Qian Liu
| Snapshot Date: 2025-03-13 13:40 -0400 (Thu, 13 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 2025-03-14 11:40 -0400 (Fri, 14 Mar 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" | 4781 |
| palomino7 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2025-03-01 r87860 ucrt) -- "Unsuffered Consequences" | 4537 |
| lconway | macOS 12.7.1 Monterey | x86_64 | R Under development (unstable) (2025-03-02 r87868) -- "Unsuffered Consequences" | 4567 |
| kjohnson3 | macOS 13.7.1 Ventura | arm64 | R Under development (unstable) (2025-03-02 r87868) -- "Unsuffered Consequences" | 4519 |
| kunpeng2 | Linux (openEuler 24.03 LTS) | aarch64 | R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" | 4451 |
| 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 1738/2309 | 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: 2025-03-14 01:25:10 -0400 (Fri, 14 Mar 2025) |
| EndedAt: 2025-03-14 01:28:03 -0400 (Fri, 14 Mar 2025) |
| EllapsedTime: 172.3 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) (2025-02-19 r87757)
* 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 6.009 0.357 6.368
* 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) (2025-02-19 r87757) -- "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...
24f15d2a8410a_GRCh38.primary_assembly.genome.fa.1.bt2 added
24f15d7f5b6edb_GRCh38.primary_assembly.genome.fa.2.bt2 added
24f15d5b84bd7e_GRCh38.primary_assembly.genome.fa.3.bt2 added
24f15d3ee14034_GRCh38.primary_assembly.genome.fa.4.bt2 added
24f15d574a9a41_GRCh38.primary_assembly.genome.fa.rev.1.bt2 added
24f15d7194f78d_GRCh38.primary_assembly.genome.fa.rev.2.bt2 added
24f15d5dd853c4_outfile.txt added
24f15d24ccf646_GRCh37_to_GRCh38.chain added
24f15d4566741d_GRCh37_to_NCBI34.chain added
24f15d756daab7_GRCh37_to_NCBI35.chain added
24f15d1162403e_GRCh37_to_NCBI36.chain added
24f15d57b4c647_GRCh38_to_GRCh37.chain added
24f15d46106117_GRCh38_to_NCBI34.chain added
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24f15d73a6647b_GRCh38_to_NCBI36.chain added
24f15d4943e53f_NCBI34_to_GRCh37.chain added
24f15d49ab098f_NCBI34_to_GRCh38.chain added
24f15d1554373a_NCBI35_to_GRCh37.chain added
24f15d1173a1cf_NCBI35_to_GRCh38.chain added
24f15d36832df5_NCBI36_to_GRCh37.chain added
24f15d10aeb1c_NCBI36_to_GRCh38.chain added
24f15d22fddeb5_GRCm38_to_NCBIM36.chain added
24f15d46c011a3_GRCm38_to_NCBIM37.chain added
24f15d29692e3a_NCBIM36_to_GRCm38.chain added
24f15d225919bc_NCBIM37_to_GRCm38.chain added
24f15d4e01e589_1000G_omni2.5.b37.vcf.gz added
24f15d58f0a086_1000G_omni2.5.b37.vcf.gz.tbi added
24f15d392876a2_Mills_and_1000G_gold_standard.indels.b37.vcf.gz added
24f15d5a80953_Mills_and_1000G_gold_standard.indels.b37.vcf.gz.tbi added
24f15d715cdedf_1000G_omni2.5.hg38.vcf.gz added
24f15d59ea2e8e_1000G_omni2.5.hg38.vcf.gz.tbi added
24f15d8504a5d_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz added
24f15d70b84dba_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz.tbi added
24f15d356eec0d_af-only-gnomad.raw.sites.vcf added
24f15d47318a91_af-only-gnomad.raw.sites.vcf.idx added
24f15d4802e7fb_Mutect2-exome-panel.vcf.idx added
24f15d2703e39a_Mutect2-WGS-panel-b37.vcf added
24f15d2509de56_Mutect2-WGS-panel-b37.vcf.idx added
24f15d6ccfde42_small_exac_common_3.vcf added
24f15d6c6a57b7_small_exac_common_3.vcf.idx added
24f15d1a77890d_1000g_pon.hg38.vcf.gz added
24f15d7e321e80_1000g_pon.hg38.vcf.gz.tbi added
24f15d441f1dfe_af-only-gnomad.hg38.vcf.gz added
24f15d6087ea24_af-only-gnomad.hg38.vcf.gz.tbi added
24f15d617a6aa_small_exac_common_3.hg38.vcf.gz added
24f15d37c58279_small_exac_common_3.hg38.vcf.gz.tbi added
24f15d29cbcf64_gencode.v41.annotation.gtf added
24f15d4fc2b039_gencode.v42.annotation.gtf added
24f15d4d19b9b4_gencode.vM30.annotation.gtf added
24f15d3b3f7133_gencode.vM31.annotation.gtf added
24f15d645de2e_gencode.v41.transcripts.fa added
24f15d4e24a4d0_gencode.v41.transcripts.fa.fai added
24f15d5e3d4fe9_gencode.v42.transcripts.fa added
24f15d4d05efd1_gencode.v42.transcripts.fa.fai added
24f15d778dd30a_gencode.vM30.pc_transcripts.fa added
24f15d9669a5_gencode.vM30.pc_transcripts.fa.fai added
24f15d1b07d55b_gencode.vM31.pc_transcripts.fa added
24f15d507e7390_gencode.vM31.pc_transcripts.fa.fai added
24f15d39bee047_GRCh38.primary_assembly.genome.fa.1.ht2 added
24f15d20afdeae_GRCh38.primary_assembly.genome.fa.2.ht2 added
24f15d41db5270_GRCh38.primary_assembly.genome.fa.3.ht2 added
24f15d13a90ed6_GRCh38.primary_assembly.genome.fa.4.ht2 added
24f15d2900290b_GRCh38.primary_assembly.genome.fa.5.ht2 added
24f15d3293a02a_GRCh38.primary_assembly.genome.fa.6.ht2 added
24f15d4917fae3_GRCh38.primary_assembly.genome.fa.7.ht2 added
24f15d7031b39d_GRCh38.primary_assembly.genome.fa.8.ht2 added
24f15d7a968826_GRCh38_full_analysis_set_plus_decoy_hla.fa.fai added
24f15d701bde7d_GRCh38_full_analysis_set_plus_decoy_hla.fa.amb added
24f15d153b91f3_GRCh38_full_analysis_set_plus_decoy_hla.fa.ann added
24f15d67666668_GRCh38_full_analysis_set_plus_decoy_hla.fa.bwt added
24f15d5c863634_GRCh38_full_analysis_set_plus_decoy_hla.fa.pac added
24f15d2fb31b00_GRCh38_full_analysis_set_plus_decoy_hla.fa.sa added
24f15d659884e8_GRCh38_full_analysis_set_plus_decoy_hla.fa added
24f15d20a55432_GRCh38.primary_assembly.genome.fa.fai added
24f15d103b0525_GRCh38.primary_assembly.genome.fa.amb added
24f15d6bb02b92_GRCh38.primary_assembly.genome.fa.ann added
24f15d586ad6ac_GRCh38.primary_assembly.genome.fa.bwt added
24f15d3a06d489_GRCh38.primary_assembly.genome.fa.pac added
24f15d3b72dbcb_GRCh38.primary_assembly.genome.fa.sa added
24f15d25849060_GRCh38.primary_assembly.genome.fa added
24f15d754645bc_hs37d5.fa.fai added
24f15d41b8b9f9_hs37d5.fa.amb added
24f15d73a93530_hs37d5.fa.ann added
24f15d538395a5_hs37d5.fa.bwt added
24f15debea9cb_hs37d5.fa.pac added
24f15d6b37083a_hs37d5.fa.sa added
24f15d5419ff4b_hs37d5.fa added
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24f15d3bb57bca_ctable.bin added
24f15ddd8df92_ctg_offsets.bin added
24f15d4a765dd4_duplicate_clusters.tsv added
24f15d7d90ce3a_info.json added
24f15d2181ee68_mphf.bin added
24f15d737686df_pos.bin added
24f15d30246e65_pre_indexing.log added
24f15d6a99e94b_rank.bin added
24f15d63a83a7c_ref_indexing.log added
24f15d2abaf68b_refAccumLengths.bin added
24f15d5ab5c7c8_reflengths.bin added
24f15d78e3cc6f_refseq.bin added
24f15d12215cf3_seq.bin added
24f15d373bfdfc_versionInfo.json added
24f15d2896e770_salmon_index added
24f15d77b9e1db_chrLength.txt added
24f15d57e1522f_chrName.txt added
24f15d38d1ec95_chrNameLength.txt added
24f15d636a0d6e_chrStart.txt added
24f15d304c28db_exonGeTrInfo.tab added
24f15d72d8c11e_exonInfo.tab added
24f15d1edce939_geneInfo.tab added
24f15d55d0b93b_Genome added
24f15d681f06da_genomeParameters.txt added
24f15d6095a333_Log.out added
24f15d4979ee6b_SA added
24f15d3ba29c80_SAindex added
24f15d6f544cfe_sjdbInfo.txt added
24f15d34b0f6a5_sjdbList.fromGTF.out.tab added
24f15dfbc9bcb_sjdbList.out.tab added
24f15d191acc24_transcriptInfo.tab added
24f15d7066726f_GRCh38.GENCODE.v42_100 added
24f15d1d957b5d_knownGene_hg38.sql added
24f15d639129f8_knownGene_hg38.txt added
24f15d6df740aa_refGene_hg38.sql added
24f15d3f1769c6_refGene_hg38.txt added
24f15d5707b0d7_knownGene_mm39.sql added
24f15d1e1baf0f_knownGene_mm39.txt added
24f15d29b15311_refGene_mm39.sql added
24f15d3aafeb54_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/RtmptQU2vZ/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
20.271 1.443 21.823
ReUseData.Rcheck/ReUseData-Ex.timings
| name | user | system | elapsed | |
| dataHub-class | 6.009 | 0.357 | 6.368 | |
| dataSearch | 1.147 | 0.043 | 1.190 | |
| dataUpdate | 0.000 | 0.001 | 0.001 | |
| getCloudData | 2.571 | 0.099 | 3.165 | |
| getData | 0 | 0 | 0 | |
| meta_data | 0.001 | 0.001 | 0.000 | |
| recipeHub-class | 0.124 | 0.005 | 0.130 | |
| recipeLoad | 1.298 | 0.024 | 1.323 | |
| recipeMake | 0.001 | 0.000 | 0.001 | |
| recipeSearch | 0.541 | 0.008 | 0.549 | |
| recipeUpdate | 0 | 0 | 0 | |