Qian Liu
| Snapshot Date: 2025-03-26 13:40 -0400 (Wed, 26 Mar 2025) |
| git_url: https://git.bioconductor.org/packages/ReUseData |
| git_branch: devel |
| git_last_commit: 85fc756 |
| git_last_commit_date: 2024-10-29 11:17:22 -0400 (Tue, 29 Oct 2024) |
| Back to Multiple platform build/check report for BioC 3.21: simplified long |
|
This page was generated on 2025-03-27 11:41 -0400 (Thu, 27 Mar 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | R Under development (unstable) (2025-03-13 r87965) -- "Unsuffered Consequences" | 4783 |
| palomino7 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2025-03-01 r87860 ucrt) -- "Unsuffered Consequences" | 4552 |
| lconway | macOS 12.7.1 Monterey | x86_64 | R Under development (unstable) (2025-03-02 r87868) -- "Unsuffered Consequences" | 4581 |
| kjohnson3 | macOS 13.7.1 Ventura | arm64 | R Under development (unstable) (2025-03-02 r87868) -- "Unsuffered Consequences" | 4533 |
| kunpeng2 | Linux (openEuler 24.03 LTS) | aarch64 | R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" | 4463 |
| 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 1741/2315 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| ReUseData 1.7.0 (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: 1.7.0 |
| Command: /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:ReUseData.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings ReUseData_1.7.0.tar.gz |
| StartedAt: 2025-03-27 01:49:59 -0400 (Thu, 27 Mar 2025) |
| EndedAt: 2025-03-27 01:52:52 -0400 (Thu, 27 Mar 2025) |
| EllapsedTime: 173.4 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: ReUseData.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:ReUseData.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings ReUseData_1.7.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/ReUseData.Rcheck’
* using R Under development (unstable) (2025-03-13 r87965)
* 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 24.04.2 LTS
* using session charset: UTF-8
* checking for file ‘ReUseData/DESCRIPTION’ ... OK
* this is package ‘ReUseData’ version ‘1.7.0’
* 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 5.835 0.328 6.168
* 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-3.21-bioc/meat/ReUseData.Rcheck/00check.log’
for details.
ReUseData.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD INSTALL ReUseData ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.21-bioc/R/site-library’ * installing *source* package ‘ReUseData’ ... ** this is package ‘ReUseData’ version ‘1.7.0’ ** 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 Under development (unstable) (2025-03-13 r87965) -- "Unsuffered Consequences"
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...
3c43d749889b26_GRCh38.primary_assembly.genome.fa.1.bt2 added
3c43d72303df26_GRCh38.primary_assembly.genome.fa.2.bt2 added
3c43d71b9e332c_GRCh38.primary_assembly.genome.fa.3.bt2 added
3c43d77a8be513_GRCh38.primary_assembly.genome.fa.4.bt2 added
3c43d7453cc99e_GRCh38.primary_assembly.genome.fa.rev.1.bt2 added
3c43d77b4ef50b_GRCh38.primary_assembly.genome.fa.rev.2.bt2 added
3c43d727f0c820_outfile.txt added
3c43d76404a110_GRCh37_to_GRCh38.chain added
3c43d76a13e5df_GRCh37_to_NCBI34.chain added
3c43d72a93b710_GRCh37_to_NCBI35.chain added
3c43d7fc02357_GRCh37_to_NCBI36.chain added
3c43d71634465b_GRCh38_to_GRCh37.chain added
3c43d75d176f15_GRCh38_to_NCBI34.chain added
3c43d77e6018e1_GRCh38_to_NCBI35.chain added
3c43d742e4759d_GRCh38_to_NCBI36.chain added
3c43d7d36ac39_NCBI34_to_GRCh37.chain added
3c43d767d141b_NCBI34_to_GRCh38.chain added
3c43d75b863b6c_NCBI35_to_GRCh37.chain added
3c43d7230bd2dd_NCBI35_to_GRCh38.chain added
3c43d76131a492_NCBI36_to_GRCh37.chain added
3c43d73258f3ee_NCBI36_to_GRCh38.chain added
3c43d71dfbd829_GRCm38_to_NCBIM36.chain added
3c43d726055bf7_GRCm38_to_NCBIM37.chain added
3c43d76cdd2fb8_NCBIM36_to_GRCm38.chain added
3c43d733be323b_NCBIM37_to_GRCm38.chain added
3c43d71fcd6e72_1000G_omni2.5.b37.vcf.gz added
3c43d728aa7739_1000G_omni2.5.b37.vcf.gz.tbi added
3c43d76de951b8_Mills_and_1000G_gold_standard.indels.b37.vcf.gz added
3c43d7457a20e6_Mills_and_1000G_gold_standard.indels.b37.vcf.gz.tbi added
3c43d73256718c_1000G_omni2.5.hg38.vcf.gz added
3c43d72f83bf09_1000G_omni2.5.hg38.vcf.gz.tbi added
3c43d7f02bc0c_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz added
3c43d7555a50b2_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz.tbi added
3c43d74b21f236_af-only-gnomad.raw.sites.vcf added
3c43d798ea120_af-only-gnomad.raw.sites.vcf.idx added
3c43d71a971a50_Mutect2-exome-panel.vcf.idx added
3c43d74670e741_Mutect2-WGS-panel-b37.vcf added
3c43d7317f6940_Mutect2-WGS-panel-b37.vcf.idx added
3c43d77e9bbb61_small_exac_common_3.vcf added
3c43d73084cd20_small_exac_common_3.vcf.idx added
3c43d75c132050_1000g_pon.hg38.vcf.gz added
3c43d7e5bdeb8_1000g_pon.hg38.vcf.gz.tbi added
3c43d746b9137c_af-only-gnomad.hg38.vcf.gz added
3c43d7392a8f65_af-only-gnomad.hg38.vcf.gz.tbi added
3c43d7cbbf799_small_exac_common_3.hg38.vcf.gz added
3c43d799d8919_small_exac_common_3.hg38.vcf.gz.tbi added
3c43d746613b9f_gencode.v41.annotation.gtf added
3c43d713390bb4_gencode.v42.annotation.gtf added
3c43d76523c485_gencode.vM30.annotation.gtf added
3c43d7696d0e7c_gencode.vM31.annotation.gtf added
3c43d7746ab046_gencode.v41.transcripts.fa added
3c43d7177cb873_gencode.v41.transcripts.fa.fai added
3c43d7768e6a6_gencode.v42.transcripts.fa added
3c43d71a700c3d_gencode.v42.transcripts.fa.fai added
3c43d7459e82b_gencode.vM30.pc_transcripts.fa added
3c43d73b2718e1_gencode.vM30.pc_transcripts.fa.fai added
3c43d73a3d7aaf_gencode.vM31.pc_transcripts.fa added
3c43d72d045f65_gencode.vM31.pc_transcripts.fa.fai added
3c43d729106a99_GRCh38.primary_assembly.genome.fa.1.ht2 added
3c43d77fb79b95_GRCh38.primary_assembly.genome.fa.2.ht2 added
3c43d75f5ad0f1_GRCh38.primary_assembly.genome.fa.3.ht2 added
3c43d7589429a3_GRCh38.primary_assembly.genome.fa.4.ht2 added
3c43d7eba57a1_GRCh38.primary_assembly.genome.fa.5.ht2 added
3c43d734b521a3_GRCh38.primary_assembly.genome.fa.6.ht2 added
3c43d723b61bd9_GRCh38.primary_assembly.genome.fa.7.ht2 added
3c43d71848f8c1_GRCh38.primary_assembly.genome.fa.8.ht2 added
3c43d74f4c3bf3_GRCh38_full_analysis_set_plus_decoy_hla.fa.fai added
3c43d76a27031a_GRCh38_full_analysis_set_plus_decoy_hla.fa.amb added
3c43d749c86201_GRCh38_full_analysis_set_plus_decoy_hla.fa.ann added
3c43d74de7f754_GRCh38_full_analysis_set_plus_decoy_hla.fa.bwt added
3c43d71aabd03b_GRCh38_full_analysis_set_plus_decoy_hla.fa.pac added
3c43d725db8252_GRCh38_full_analysis_set_plus_decoy_hla.fa.sa added
3c43d75c43d60c_GRCh38_full_analysis_set_plus_decoy_hla.fa added
3c43d76164e3b7_GRCh38.primary_assembly.genome.fa.fai added
3c43d75f0611b7_GRCh38.primary_assembly.genome.fa.amb added
3c43d768ffcda5_GRCh38.primary_assembly.genome.fa.ann added
3c43d76b026cd0_GRCh38.primary_assembly.genome.fa.bwt added
3c43d725674d56_GRCh38.primary_assembly.genome.fa.pac added
3c43d77c38d959_GRCh38.primary_assembly.genome.fa.sa added
3c43d750263155_GRCh38.primary_assembly.genome.fa added
3c43d7ed45bd3_hs37d5.fa.fai added
3c43d770a3899f_hs37d5.fa.amb added
3c43d767a2e9c8_hs37d5.fa.ann added
3c43d7163d4279_hs37d5.fa.bwt added
3c43d7b1395dc_hs37d5.fa.pac added
3c43d76bfcd1f3_hs37d5.fa.sa added
3c43d751645b5a_hs37d5.fa added
3c43d74551108b_complete_ref_lens.bin added
3c43d719013158_ctable.bin added
3c43d77a74c5f3_ctg_offsets.bin added
3c43d74508ac20_duplicate_clusters.tsv added
3c43d7785c0249_info.json added
3c43d75308ef96_mphf.bin added
3c43d753c303c2_pos.bin added
3c43d72d1123ec_pre_indexing.log added
3c43d776bf0b6f_rank.bin added
3c43d76c0bfc83_ref_indexing.log added
3c43d77c5d5fe0_refAccumLengths.bin added
3c43d760e60e8a_reflengths.bin added
3c43d735d45e85_refseq.bin added
3c43d74a455734_seq.bin added
3c43d77b91dec5_versionInfo.json added
3c43d75bafe0d7_salmon_index added
3c43d726892d41_chrLength.txt added
3c43d75cf6c27c_chrName.txt added
3c43d73ab5f28e_chrNameLength.txt added
3c43d7f88fae6_chrStart.txt added
3c43d747f92f4c_exonGeTrInfo.tab added
3c43d7601d3fe5_exonInfo.tab added
3c43d7bc1d440_geneInfo.tab added
3c43d7181f60a1_Genome added
3c43d76ef19bb8_genomeParameters.txt added
3c43d77c655ddf_Log.out added
3c43d77fc24a69_SA added
3c43d752ede31_SAindex added
3c43d7778f3bc_sjdbInfo.txt added
3c43d76bbf1c5c_sjdbList.fromGTF.out.tab added
3c43d75693398b_sjdbList.out.tab added
3c43d74cca0447_transcriptInfo.tab added
3c43d74c04db5_GRCh38.GENCODE.v42_100 added
3c43d75107ff7e_knownGene_hg38.sql added
3c43d711d2b068_knownGene_hg38.txt added
3c43d77d1c4ffe_refGene_hg38.sql added
3c43d72410ef15_refGene_hg38.txt added
3c43d76595b42a_knownGene_mm39.sql added
3c43d72a2d73eb_knownGene_mm39.txt added
3c43d71acffa84_refGene_mm39.sql added
3c43d751a1b0ad_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/Rtmp9xDhvK/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
19.962 1.576 21.777
ReUseData.Rcheck/ReUseData-Ex.timings
| name | user | system | elapsed | |
| dataHub-class | 5.835 | 0.328 | 6.168 | |
| dataSearch | 1.078 | 0.026 | 1.105 | |
| dataUpdate | 0.001 | 0.000 | 0.001 | |
| getCloudData | 2.661 | 0.110 | 3.345 | |
| getData | 0 | 0 | 0 | |
| meta_data | 0.001 | 0.000 | 0.001 | |
| recipeHub-class | 0.122 | 0.002 | 0.124 | |
| recipeLoad | 1.283 | 0.092 | 1.375 | |
| recipeMake | 0.001 | 0.000 | 0.001 | |
| recipeSearch | 0.531 | 0.033 | 0.564 | |
| recipeUpdate | 0 | 0 | 0 | |