Qian Liu
| Snapshot Date: 2025-04-21 13:40 -0400 (Mon, 21 Apr 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 2025-04-22 13:18 -0400 (Tue, 22 Apr 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.5.0 RC (2025-04-04 r88126) -- "How About a Twenty-Six" | 4831 |
| palomino7 | Windows Server 2022 Datacenter | x64 | 4.5.0 RC (2025-04-04 r88126 ucrt) -- "How About a Twenty-Six" | 4573 |
| lconway | macOS 12.7.1 Monterey | x86_64 | 4.5.0 RC (2025-04-04 r88126) -- "How About a Twenty-Six" | 4599 |
| kjohnson3 | macOS 13.7.1 Ventura | arm64 | 4.5.0 RC (2025-04-04 r88126) -- "How About a Twenty-Six" | 4553 |
| kunpeng2 | Linux (openEuler 24.03 LTS) | aarch64 | R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" | 4570 |
| 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 24.04.1 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino7 | 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 | | ||||||||
| 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: 2025-04-21 21:12:17 -0400 (Mon, 21 Apr 2025) |
| EndedAt: 2025-04-21 21:13:09 -0400 (Mon, 21 Apr 2025) |
| EllapsedTime: 52.6 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 4.5.0 RC (2025-04-04 r88126)
* using platform: aarch64-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 Ventura 13.7.1
* 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
* 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 4.5.0 RC (2025-04-04 r88126) -- "How About a Twenty-Six"
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...
f0786118d972_GRCh38.primary_assembly.genome.fa.1.bt2 added
f078266bfd2b_GRCh38.primary_assembly.genome.fa.2.bt2 added
f0787bba25c1_GRCh38.primary_assembly.genome.fa.3.bt2 added
f0787a04e15c_GRCh38.primary_assembly.genome.fa.4.bt2 added
f07856679d99_GRCh38.primary_assembly.genome.fa.rev.1.bt2 added
f0782c9bd420_GRCh38.primary_assembly.genome.fa.rev.2.bt2 added
f0782a8397c1_outfile.txt added
f078256015b5_GRCh37_to_GRCh38.chain added
f0784731313e_GRCh37_to_NCBI34.chain added
f0786e9801f5_GRCh37_to_NCBI35.chain added
f0783da8b48c_GRCh37_to_NCBI36.chain added
f078ee572f4_GRCh38_to_GRCh37.chain added
f07879ddf8cf_GRCh38_to_NCBI34.chain added
f0785bfa1c8a_GRCh38_to_NCBI35.chain added
f078167d733_GRCh38_to_NCBI36.chain added
f078486155fd_NCBI34_to_GRCh37.chain added
f0786e547a2a_NCBI34_to_GRCh38.chain added
f0786c2093fc_NCBI35_to_GRCh37.chain added
f0784ed3bcd9_NCBI35_to_GRCh38.chain added
f0782f1372fd_NCBI36_to_GRCh37.chain added
f07825e25830_NCBI36_to_GRCh38.chain added
f0782f0bcabe_GRCm38_to_NCBIM36.chain added
f0782f2b9813_GRCm38_to_NCBIM37.chain added
f078570d1f96_NCBIM36_to_GRCm38.chain added
f0781e94dd80_NCBIM37_to_GRCm38.chain added
f0783f5a0e2f_1000G_omni2.5.b37.vcf.gz added
f07831595027_1000G_omni2.5.b37.vcf.gz.tbi added
f0785e9d49c0_Mills_and_1000G_gold_standard.indels.b37.vcf.gz added
f07828550cc7_Mills_and_1000G_gold_standard.indels.b37.vcf.gz.tbi added
f07867b9f180_1000G_omni2.5.hg38.vcf.gz added
f078609e3fb3_1000G_omni2.5.hg38.vcf.gz.tbi added
f07835683253_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz added
f0784bc00289_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz.tbi added
f0782ae69739_af-only-gnomad.raw.sites.vcf added
f0788d23530_af-only-gnomad.raw.sites.vcf.idx added
f07820a1e6d6_Mutect2-exome-panel.vcf.idx added
f0786539fc56_Mutect2-WGS-panel-b37.vcf added
f07841e5a605_Mutect2-WGS-panel-b37.vcf.idx added
f0784bf6b40f_small_exac_common_3.vcf added
f07831a76bbf_small_exac_common_3.vcf.idx added
f0786692e210_1000g_pon.hg38.vcf.gz added
f0783537bd0c_1000g_pon.hg38.vcf.gz.tbi added
f0785e5c7a1f_af-only-gnomad.hg38.vcf.gz added
f078955b99f_af-only-gnomad.hg38.vcf.gz.tbi added
f0785b0d7a82_small_exac_common_3.hg38.vcf.gz added
f07851e61b81_small_exac_common_3.hg38.vcf.gz.tbi added
f0785a17dc28_gencode.v41.annotation.gtf added
f0785476f44d_gencode.v42.annotation.gtf added
f0784da1168d_gencode.vM30.annotation.gtf added
f078acfaacc_gencode.vM31.annotation.gtf added
f07847d63c9f_gencode.v41.transcripts.fa added
f07842260f91_gencode.v41.transcripts.fa.fai added
f07850c81a84_gencode.v42.transcripts.fa added
f078144f98b_gencode.v42.transcripts.fa.fai added
f078575b1553_gencode.vM30.pc_transcripts.fa added
f0781cd528f3_gencode.vM30.pc_transcripts.fa.fai added
f0786e73784e_gencode.vM31.pc_transcripts.fa added
f0785edf8188_gencode.vM31.pc_transcripts.fa.fai added
f07823b13861_GRCh38.primary_assembly.genome.fa.1.ht2 added
f07847ec7a95_GRCh38.primary_assembly.genome.fa.2.ht2 added
f0787663f116_GRCh38.primary_assembly.genome.fa.3.ht2 added
f0781b691813_GRCh38.primary_assembly.genome.fa.4.ht2 added
f07810ab9574_GRCh38.primary_assembly.genome.fa.5.ht2 added
f07870e0fb38_GRCh38.primary_assembly.genome.fa.6.ht2 added
f078428d536d_GRCh38.primary_assembly.genome.fa.7.ht2 added
f0784c603b3d_GRCh38.primary_assembly.genome.fa.8.ht2 added
f07841d148f7_GRCh38_full_analysis_set_plus_decoy_hla.fa.fai added
f078130d71e3_GRCh38_full_analysis_set_plus_decoy_hla.fa.amb added
f07857aff7da_GRCh38_full_analysis_set_plus_decoy_hla.fa.ann added
f07861b9362f_GRCh38_full_analysis_set_plus_decoy_hla.fa.bwt added
f078469479c8_GRCh38_full_analysis_set_plus_decoy_hla.fa.pac added
f0783dc75dab_GRCh38_full_analysis_set_plus_decoy_hla.fa.sa added
f0786bd6a53c_GRCh38_full_analysis_set_plus_decoy_hla.fa added
f07858fa3d73_GRCh38.primary_assembly.genome.fa.fai added
f07814d876a8_GRCh38.primary_assembly.genome.fa.amb added
f078f561a49_GRCh38.primary_assembly.genome.fa.ann added
f0785dd7b67c_GRCh38.primary_assembly.genome.fa.bwt added
f0787d0db705_GRCh38.primary_assembly.genome.fa.pac added
f078f6ae967_GRCh38.primary_assembly.genome.fa.sa added
f07834017119_GRCh38.primary_assembly.genome.fa added
f0784aa83afb_hs37d5.fa.fai added
f0786ab85b07_hs37d5.fa.amb added
f0786d605f4d_hs37d5.fa.ann added
f0785210f054_hs37d5.fa.bwt added
f078561244e3_hs37d5.fa.pac added
f0784968bf3a_hs37d5.fa.sa added
f0787be29e7c_hs37d5.fa added
f0785b131e6e_complete_ref_lens.bin added
f0784432f678_ctable.bin added
f0786dd36342_ctg_offsets.bin added
f0785119ba62_duplicate_clusters.tsv added
f078701ba186_info.json added
f07826099dea_mphf.bin added
f078415e8128_pos.bin added
f07823718a9f_pre_indexing.log added
f0787343dee6_rank.bin added
f0786cdf0928_ref_indexing.log added
f07826d258ef_refAccumLengths.bin added
f0783bccc6d2_reflengths.bin added
f07811123aa_refseq.bin added
f078c3c6e72_seq.bin added
f078537704a4_versionInfo.json added
f0782ad1d5cb_salmon_index added
f078362b1863_chrLength.txt added
f078474e275d_chrName.txt added
f0785bfa6f3d_chrNameLength.txt added
f078169d3cf8_chrStart.txt added
f0782d0dc961_exonGeTrInfo.tab added
f07864201662_exonInfo.tab added
f078769daf48_geneInfo.tab added
f0786a5edcce_Genome added
f07879f28ef0_genomeParameters.txt added
f07823866d1c_Log.out added
f0784e655b7c_SA added
f07860595219_SAindex added
f07881d18ba_sjdbInfo.txt added
f0782e425f7f_sjdbList.fromGTF.out.tab added
f07878ba293_sjdbList.out.tab added
f078605e64c3_transcriptInfo.tab added
f07855296fa2_GRCh38.GENCODE.v42_100 added
f0781360205c_knownGene_hg38.sql added
f078bec81f4_knownGene_hg38.txt added
f0785447c049_refGene_hg38.sql added
f07832a123d9_refGene_hg38.txt added
f07871389586_knownGene_mm39.sql added
f07839e0ca7c_knownGene_mm39.txt added
f078550db093_refGene_mm39.sql added
f07875c3ae84_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:
/var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmplKcyfq/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
8.025 1.238 10.053
ReUseData.Rcheck/ReUseData-Ex.timings
| name | user | system | elapsed | |
| dataHub-class | 2.049 | 0.244 | 2.320 | |
| dataSearch | 0.370 | 0.017 | 0.387 | |
| dataUpdate | 0 | 0 | 0 | |
| getCloudData | 0.976 | 0.061 | 1.680 | |
| getData | 0 | 0 | 0 | |
| meta_data | 0 | 0 | 0 | |
| recipeHub-class | 0.039 | 0.005 | 0.045 | |
| recipeLoad | 0.404 | 0.028 | 0.437 | |
| recipeMake | 0 | 0 | 0 | |
| recipeSearch | 0.168 | 0.012 | 0.179 | |
| recipeUpdate | 0 | 0 | 0 | |