Qian Liu
| Snapshot Date: 2025-03-17 13:00 -0400 (Mon, 17 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 -0400 (Tue, 29 Oct 2024) |
| Back to Multiple platform build/check report for BioC 3.20: simplified long |
|
This page was generated on 2025-03-20 12:05 -0400 (Thu, 20 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" | 4756 |
| palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.3 (2025-02-28 ucrt) -- "Trophy Case" | 4487 |
| merida1 | macOS 12.7.5 Monterey | x86_64 | 4.4.3 (2025-02-28) -- "Trophy Case" | 4514 |
| kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.3 (2025-02-28) -- "Trophy Case" | 4441 |
| taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.4.3 (2025-02-28) -- "Trophy Case" | 4406 |
| 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: 2025-03-18 02:18:02 -0400 (Tue, 18 Mar 2025) |
| EndedAt: 2025-03-18 02:20:45 -0400 (Tue, 18 Mar 2025) |
| EllapsedTime: 163.1 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 6.37 0.255 6.631
* 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...
6668a3ce20fa3_GRCh38.primary_assembly.genome.fa.1.bt2 added
6668a9a95285_GRCh38.primary_assembly.genome.fa.2.bt2 added
6668a673df6e8_GRCh38.primary_assembly.genome.fa.3.bt2 added
6668a5fdb66d7_GRCh38.primary_assembly.genome.fa.4.bt2 added
6668a7fba5871_GRCh38.primary_assembly.genome.fa.rev.1.bt2 added
6668a63d77e45_GRCh38.primary_assembly.genome.fa.rev.2.bt2 added
6668a45df1dbd_outfile.txt added
6668a3d810ee0_GRCh37_to_GRCh38.chain added
6668a2ce0e4e1_GRCh37_to_NCBI34.chain added
6668a1dad8f7e_GRCh37_to_NCBI35.chain added
6668a63088981_GRCh37_to_NCBI36.chain added
6668a594e8598_GRCh38_to_GRCh37.chain added
6668a72c0ed0c_GRCh38_to_NCBI34.chain added
6668a7e428e52_GRCh38_to_NCBI35.chain added
6668a1815cb92_GRCh38_to_NCBI36.chain added
6668a16843f7c_NCBI34_to_GRCh37.chain added
6668a19f12930_NCBI34_to_GRCh38.chain added
6668a1ad9090c_NCBI35_to_GRCh37.chain added
6668a539f8808_NCBI35_to_GRCh38.chain added
6668a1c20a5ff_NCBI36_to_GRCh37.chain added
6668a2df7dd4d_NCBI36_to_GRCh38.chain added
6668a91e0036_GRCm38_to_NCBIM36.chain added
6668a38f681c_GRCm38_to_NCBIM37.chain added
6668a4bd27514_NCBIM36_to_GRCm38.chain added
6668a31f3b382_NCBIM37_to_GRCm38.chain added
6668a4eb0f537_1000G_omni2.5.b37.vcf.gz added
6668a30dadc8b_1000G_omni2.5.b37.vcf.gz.tbi added
6668a64ca842c_Mills_and_1000G_gold_standard.indels.b37.vcf.gz added
6668a7a1ea8c9_Mills_and_1000G_gold_standard.indels.b37.vcf.gz.tbi added
6668a1427ec56_1000G_omni2.5.hg38.vcf.gz added
6668a575ceea8_1000G_omni2.5.hg38.vcf.gz.tbi added
6668a3700b86c_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz added
6668a1dd13edc_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz.tbi added
6668a3e9ae590_af-only-gnomad.raw.sites.vcf added
6668a16dc1f44_af-only-gnomad.raw.sites.vcf.idx added
6668a1d8b974d_Mutect2-exome-panel.vcf.idx added
6668a227263d5_Mutect2-WGS-panel-b37.vcf added
6668a5cbb3d01_Mutect2-WGS-panel-b37.vcf.idx added
6668a5b0ca62d_small_exac_common_3.vcf added
6668a4f5348b7_small_exac_common_3.vcf.idx added
6668a7a68cc80_1000g_pon.hg38.vcf.gz added
6668a3e152faf_1000g_pon.hg38.vcf.gz.tbi added
6668a28a1ce4f_af-only-gnomad.hg38.vcf.gz added
6668a6d29b98c_af-only-gnomad.hg38.vcf.gz.tbi added
6668a3c57be01_small_exac_common_3.hg38.vcf.gz added
6668a40b799e2_small_exac_common_3.hg38.vcf.gz.tbi added
6668a3adf909_gencode.v41.annotation.gtf added
6668a5648e731_gencode.v42.annotation.gtf added
6668a5b90a2ee_gencode.vM30.annotation.gtf added
6668a574d8111_gencode.vM31.annotation.gtf added
6668a72698d30_gencode.v41.transcripts.fa added
6668a988803b_gencode.v41.transcripts.fa.fai added
6668a606b8147_gencode.v42.transcripts.fa added
6668a75f8f54c_gencode.v42.transcripts.fa.fai added
6668a555af550_gencode.vM30.pc_transcripts.fa added
6668a125f34c9_gencode.vM30.pc_transcripts.fa.fai added
6668a44a9ea83_gencode.vM31.pc_transcripts.fa added
6668a635d1db_gencode.vM31.pc_transcripts.fa.fai added
6668a7729b8f5_GRCh38.primary_assembly.genome.fa.1.ht2 added
6668a3ec8934c_GRCh38.primary_assembly.genome.fa.2.ht2 added
6668a1a5dbe31_GRCh38.primary_assembly.genome.fa.3.ht2 added
6668a4e86a79d_GRCh38.primary_assembly.genome.fa.4.ht2 added
6668a75c94bb9_GRCh38.primary_assembly.genome.fa.5.ht2 added
6668a382efd0d_GRCh38.primary_assembly.genome.fa.6.ht2 added
6668ad218d2d_GRCh38.primary_assembly.genome.fa.7.ht2 added
6668aca56afd_GRCh38.primary_assembly.genome.fa.8.ht2 added
6668a55ba945b_GRCh38_full_analysis_set_plus_decoy_hla.fa.fai added
6668a2f93f103_GRCh38_full_analysis_set_plus_decoy_hla.fa.amb added
6668a6960a7fe_GRCh38_full_analysis_set_plus_decoy_hla.fa.ann added
6668a30c73a88_GRCh38_full_analysis_set_plus_decoy_hla.fa.bwt added
6668a7ee739ba_GRCh38_full_analysis_set_plus_decoy_hla.fa.pac added
6668a63c9747e_GRCh38_full_analysis_set_plus_decoy_hla.fa.sa added
6668a6edc6a37_GRCh38_full_analysis_set_plus_decoy_hla.fa added
6668a27890809_GRCh38.primary_assembly.genome.fa.fai added
6668a50f32e0b_GRCh38.primary_assembly.genome.fa.amb added
6668a2b342838_GRCh38.primary_assembly.genome.fa.ann added
6668a6840a1eb_GRCh38.primary_assembly.genome.fa.bwt added
6668a54a12714_GRCh38.primary_assembly.genome.fa.pac added
6668a17d0f69_GRCh38.primary_assembly.genome.fa.sa added
6668a43d144d9_GRCh38.primary_assembly.genome.fa added
6668a2beea825_hs37d5.fa.fai added
6668a73e69c99_hs37d5.fa.amb added
6668a4d59c515_hs37d5.fa.ann added
6668ac5a296c_hs37d5.fa.bwt added
6668a69df91e6_hs37d5.fa.pac added
6668a22b4ba65_hs37d5.fa.sa added
6668a1eb95e35_hs37d5.fa added
6668a2e897c69_complete_ref_lens.bin added
6668a28ea8c40_ctable.bin added
6668a15e3172a_ctg_offsets.bin added
6668a6d520fb6_duplicate_clusters.tsv added
6668a43484a71_info.json added
6668a6469bec8_mphf.bin added
6668a631b5b6f_pos.bin added
6668a7b77477f_pre_indexing.log added
6668a718b4bf5_rank.bin added
6668a6fc0c66c_ref_indexing.log added
6668a5131dbda_refAccumLengths.bin added
6668a211f3cf8_reflengths.bin added
6668a59216e6a_refseq.bin added
6668a1f91662_seq.bin added
6668a200676b2_versionInfo.json added
6668a3ceae2e9_salmon_index added
6668a70d5809a_chrLength.txt added
6668a478f7ebc_chrName.txt added
6668adde10f4_chrNameLength.txt added
6668a1c09a8d2_chrStart.txt added
6668a2fd020a7_exonGeTrInfo.tab added
6668a627f3808_exonInfo.tab added
6668a1d86b83c_geneInfo.tab added
6668a73a16581_Genome added
6668ae6de02d_genomeParameters.txt added
6668a116d54d5_Log.out added
6668a40fb2a96_SA added
6668a1ac80999_SAindex added
6668a7b4ce6bb_sjdbInfo.txt added
6668a63afe4fb_sjdbList.fromGTF.out.tab added
6668a398167ce_sjdbList.out.tab added
6668a29d66325_transcriptInfo.tab added
6668ac9a713b_GRCh38.GENCODE.v42_100 added
6668a4f647ef8_knownGene_hg38.sql added
6668a172872db_knownGene_hg38.txt added
6668a4fe2bbac_refGene_hg38.sql added
6668a33ce3dc0_refGene_hg38.txt added
6668a7a43ce4a_knownGene_mm39.sql added
6668a4b5a032b_knownGene_mm39.txt added
6668a255989b6_refGene_mm39.sql added
6668a6a0494b6_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/Rtmp2G0U0w/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
18.269 1.249 19.682
ReUseData.Rcheck/ReUseData-Ex.timings
| name | user | system | elapsed | |
| dataHub-class | 6.370 | 0.255 | 6.631 | |
| dataSearch | 1.276 | 0.038 | 1.314 | |
| dataUpdate | 0 | 0 | 0 | |
| getCloudData | 2.791 | 0.126 | 3.331 | |
| getData | 0 | 0 | 0 | |
| meta_data | 0 | 0 | 0 | |
| recipeHub-class | 0.131 | 0.002 | 0.133 | |
| recipeLoad | 1.341 | 0.065 | 1.408 | |
| recipeMake | 0 | 0 | 0 | |
| recipeSearch | 0.541 | 0.005 | 0.546 | |
| recipeUpdate | 0 | 0 | 0 | |