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 13:17 -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 23:00:20 -0400 (Mon, 21 Apr 2025) |
| EndedAt: 2025-04-21 23:02:54 -0400 (Mon, 21 Apr 2025) |
| EllapsedTime: 154.0 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: 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 7.345 0.892 8.370
getCloudData 2.807 0.154 7.033
* 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 4.5.0 RC (2025-04-04 r88126) -- "How About a Twenty-Six"
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...
2bba6f91aa9d_GRCh38.primary_assembly.genome.fa.1.bt2 added
2bba445862a4_GRCh38.primary_assembly.genome.fa.2.bt2 added
2bba6b4200a_GRCh38.primary_assembly.genome.fa.3.bt2 added
2bba1ba373f6_GRCh38.primary_assembly.genome.fa.4.bt2 added
2bba81229a7_GRCh38.primary_assembly.genome.fa.rev.1.bt2 added
2bba606c9714_GRCh38.primary_assembly.genome.fa.rev.2.bt2 added
2bba7932d380_outfile.txt added
2bba77dbb6a9_GRCh37_to_GRCh38.chain added
2bba79b54eb8_GRCh37_to_NCBI34.chain added
2bba6e435074_GRCh37_to_NCBI35.chain added
2bba557283a_GRCh37_to_NCBI36.chain added
2bba1d11fa93_GRCh38_to_GRCh37.chain added
2bba759d7ce_GRCh38_to_NCBI34.chain added
2bba1b671927_GRCh38_to_NCBI35.chain added
2bbada45d7f_GRCh38_to_NCBI36.chain added
2bba21f643d8_NCBI34_to_GRCh37.chain added
2bba2ee02b53_NCBI34_to_GRCh38.chain added
2bba7f3c6e2f_NCBI35_to_GRCh37.chain added
2bba586610eb_NCBI35_to_GRCh38.chain added
2bba14e0e1a4_NCBI36_to_GRCh37.chain added
2bba37fde0b1_NCBI36_to_GRCh38.chain added
2bba7caaa12e_GRCm38_to_NCBIM36.chain added
2bba263c12f3_GRCm38_to_NCBIM37.chain added
2bba32002321_NCBIM36_to_GRCm38.chain added
2bba2702652c_NCBIM37_to_GRCm38.chain added
2bbae403fb6_1000G_omni2.5.b37.vcf.gz added
2bba1c16cd09_1000G_omni2.5.b37.vcf.gz.tbi added
2bba1cef1847_Mills_and_1000G_gold_standard.indels.b37.vcf.gz added
2bba1522ec28_Mills_and_1000G_gold_standard.indels.b37.vcf.gz.tbi added
2bba27be40ef_1000G_omni2.5.hg38.vcf.gz added
2bba3b991f4b_1000G_omni2.5.hg38.vcf.gz.tbi added
2bba41d5937e_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz added
2bba2cc656f6_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz.tbi added
2bba11774771_af-only-gnomad.raw.sites.vcf added
2bba2df354ac_af-only-gnomad.raw.sites.vcf.idx added
2bba423bffc5_Mutect2-exome-panel.vcf.idx added
2bba7115007b_Mutect2-WGS-panel-b37.vcf added
2bba19d2c53d_Mutect2-WGS-panel-b37.vcf.idx added
2bba5c933509_small_exac_common_3.vcf added
2bba447f115a_small_exac_common_3.vcf.idx added
2bba724c4ed7_1000g_pon.hg38.vcf.gz added
2bba6fcc3fe0_1000g_pon.hg38.vcf.gz.tbi added
2bba4a75c477_af-only-gnomad.hg38.vcf.gz added
2bba79b586d1_af-only-gnomad.hg38.vcf.gz.tbi added
2bba7ca641c3_small_exac_common_3.hg38.vcf.gz added
2bba727a924_small_exac_common_3.hg38.vcf.gz.tbi added
2bba3cd17e27_gencode.v41.annotation.gtf added
2bba5db151a2_gencode.v42.annotation.gtf added
2bba246692bc_gencode.vM30.annotation.gtf added
2bba4a2b874f_gencode.vM31.annotation.gtf added
2bba6fc07993_gencode.v41.transcripts.fa added
2bba456ddb36_gencode.v41.transcripts.fa.fai added
2bba2f52d9d6_gencode.v42.transcripts.fa added
2bba685b88df_gencode.v42.transcripts.fa.fai added
2bba51771dff_gencode.vM30.pc_transcripts.fa added
2bba63527a21_gencode.vM30.pc_transcripts.fa.fai added
2bba3bd03f78_gencode.vM31.pc_transcripts.fa added
2bba64f6fdf5_gencode.vM31.pc_transcripts.fa.fai added
2bba139b139c_GRCh38.primary_assembly.genome.fa.1.ht2 added
2bba2a2470d2_GRCh38.primary_assembly.genome.fa.2.ht2 added
2bba3e6b009b_GRCh38.primary_assembly.genome.fa.3.ht2 added
2bba62f4e020_GRCh38.primary_assembly.genome.fa.4.ht2 added
2bba3aa687a1_GRCh38.primary_assembly.genome.fa.5.ht2 added
2bbab12791c_GRCh38.primary_assembly.genome.fa.6.ht2 added
2bba69cd22f1_GRCh38.primary_assembly.genome.fa.7.ht2 added
2bba1ab1327b_GRCh38.primary_assembly.genome.fa.8.ht2 added
2bba676936ed_GRCh38_full_analysis_set_plus_decoy_hla.fa.fai added
2bba2c9536a5_GRCh38_full_analysis_set_plus_decoy_hla.fa.amb added
2bba7836a180_GRCh38_full_analysis_set_plus_decoy_hla.fa.ann added
2bba4aa51828_GRCh38_full_analysis_set_plus_decoy_hla.fa.bwt added
2bba1cd51061_GRCh38_full_analysis_set_plus_decoy_hla.fa.pac added
2bba68265f10_GRCh38_full_analysis_set_plus_decoy_hla.fa.sa added
2bba2f2b48db_GRCh38_full_analysis_set_plus_decoy_hla.fa added
2bba42bc3a0e_GRCh38.primary_assembly.genome.fa.fai added
2bba53878f5c_GRCh38.primary_assembly.genome.fa.amb added
2bba68d50bdb_GRCh38.primary_assembly.genome.fa.ann added
2bba7afd8ca1_GRCh38.primary_assembly.genome.fa.bwt added
2bba1c1bdd1c_GRCh38.primary_assembly.genome.fa.pac added
2bba695167ae_GRCh38.primary_assembly.genome.fa.sa added
2bba5f6e0686_GRCh38.primary_assembly.genome.fa added
2bba306e785c_hs37d5.fa.fai added
2bba249ff8db_hs37d5.fa.amb added
2bba28b04a6_hs37d5.fa.ann added
2bba74de2f97_hs37d5.fa.bwt added
2bba27069e72_hs37d5.fa.pac added
2bba238c6262_hs37d5.fa.sa added
2bba558f2229_hs37d5.fa added
2bba280bdda1_complete_ref_lens.bin added
2bba23038991_ctable.bin added
2bba3d3ca08c_ctg_offsets.bin added
2bba575066bc_duplicate_clusters.tsv added
2bba5f88ed6c_info.json added
2bba169b7e74_mphf.bin added
2bba3a8afd44_pos.bin added
2bba7af99962_pre_indexing.log added
2bba18c53001_rank.bin added
2bba39d29e5b_ref_indexing.log added
2bba329a8605_refAccumLengths.bin added
2bba3ed4cc37_reflengths.bin added
2bba4ab4f1b_refseq.bin added
2bbaad67802_seq.bin added
2bba660d0dd_versionInfo.json added
2bba3e306070_salmon_index added
2bba5a0b78f5_chrLength.txt added
2bba27324b02_chrName.txt added
2bba56da8468_chrNameLength.txt added
2bba242af464_chrStart.txt added
2bba12e3c9_exonGeTrInfo.tab added
2bba5828a128_exonInfo.tab added
2bba536c764f_geneInfo.tab added
2bba75cb6752_Genome added
2bba7cec74e8_genomeParameters.txt added
2bba7ef6b6b_Log.out added
2bba777541de_SA added
2bba33379317_SAindex added
2bba599e546_sjdbInfo.txt added
2bba3a9b5989_sjdbList.fromGTF.out.tab added
2bba2d134f6e_sjdbList.out.tab added
2bba4ec3d5e0_transcriptInfo.tab added
2bba1b0e8d86_GRCh38.GENCODE.v42_100 added
2bba586d664a_knownGene_hg38.sql added
2bba7656b1a0_knownGene_hg38.txt added
2bba35a7bc12_refGene_hg38.sql added
2bba172c5d43_refGene_hg38.txt added
2bba619ee597_knownGene_mm39.sql added
2bba6f34e93_knownGene_mm39.txt added
2bba4fab9875_refGene_mm39.sql added
2bbaaa65230_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/RtmpgfoEST/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
24.989 3.697 29.931
ReUseData.Rcheck/ReUseData-Ex.timings
| name | user | system | elapsed | |
| dataHub-class | 7.345 | 0.892 | 8.370 | |
| dataSearch | 1.343 | 0.060 | 1.410 | |
| dataUpdate | 0.001 | 0.000 | 0.001 | |
| getCloudData | 2.807 | 0.154 | 7.033 | |
| getData | 0.000 | 0.001 | 0.000 | |
| meta_data | 0.001 | 0.000 | 0.001 | |
| recipeHub-class | 0.148 | 0.012 | 0.160 | |
| recipeLoad | 1.527 | 0.102 | 1.643 | |
| recipeMake | 0.000 | 0.001 | 0.001 | |
| recipeSearch | 0.665 | 0.044 | 0.714 | |
| recipeUpdate | 0 | 0 | 0 | |