Qian Liu
| Snapshot Date: 2025-09-29 13:40 -0400 (Mon, 29 Sep 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 2025-10-02 11:41 -0400 (Thu, 02 Oct 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" | 4831 |
| merida1 | macOS 12.7.5 Monterey | x86_64 | 4.5.1 RC (2025-06-05 r88288) -- "Great Square Root" | 4612 |
| kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" | 4553 |
| kunpeng2 | Linux (openEuler 24.03 LTS) | aarch64 | R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" | 4584 |
| 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 | | ||||||||
| 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: 2025-10-01 09:33:26 -0400 (Wed, 01 Oct 2025) |
| EndedAt: 2025-10-01 09:36:03 -0400 (Wed, 01 Oct 2025) |
| EllapsedTime: 156.5 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_1.8.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/ReUseData.Rcheck’
* using R version 4.5.1 Patched (2025-06-14 r88325)
* using platform: aarch64-apple-darwin20
* R was compiled by
Apple clang version 16.0.0 (clang-1600.0.26.6)
GNU Fortran (GCC) 14.2.0
* running under: macOS Ventura 13.7.5
* 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 7.139 0.878 8.235
getCloudData 2.897 0.183 5.161
* 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-arm64/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 Patched (2025-06-14 r88325) -- "Great Square Root"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: aarch64-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...
100f051b13363_GRCh38.primary_assembly.genome.fa.1.bt2 added
100f048a4d27b_GRCh38.primary_assembly.genome.fa.2.bt2 added
100f03cf6ae7f_GRCh38.primary_assembly.genome.fa.3.bt2 added
100f0673a331d_GRCh38.primary_assembly.genome.fa.4.bt2 added
100f01df1e9dd_GRCh38.primary_assembly.genome.fa.rev.1.bt2 added
100f07530bb86_GRCh38.primary_assembly.genome.fa.rev.2.bt2 added
100f052679685_outfile.txt added
100f0ecb2007_GRCh37_to_GRCh38.chain added
100f039a3b327_GRCh37_to_NCBI34.chain added
100f02a46e301_GRCh37_to_NCBI35.chain added
100f013e16c56_GRCh37_to_NCBI36.chain added
100f0348f8c4c_GRCh38_to_GRCh37.chain added
100f03c43ec89_GRCh38_to_NCBI34.chain added
100f0f5e3548_GRCh38_to_NCBI35.chain added
100f071fc11d9_GRCh38_to_NCBI36.chain added
100f05bf7f805_NCBI34_to_GRCh37.chain added
100f074bc3f6e_NCBI34_to_GRCh38.chain added
100f072e88aa1_NCBI35_to_GRCh37.chain added
100f0e58af7_NCBI35_to_GRCh38.chain added
100f05e065e96_NCBI36_to_GRCh37.chain added
100f0742bfa13_NCBI36_to_GRCh38.chain added
100f0732f30fa_GRCm38_to_NCBIM36.chain added
100f01f38a82a_GRCm38_to_NCBIM37.chain added
100f040a86d69_NCBIM36_to_GRCm38.chain added
100f071a729a8_NCBIM37_to_GRCm38.chain added
100f015a00ee3_1000G_omni2.5.b37.vcf.gz added
100f03f31642c_1000G_omni2.5.b37.vcf.gz.tbi added
100f043a7a51d_Mills_and_1000G_gold_standard.indels.b37.vcf.gz added
100f03349359e_Mills_and_1000G_gold_standard.indels.b37.vcf.gz.tbi added
100f0b5f3260_1000G_omni2.5.hg38.vcf.gz added
100f016e44275_1000G_omni2.5.hg38.vcf.gz.tbi added
100f063c71b10_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz added
100f024c1ea9d_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz.tbi added
100f03711fc45_af-only-gnomad.raw.sites.vcf added
100f07dc93241_af-only-gnomad.raw.sites.vcf.idx added
100f0240289eb_Mutect2-exome-panel.vcf.idx added
100f022acb5c5_Mutect2-WGS-panel-b37.vcf added
100f078d1aa4b_Mutect2-WGS-panel-b37.vcf.idx added
100f0d035fe5_small_exac_common_3.vcf added
100f0588cba0f_small_exac_common_3.vcf.idx added
100f07f0b5c33_1000g_pon.hg38.vcf.gz added
100f042d2596e_1000g_pon.hg38.vcf.gz.tbi added
100f07fed6707_af-only-gnomad.hg38.vcf.gz added
100f03b073e2e_af-only-gnomad.hg38.vcf.gz.tbi added
100f058835c48_small_exac_common_3.hg38.vcf.gz added
100f0181fa85e_small_exac_common_3.hg38.vcf.gz.tbi added
100f04666bfb1_gencode.v41.annotation.gtf added
100f03b32193_gencode.v42.annotation.gtf added
100f065613bca_gencode.vM30.annotation.gtf added
100f0529c7ec5_gencode.vM31.annotation.gtf added
100f02046e1e2_gencode.v41.transcripts.fa added
100f0d97ccfc_gencode.v41.transcripts.fa.fai added
100f06912bb5c_gencode.v42.transcripts.fa added
100f04ccacae8_gencode.v42.transcripts.fa.fai added
100f015cf6cbb_gencode.vM30.pc_transcripts.fa added
100f064eb742c_gencode.vM30.pc_transcripts.fa.fai added
100f01e182877_gencode.vM31.pc_transcripts.fa added
100f04408ac10_gencode.vM31.pc_transcripts.fa.fai added
100f015587155_GRCh38.primary_assembly.genome.fa.1.ht2 added
100f061788e65_GRCh38.primary_assembly.genome.fa.2.ht2 added
100f031ccbae1_GRCh38.primary_assembly.genome.fa.3.ht2 added
100f078012351_GRCh38.primary_assembly.genome.fa.4.ht2 added
100f012b5d864_GRCh38.primary_assembly.genome.fa.5.ht2 added
100f0609196d4_GRCh38.primary_assembly.genome.fa.6.ht2 added
100f0764569d3_GRCh38.primary_assembly.genome.fa.7.ht2 added
100f04726d84e_GRCh38.primary_assembly.genome.fa.8.ht2 added
100f047430d60_GRCh38_full_analysis_set_plus_decoy_hla.fa.fai added
100f03233e2d_GRCh38_full_analysis_set_plus_decoy_hla.fa.amb added
100f07ec6fdf6_GRCh38_full_analysis_set_plus_decoy_hla.fa.ann added
100f03a4b6280_GRCh38_full_analysis_set_plus_decoy_hla.fa.bwt added
100f02b2fdf66_GRCh38_full_analysis_set_plus_decoy_hla.fa.pac added
100f053f3b7b0_GRCh38_full_analysis_set_plus_decoy_hla.fa.sa added
100f025a0aedf_GRCh38_full_analysis_set_plus_decoy_hla.fa added
100f05838c5c5_GRCh38.primary_assembly.genome.fa.fai added
100f0774035c2_GRCh38.primary_assembly.genome.fa.amb added
100f0188990b8_GRCh38.primary_assembly.genome.fa.ann added
100f06f7c2c9d_GRCh38.primary_assembly.genome.fa.bwt added
100f041553099_GRCh38.primary_assembly.genome.fa.pac added
100f03fe9ae51_GRCh38.primary_assembly.genome.fa.sa added
100f06b3689f_GRCh38.primary_assembly.genome.fa added
100f06c99a228_hs37d5.fa.fai added
100f05a6527cb_hs37d5.fa.amb added
100f02717aeca_hs37d5.fa.ann added
100f03d463d3_hs37d5.fa.bwt added
100f06ce5b39b_hs37d5.fa.pac added
100f05c72bcf7_hs37d5.fa.sa added
100f070d42b8b_hs37d5.fa added
100f07976ec8b_complete_ref_lens.bin added
100f06ea3d7f9_ctable.bin added
100f046b8552e_ctg_offsets.bin added
100f06fe06347_duplicate_clusters.tsv added
100f0749603b2_info.json added
100f024ccd6ea_mphf.bin added
100f0431af86_pos.bin added
100f059fa8890_pre_indexing.log added
100f04f1bd416_rank.bin added
100f02c0118ed_ref_indexing.log added
100f07c0b862c_refAccumLengths.bin added
100f05895f253_reflengths.bin added
100f05c585494_refseq.bin added
100f02b18efe9_seq.bin added
100f0722ec019_versionInfo.json added
100f05b45e3df_salmon_index added
100f049737449_chrLength.txt added
100f03ad78a4b_chrName.txt added
100f01cb8601b_chrNameLength.txt added
100f0cad9b58_chrStart.txt added
100f059b1b4e8_exonGeTrInfo.tab added
100f021dc1959_exonInfo.tab added
100f07904336c_geneInfo.tab added
100f02cc3586_Genome added
100f02ccdf1d9_genomeParameters.txt added
100f04c0f48a_Log.out added
100f017f69276_SA added
100f03d098d44_SAindex added
100f03e198aaa_sjdbInfo.txt added
100f07edebebf_sjdbList.fromGTF.out.tab added
100f051bd2eab_sjdbList.out.tab added
100f05b430679_transcriptInfo.tab added
100f0d5e20be_GRCh38.GENCODE.v42_100 added
100f01eb7a0cd_knownGene_hg38.sql added
100f0299e027c_knownGene_hg38.txt added
100f044b5303c_refGene_hg38.sql added
100f05371d661_refGene_hg38.txt added
100f056b1a513_knownGene_mm39.sql added
100f028ccaedc_knownGene_mm39.txt added
100f015ec0271_refGene_mm39.sql added
100f0399453f5_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/RtmpgSRt5C/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
26.961 4.229 33.749
ReUseData.Rcheck/ReUseData-Ex.timings
| name | user | system | elapsed | |
| dataHub-class | 7.139 | 0.878 | 8.235 | |
| dataSearch | 1.206 | 0.058 | 1.273 | |
| dataUpdate | 0.000 | 0.001 | 0.001 | |
| getCloudData | 2.897 | 0.183 | 5.161 | |
| getData | 0 | 0 | 0 | |
| meta_data | 0.001 | 0.001 | 0.001 | |
| recipeHub-class | 0.138 | 0.012 | 0.150 | |
| recipeLoad | 1.400 | 0.095 | 1.501 | |
| recipeMake | 0.000 | 0.001 | 0.000 | |
| recipeSearch | 0.637 | 0.043 | 0.684 | |
| recipeUpdate | 0.000 | 0.000 | 0.001 | |