Qian Liu
| Snapshot Date: 2025-09-02 13:45 -0400 (Tue, 02 Sep 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 2025-09-03 12:04 -0400 (Wed, 03 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" | 4826 |
| lconway | macOS 12.7.1 Monterey | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4616 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" | 4563 |
| 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 1742/2321 | 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: 2025-09-03 03:24:09 -0400 (Wed, 03 Sep 2025) |
| EndedAt: 2025-09-03 03:26:56 -0400 (Wed, 03 Sep 2025) |
| EllapsedTime: 167.2 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 5.895 0.239 6.136
* 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...
eb6b03d2c77a1_GRCh38.primary_assembly.genome.fa.1.bt2 added
eb6b02b37dbb4_GRCh38.primary_assembly.genome.fa.2.bt2 added
eb6b06f0659f8_GRCh38.primary_assembly.genome.fa.3.bt2 added
eb6b03198678d_GRCh38.primary_assembly.genome.fa.4.bt2 added
eb6b03aa50be5_GRCh38.primary_assembly.genome.fa.rev.1.bt2 added
eb6b077aae217_GRCh38.primary_assembly.genome.fa.rev.2.bt2 added
eb6b027aa43ac_outfile.txt added
eb6b07a7de01e_GRCh37_to_GRCh38.chain added
eb6b043d05896_GRCh37_to_NCBI34.chain added
eb6b01fe31744_GRCh37_to_NCBI35.chain added
eb6b07623bcec_GRCh37_to_NCBI36.chain added
eb6b0777d59c6_GRCh38_to_GRCh37.chain added
eb6b02807d646_GRCh38_to_NCBI34.chain added
eb6b03d74a650_GRCh38_to_NCBI35.chain added
eb6b0797da008_GRCh38_to_NCBI36.chain added
eb6b052b5f2a_NCBI34_to_GRCh37.chain added
eb6b043825d6_NCBI34_to_GRCh38.chain added
eb6b04a455ed5_NCBI35_to_GRCh37.chain added
eb6b0618ceccd_NCBI35_to_GRCh38.chain added
eb6b075e7017e_NCBI36_to_GRCh37.chain added
eb6b045ef7672_NCBI36_to_GRCh38.chain added
eb6b03bb69a5d_GRCm38_to_NCBIM36.chain added
eb6b07a05cc36_GRCm38_to_NCBIM37.chain added
eb6b04ce365c8_NCBIM36_to_GRCm38.chain added
eb6b0832f94e_NCBIM37_to_GRCm38.chain added
eb6b0695bb768_1000G_omni2.5.b37.vcf.gz added
eb6b052e308f6_1000G_omni2.5.b37.vcf.gz.tbi added
eb6b06af7f928_Mills_and_1000G_gold_standard.indels.b37.vcf.gz added
eb6b07478009a_Mills_and_1000G_gold_standard.indels.b37.vcf.gz.tbi added
eb6b01e8af444_1000G_omni2.5.hg38.vcf.gz added
eb6b0344d2d7f_1000G_omni2.5.hg38.vcf.gz.tbi added
eb6b031a4783c_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz added
eb6b049c2cff8_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz.tbi added
eb6b023538777_af-only-gnomad.raw.sites.vcf added
eb6b0633cdfc9_af-only-gnomad.raw.sites.vcf.idx added
eb6b0467dbdd_Mutect2-exome-panel.vcf.idx added
eb6b01afe698e_Mutect2-WGS-panel-b37.vcf added
eb6b0ae72375_Mutect2-WGS-panel-b37.vcf.idx added
eb6b07ee5bbfc_small_exac_common_3.vcf added
eb6b05ecec225_small_exac_common_3.vcf.idx added
eb6b02aca3aba_1000g_pon.hg38.vcf.gz added
eb6b0750978e8_1000g_pon.hg38.vcf.gz.tbi added
eb6b0564c1beb_af-only-gnomad.hg38.vcf.gz added
eb6b052d21100_af-only-gnomad.hg38.vcf.gz.tbi added
eb6b0327e1f38_small_exac_common_3.hg38.vcf.gz added
eb6b04fc9bbf3_small_exac_common_3.hg38.vcf.gz.tbi added
eb6b057fd702a_gencode.v41.annotation.gtf added
eb6b036b6450e_gencode.v42.annotation.gtf added
eb6b01a0f1ac9_gencode.vM30.annotation.gtf added
eb6b0398a5cf7_gencode.vM31.annotation.gtf added
eb6b02c9d468d_gencode.v41.transcripts.fa added
eb6b05ffe913b_gencode.v41.transcripts.fa.fai added
eb6b07540f754_gencode.v42.transcripts.fa added
eb6b026a312c3_gencode.v42.transcripts.fa.fai added
eb6b02ce1f704_gencode.vM30.pc_transcripts.fa added
eb6b07d73f0a2_gencode.vM30.pc_transcripts.fa.fai added
eb6b0ffeca2b_gencode.vM31.pc_transcripts.fa added
eb6b07fc4fffa_gencode.vM31.pc_transcripts.fa.fai added
eb6b0686be9ca_GRCh38.primary_assembly.genome.fa.1.ht2 added
eb6b0476cac6_GRCh38.primary_assembly.genome.fa.2.ht2 added
eb6b01e4ff43e_GRCh38.primary_assembly.genome.fa.3.ht2 added
eb6b01cb91749_GRCh38.primary_assembly.genome.fa.4.ht2 added
eb6b0361b4302_GRCh38.primary_assembly.genome.fa.5.ht2 added
eb6b06812c436_GRCh38.primary_assembly.genome.fa.6.ht2 added
eb6b0400c9ec1_GRCh38.primary_assembly.genome.fa.7.ht2 added
eb6b0195822cb_GRCh38.primary_assembly.genome.fa.8.ht2 added
eb6b06c7aa014_GRCh38_full_analysis_set_plus_decoy_hla.fa.fai added
eb6b05b0b084f_GRCh38_full_analysis_set_plus_decoy_hla.fa.amb added
eb6b0243f4641_GRCh38_full_analysis_set_plus_decoy_hla.fa.ann added
eb6b06b605c10_GRCh38_full_analysis_set_plus_decoy_hla.fa.bwt added
eb6b039d9ca74_GRCh38_full_analysis_set_plus_decoy_hla.fa.pac added
eb6b04f0980fb_GRCh38_full_analysis_set_plus_decoy_hla.fa.sa added
eb6b06069d4f8_GRCh38_full_analysis_set_plus_decoy_hla.fa added
eb6b01025e65f_GRCh38.primary_assembly.genome.fa.fai added
eb6b021db91fb_GRCh38.primary_assembly.genome.fa.amb added
eb6b012e7f431_GRCh38.primary_assembly.genome.fa.ann added
eb6b05fefa253_GRCh38.primary_assembly.genome.fa.bwt added
eb6b079d90225_GRCh38.primary_assembly.genome.fa.pac added
eb6b0499e393f_GRCh38.primary_assembly.genome.fa.sa added
eb6b079febd1c_GRCh38.primary_assembly.genome.fa added
eb6b033635f1d_hs37d5.fa.fai added
eb6b0763b7fcc_hs37d5.fa.amb added
eb6b059fd4e57_hs37d5.fa.ann added
eb6b028a45671_hs37d5.fa.bwt added
eb6b01cde9290_hs37d5.fa.pac added
eb6b06df455b_hs37d5.fa.sa added
eb6b026184714_hs37d5.fa added
eb6b02cdd5cbb_complete_ref_lens.bin added
eb6b06a44556_ctable.bin added
eb6b0e8430de_ctg_offsets.bin added
eb6b031542781_duplicate_clusters.tsv added
eb6b024f43994_info.json added
eb6b02b3d4828_mphf.bin added
eb6b0676f6a83_pos.bin added
eb6b0d06fdcb_pre_indexing.log added
eb6b06b49e6e9_rank.bin added
eb6b0c78d4f_ref_indexing.log added
eb6b079819ddf_refAccumLengths.bin added
eb6b04654ef38_reflengths.bin added
eb6b02506d390_refseq.bin added
eb6b064e1f9ef_seq.bin added
eb6b02eb9ad_versionInfo.json added
eb6b07410548b_salmon_index added
eb6b0454bcee7_chrLength.txt added
eb6b01054a00c_chrName.txt added
eb6b015ebe686_chrNameLength.txt added
eb6b05833c318_chrStart.txt added
eb6b07044425f_exonGeTrInfo.tab added
eb6b0fc4e8ab_exonInfo.tab added
eb6b021d1fc58_geneInfo.tab added
eb6b06a42ff7b_Genome added
eb6b0432847c8_genomeParameters.txt added
eb6b0180d7c24_Log.out added
eb6b044404dd3_SA added
eb6b06bcc9e3a_SAindex added
eb6b034ec0eb4_sjdbInfo.txt added
eb6b04b1f932e_sjdbList.fromGTF.out.tab added
eb6b011e4e54e_sjdbList.out.tab added
eb6b061c96b70_transcriptInfo.tab added
eb6b051c3d884_GRCh38.GENCODE.v42_100 added
eb6b02069162c_knownGene_hg38.sql added
eb6b0131d92f1_knownGene_hg38.txt added
eb6b076b81219_refGene_hg38.sql added
eb6b04ba65e54_refGene_hg38.txt added
eb6b07a8cfd75_knownGene_mm39.sql added
eb6b03bf0fe4_knownGene_mm39.txt added
eb6b036f0453d_refGene_mm39.sql added
eb6b07b548ac4_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/RtmpwBTguM/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
18.855 1.153 20.349
ReUseData.Rcheck/ReUseData-Ex.timings
| name | user | system | elapsed | |
| dataHub-class | 5.895 | 0.239 | 6.136 | |
| dataSearch | 1.157 | 0.013 | 1.170 | |
| dataUpdate | 0.001 | 0.000 | 0.000 | |
| getCloudData | 2.797 | 0.140 | 4.079 | |
| getData | 0 | 0 | 0 | |
| meta_data | 0.000 | 0.000 | 0.001 | |
| recipeHub-class | 0.129 | 0.004 | 0.133 | |
| recipeLoad | 1.299 | 0.062 | 1.362 | |
| recipeMake | 0 | 0 | 0 | |
| recipeSearch | 0.541 | 0.007 | 0.548 | |
| recipeUpdate | 0.001 | 0.000 | 0.000 | |