Qian Liu
| Snapshot Date: 2025-09-22 13:40 -0400 (Mon, 22 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 2025-09-25 11:40 -0400 (Thu, 25 Sep 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" | 4827 |
| merida1 | macOS 12.7.5 Monterey | x86_64 | 4.5.1 RC (2025-06-05 r88288) -- "Great Square Root" | 4608 |
| kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" | 4549 |
| kunpeng2 | Linux (openEuler 24.03 LTS) | aarch64 | R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" | 4581 |
| 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: 2025-09-23 08:46:57 -0400 (Tue, 23 Sep 2025) |
| EndedAt: 2025-09-23 08:58:01 -0400 (Tue, 23 Sep 2025) |
| EllapsedTime: 663.5 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 RC (2025-06-05 r88288)
* 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 ‘1.8.0’
* 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 7.238 0.797 229.914
getCloudData 2.594 0.126 19.950
recipeLoad 1.682 0.076 5.603
* 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-x86_64/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 RC (2025-06-05 r88288) -- "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...
161871263362f_GRCh38.primary_assembly.genome.fa.1.bt2 added
161872f7a5117_GRCh38.primary_assembly.genome.fa.2.bt2 added
16187761d55b_GRCh38.primary_assembly.genome.fa.3.bt2 added
1618727fe4d26_GRCh38.primary_assembly.genome.fa.4.bt2 added
16187287b0e4d_GRCh38.primary_assembly.genome.fa.rev.1.bt2 added
1618726e7f5fe_GRCh38.primary_assembly.genome.fa.rev.2.bt2 added
1618746c70aa6_outfile.txt added
16187358c3c97_GRCh37_to_GRCh38.chain added
161879ddf8f8_GRCh37_to_NCBI34.chain added
161874c0466d7_GRCh37_to_NCBI35.chain added
1618734fbd43e_GRCh37_to_NCBI36.chain added
1618712b4d9f_GRCh38_to_GRCh37.chain added
1618741f50252_GRCh38_to_NCBI34.chain added
161873c6b7752_GRCh38_to_NCBI35.chain added
161873366c77b_GRCh38_to_NCBI36.chain added
1618720b2769a_NCBI34_to_GRCh37.chain added
161872488893b_NCBI34_to_GRCh38.chain added
161877fe99339_NCBI35_to_GRCh37.chain added
161873fc0c4ca_NCBI35_to_GRCh38.chain added
161878b7ca79_NCBI36_to_GRCh37.chain added
161875a4dd267_NCBI36_to_GRCh38.chain added
161872b309682_GRCm38_to_NCBIM36.chain added
161872e946f5_GRCm38_to_NCBIM37.chain added
1618721318051_NCBIM36_to_GRCm38.chain added
1618738df56dd_NCBIM37_to_GRCm38.chain added
161874ebfe456_1000G_omni2.5.b37.vcf.gz added
161871827f27e_1000G_omni2.5.b37.vcf.gz.tbi added
1618766a13a95_Mills_and_1000G_gold_standard.indels.b37.vcf.gz added
16187630d40d6_Mills_and_1000G_gold_standard.indels.b37.vcf.gz.tbi added
161877b1bd467_1000G_omni2.5.hg38.vcf.gz added
161876015f555_1000G_omni2.5.hg38.vcf.gz.tbi added
16187419dd0bb_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz added
161875ff2c6a4_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz.tbi added
161873bcf6a32_af-only-gnomad.raw.sites.vcf added
161872e45174b_af-only-gnomad.raw.sites.vcf.idx added
1618739fc54a8_Mutect2-exome-panel.vcf.idx added
161876519ff55_Mutect2-WGS-panel-b37.vcf added
16187dca594e_Mutect2-WGS-panel-b37.vcf.idx added
161875fad16f4_small_exac_common_3.vcf added
161875cbe1e3e_small_exac_common_3.vcf.idx added
1618745b3a803_1000g_pon.hg38.vcf.gz added
1618715db80b5_1000g_pon.hg38.vcf.gz.tbi added
161877ddef648_af-only-gnomad.hg38.vcf.gz added
1618738fb3187_af-only-gnomad.hg38.vcf.gz.tbi added
161877370b34a_small_exac_common_3.hg38.vcf.gz added
161876c0afa7b_small_exac_common_3.hg38.vcf.gz.tbi added
1618744c2d8a7_gencode.v41.annotation.gtf added
16187541ddf35_gencode.v42.annotation.gtf added
1618775293bb7_gencode.vM30.annotation.gtf added
16187660fa778_gencode.vM31.annotation.gtf added
16187dbbeba1_gencode.v41.transcripts.fa added
161872c6a9e12_gencode.v41.transcripts.fa.fai added
16187bafc686_gencode.v42.transcripts.fa added
1618741128d68_gencode.v42.transcripts.fa.fai added
161872901c838_gencode.vM30.pc_transcripts.fa added
1618733ffe990_gencode.vM30.pc_transcripts.fa.fai added
16187663f079b_gencode.vM31.pc_transcripts.fa added
16187340c858e_gencode.vM31.pc_transcripts.fa.fai added
1618722144854_GRCh38.primary_assembly.genome.fa.1.ht2 added
1618761989446_GRCh38.primary_assembly.genome.fa.2.ht2 added
16187682eb1b8_GRCh38.primary_assembly.genome.fa.3.ht2 added
161875195dc77_GRCh38.primary_assembly.genome.fa.4.ht2 added
1618745bd3279_GRCh38.primary_assembly.genome.fa.5.ht2 added
1618783cc9b4_GRCh38.primary_assembly.genome.fa.6.ht2 added
161874ede4ca5_GRCh38.primary_assembly.genome.fa.7.ht2 added
16187647a0d16_GRCh38.primary_assembly.genome.fa.8.ht2 added
161878f152e3_GRCh38_full_analysis_set_plus_decoy_hla.fa.fai added
161871b78b9ab_GRCh38_full_analysis_set_plus_decoy_hla.fa.amb added
1618712e597a4_GRCh38_full_analysis_set_plus_decoy_hla.fa.ann added
161871f4699ad_GRCh38_full_analysis_set_plus_decoy_hla.fa.bwt added
1618754133ce5_GRCh38_full_analysis_set_plus_decoy_hla.fa.pac added
161873b030982_GRCh38_full_analysis_set_plus_decoy_hla.fa.sa added
1618744655412_GRCh38_full_analysis_set_plus_decoy_hla.fa added
1618758728cd2_GRCh38.primary_assembly.genome.fa.fai added
16187487b5c5b_GRCh38.primary_assembly.genome.fa.amb added
161871aec7f8a_GRCh38.primary_assembly.genome.fa.ann added
161871ca94ad5_GRCh38.primary_assembly.genome.fa.bwt added
161872e6ff4a6_GRCh38.primary_assembly.genome.fa.pac added
161873826d61b_GRCh38.primary_assembly.genome.fa.sa added
161877db2a369_GRCh38.primary_assembly.genome.fa added
161875b0682f7_hs37d5.fa.fai added
1618788054d1_hs37d5.fa.amb added
16187214069b3_hs37d5.fa.ann added
16187bdb77d3_hs37d5.fa.bwt added
161877597c3b9_hs37d5.fa.pac added
161873eb2e2ff_hs37d5.fa.sa added
161875254f381_hs37d5.fa added
16187473ec461_complete_ref_lens.bin added
1618769cee0d1_ctable.bin added
16187d09ef9c_ctg_offsets.bin added
16187751f174_duplicate_clusters.tsv added
1618714c2fa6d_info.json added
16187cc714c1_mphf.bin added
1618762239174_pos.bin added
16187d228902_pre_indexing.log added
161875650e90a_rank.bin added
1618759f3bbcb_ref_indexing.log added
1618710ae3a90_refAccumLengths.bin added
161871e86cc7e_reflengths.bin added
1618723db73da_refseq.bin added
161871c92ff9a_seq.bin added
1618776cae61d_versionInfo.json added
161872c9b6d9_salmon_index added
1618790361fd_chrLength.txt added
161873d162daa_chrName.txt added
161877b10133a_chrNameLength.txt added
161875c5e83f4_chrStart.txt added
161874129378c_exonGeTrInfo.tab added
1618778fde9bf_exonInfo.tab added
1618765fd38a7_geneInfo.tab added
1618753929040_Genome added
161873b3c849d_genomeParameters.txt added
161872267dcd_Log.out added
161872d0d1ed5_SA added
161873863490e_SAindex added
161877e51530d_sjdbInfo.txt added
16187d23bb45_sjdbList.fromGTF.out.tab added
1618724dbb5c0_sjdbList.out.tab added
1618754796327_transcriptInfo.tab added
161876d5cc0c4_GRCh38.GENCODE.v42_100 added
161876473bbf3_knownGene_hg38.sql added
161876a38820a_knownGene_hg38.txt added
1618723e19501_refGene_hg38.sql added
161872efd870e_refGene_hg38.txt added
161876adc03c_knownGene_mm39.sql added
161877927a690_knownGene_mm39.txt added
161871a287614_refGene_mm39.sql added
1618756602876_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/RtmpfabSE9/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
38.554 5.413 106.737
ReUseData.Rcheck/ReUseData-Ex.timings
| name | user | system | elapsed | |
| dataHub-class | 7.238 | 0.797 | 229.914 | |
| dataSearch | 1.323 | 0.042 | 1.365 | |
| dataUpdate | 0.000 | 0.000 | 0.001 | |
| getCloudData | 2.594 | 0.126 | 19.950 | |
| getData | 0.000 | 0.000 | 0.001 | |
| meta_data | 0.001 | 0.000 | 0.002 | |
| recipeHub-class | 0.145 | 0.011 | 2.495 | |
| recipeLoad | 1.682 | 0.076 | 5.603 | |
| recipeMake | 0.001 | 0.002 | 0.002 | |
| recipeSearch | 1.092 | 0.059 | 1.174 | |
| recipeUpdate | 0 | 0 | 0 | |