed | |
| dataHub-class | 7.607 | 0.907 | 8.620 | |
| dataSearch | 1.433 | 0.061 | 1.510 | |
| dataUpdate | 0.000 | 0.000 | 0.001 | |
| getCloudData | 2.879 | 0.170 | 4.216 | |
| getData | 0.000 | 0.000 | 0.001 | |
| meta_data | 0.001 | 0.000 | 0.000 | |
| recipeHub-class | 0.138 | 0.014 | 0.153 | |
| recipeLoad | 1.549 | 0.098 | 1.661 | |
| recipeMake | 0.000 | 0.001 | 0.000 | |
| recipeSearch | 0.605 | 0.038 | 0.647 | |
| recipeUpdate | 0 | 0 | 0 | |