Qian Liu
| Snapshot Date: 2025-03-06 13:00 -0500 (Thu, 06 Mar 2025) |
| git_url: https://git.bioconductor.org/packages/ReUseData |
| git_branch: RELEASE_3_20 |
| git_last_commit: 5d8c0ee |
| git_last_commit_date: 2024-10-29 11:17:22 -0500 (Tue, 29 Oct 2024) |
| Back to Multiple platform build/check report for BioC 3.20: simplified long |
|
This page was generated on 2025-03-10 12:06 -0400 (Mon, 10 Mar 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.3 (2025-02-28) -- "Trophy Case" | 4670 |
| palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.3 (2025-02-28 ucrt) -- "Trophy Case" | 4355 |
| merida1 | macOS 12.7.5 Monterey | x86_64 | 4.4.3 (2025-02-28) -- "Trophy Case" | 4446 |
| kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.3 (2025-02-28) -- "Trophy Case" | 4439 |
| taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.4.3 (2025-02-28) -- "Trophy Case" | 4306 |
| 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 1727/2289 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| ReUseData 1.6.0 (landing page) Qian Liu
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino8 | Windows Server 2022 Datacenter / x64 | ... NOT SUPPORTED ... | ||||||||||||
| merida1 | macOS 12.7.5 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson1 | macOS 13.6.6 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: 1.6.0 |
| Command: /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:ReUseData.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings ReUseData_1.6.0.tar.gz |
| StartedAt: 2025-03-07 02:03:25 -0500 (Fri, 07 Mar 2025) |
| EndedAt: 2025-03-07 02:06:12 -0500 (Fri, 07 Mar 2025) |
| EllapsedTime: 166.2 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: ReUseData.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:ReUseData.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings ReUseData_1.6.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/ReUseData.Rcheck’
* using R version 4.4.3 (2025-02-28)
* 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 ‘1.6.0’
* 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 5.89 0.275 6.169
* 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-3.20-bioc/meat/ReUseData.Rcheck/00check.log’
for details.
ReUseData.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD INSTALL ReUseData ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.20-bioc/R/site-library’ * installing *source* package ‘ReUseData’ ... ** 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 4.4.3 (2025-02-28) -- "Trophy Case"
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...
3939c62117d6ab_GRCh38.primary_assembly.genome.fa.1.bt2 added
3939c668995f3b_GRCh38.primary_assembly.genome.fa.2.bt2 added
3939c678e48341_GRCh38.primary_assembly.genome.fa.3.bt2 added
3939c6c753196_GRCh38.primary_assembly.genome.fa.4.bt2 added
3939c62258be5d_GRCh38.primary_assembly.genome.fa.rev.1.bt2 added
3939c64f433eae_GRCh38.primary_assembly.genome.fa.rev.2.bt2 added
3939c63506b21c_outfile.txt added
3939c64ae1f792_GRCh37_to_GRCh38.chain added
3939c66ba39f99_GRCh37_to_NCBI34.chain added
3939c6313847ec_GRCh37_to_NCBI35.chain added
3939c616447747_GRCh37_to_NCBI36.chain added
3939c65d38984c_GRCh38_to_GRCh37.chain added
3939c632c39fd1_GRCh38_to_NCBI34.chain added
3939c61a2ced48_GRCh38_to_NCBI35.chain added
3939c6532fc689_GRCh38_to_NCBI36.chain added
3939c62fa47805_NCBI34_to_GRCh37.chain added
3939c64bd7763d_NCBI34_to_GRCh38.chain added
3939c662fcac30_NCBI35_to_GRCh37.chain added
3939c6efa7c1c_NCBI35_to_GRCh38.chain added
3939c64960ab36_NCBI36_to_GRCh37.chain added
3939c631924179_NCBI36_to_GRCh38.chain added
3939c6209b8c53_GRCm38_to_NCBIM36.chain added
3939c647c754ee_GRCm38_to_NCBIM37.chain added
3939c65e794fa0_NCBIM36_to_GRCm38.chain added
3939c659fe4d56_NCBIM37_to_GRCm38.chain added
3939c671388465_1000G_omni2.5.b37.vcf.gz added
3939c62bced521_1000G_omni2.5.b37.vcf.gz.tbi added
3939c6acb811a_Mills_and_1000G_gold_standard.indels.b37.vcf.gz added
3939c6dfa38a0_Mills_and_1000G_gold_standard.indels.b37.vcf.gz.tbi added
3939c6d50c481_1000G_omni2.5.hg38.vcf.gz added
3939c6605bf5e9_1000G_omni2.5.hg38.vcf.gz.tbi added
3939c62f120f4b_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz added
3939c675ea23bc_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz.tbi added
3939c65940792b_af-only-gnomad.raw.sites.vcf added
3939c63b8740e1_af-only-gnomad.raw.sites.vcf.idx added
3939c61842e219_Mutect2-exome-panel.vcf.idx added
3939c62883b7d9_Mutect2-WGS-panel-b37.vcf added
3939c6708df2fe_Mutect2-WGS-panel-b37.vcf.idx added
3939c66324d9ab_small_exac_common_3.vcf added
3939c614275772_small_exac_common_3.vcf.idx added
3939c621c63aea_1000g_pon.hg38.vcf.gz added
3939c6796950f3_1000g_pon.hg38.vcf.gz.tbi added
3939c6715fefbe_af-only-gnomad.hg38.vcf.gz added
3939c65489dabb_af-only-gnomad.hg38.vcf.gz.tbi added
3939c613963e3b_small_exac_common_3.hg38.vcf.gz added
3939c6448fb648_small_exac_common_3.hg38.vcf.gz.tbi added
3939c642e52c1_gencode.v41.annotation.gtf added
3939c65f6db478_gencode.v42.annotation.gtf added
3939c6278c6278_gencode.vM30.annotation.gtf added
3939c61328cedd_gencode.vM31.annotation.gtf added
3939c628ce5faf_gencode.v41.transcripts.fa added
3939c6591ea3f2_gencode.v41.transcripts.fa.fai added
3939c633c45b30_gencode.v42.transcripts.fa added
3939c67095b49d_gencode.v42.transcripts.fa.fai added
3939c63797f392_gencode.vM30.pc_transcripts.fa added
3939c6dc2a886_gencode.vM30.pc_transcripts.fa.fai added
3939c661ce3902_gencode.vM31.pc_transcripts.fa added
3939c66366c8b3_gencode.vM31.pc_transcripts.fa.fai added
3939c6188e29a1_GRCh38.primary_assembly.genome.fa.1.ht2 added
3939c66fc871a3_GRCh38.primary_assembly.genome.fa.2.ht2 added
3939c670b78d34_GRCh38.primary_assembly.genome.fa.3.ht2 added
3939c678ea1f8a_GRCh38.primary_assembly.genome.fa.4.ht2 added
3939c61eda80ee_GRCh38.primary_assembly.genome.fa.5.ht2 added
3939c666a1b0f1_GRCh38.primary_assembly.genome.fa.6.ht2 added
3939c6522a98b5_GRCh38.primary_assembly.genome.fa.7.ht2 added
3939c65a61c1d0_GRCh38.primary_assembly.genome.fa.8.ht2 added
3939c67ee4930a_GRCh38_full_analysis_set_plus_decoy_hla.fa.fai added
3939c67aae508f_GRCh38_full_analysis_set_plus_decoy_hla.fa.amb added
3939c64aefb4ce_GRCh38_full_analysis_set_plus_decoy_hla.fa.ann added
3939c662096cb6_GRCh38_full_analysis_set_plus_decoy_hla.fa.bwt added
3939c6ed5a801_GRCh38_full_analysis_set_plus_decoy_hla.fa.pac added
3939c66cb5efb8_GRCh38_full_analysis_set_plus_decoy_hla.fa.sa added
3939c65b72bda9_GRCh38_full_analysis_set_plus_decoy_hla.fa added
3939c63597c0_GRCh38.primary_assembly.genome.fa.fai added
3939c6413fca74_GRCh38.primary_assembly.genome.fa.amb added
3939c66f08fbe4_GRCh38.primary_assembly.genome.fa.ann added
3939c644c54e08_GRCh38.primary_assembly.genome.fa.bwt added
3939c6456e1d35_GRCh38.primary_assembly.genome.fa.pac added
3939c64e76b05d_GRCh38.primary_assembly.genome.fa.sa added
3939c66c51b080_GRCh38.primary_assembly.genome.fa added
3939c65896ec12_hs37d5.fa.fai added
3939c67745100c_hs37d5.fa.amb added
3939c645705472_hs37d5.fa.ann added
3939c6c5b4742_hs37d5.fa.bwt added
3939c667dac4a9_hs37d5.fa.pac added
3939c67d084804_hs37d5.fa.sa added
3939c61a1defc8_hs37d5.fa added
3939c649a8fdab_complete_ref_lens.bin added
3939c6606f10b8_ctable.bin added
3939c632ac1969_ctg_offsets.bin added
3939c639716f4e_duplicate_clusters.tsv added
3939c651269dec_info.json added
3939c62b9638f4_mphf.bin added
3939c6584bf03d_pos.bin added
3939c637c84edd_pre_indexing.log added
3939c67dc0d1a9_rank.bin added
3939c632adb20d_ref_indexing.log added
3939c636ace1e8_refAccumLengths.bin added
3939c6786f2238_reflengths.bin added
3939c67d9d66db_refseq.bin added
3939c618b64e9e_seq.bin added
3939c6744ca3a_versionInfo.json added
3939c66a535693_salmon_index added
3939c674290c47_chrLength.txt added
3939c677a61fa_chrName.txt added
3939c62b932107_chrNameLength.txt added
3939c66332082b_chrStart.txt added
3939c64c3fb002_exonGeTrInfo.tab added
3939c671013e3c_exonInfo.tab added
3939c631a8b888_geneInfo.tab added
3939c638916082_Genome added
3939c649982a4e_genomeParameters.txt added
3939c628edc894_Log.out added
3939c67e01b4f5_SA added
3939c655f37190_SAindex added
3939c610c88d3d_sjdbInfo.txt added
3939c67b09fcf9_sjdbList.fromGTF.out.tab added
3939c670116159_sjdbList.out.tab added
3939c65a718ae9_transcriptInfo.tab added
3939c65b790db1_GRCh38.GENCODE.v42_100 added
3939c622bd7ac2_knownGene_hg38.sql added
3939c613e2fa37_knownGene_hg38.txt added
3939c62c9fab9e_refGene_hg38.sql added
3939c64e53b3b6_refGene_hg38.txt added
3939c66c2eea74_knownGene_mm39.sql added
3939c66467fa7b_knownGene_mm39.txt added
3939c64c148560_refGene_mm39.sql added
3939c61edc9c81_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:
/home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpgmNeOK/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
18.796 1.031 19.980
ReUseData.Rcheck/ReUseData-Ex.timings
| name | user | system | elapsed | |
| dataHub-class | 5.890 | 0.275 | 6.169 | |
| dataSearch | 1.100 | 0.019 | 1.119 | |
| dataUpdate | 0 | 0 | 0 | |
| getCloudData | 2.749 | 0.087 | 3.433 | |
| getData | 0.001 | 0.000 | 0.000 | |
| meta_data | 0.000 | 0.001 | 0.001 | |
| recipeHub-class | 0.125 | 0.008 | 0.133 | |
| recipeLoad | 1.285 | 0.026 | 1.312 | |
| recipeMake | 0 | 0 | 0 | |
| recipeSearch | 0.557 | 0.010 | 0.567 | |
| recipeUpdate | 0 | 0 | 0 | |