Qian Liu
| Snapshot Date: 2025-01-19 12:27 -0500 (Sun, 19 Jan 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 2025-01-20 12:16 -0500 (Mon, 20 Jan 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4746 |
| palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" | 4493 |
| 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 ... | ||||||||||||
|
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: 2025-01-20 00:15:11 -0500 (Mon, 20 Jan 2025) |
| EndedAt: 2025-01-20 00:17:55 -0500 (Mon, 20 Jan 2025) |
| EllapsedTime: 164.2 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 4.4.2 (2024-10-31)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0
GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0
* running under: Ubuntu 24.04.1 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 5.863 0.276 6.142
* 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 4.4.2 (2024-10-31) -- "Pile of Leaves"
Copyright (C) 2024 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...
2c20b87106416d_GRCh38.primary_assembly.genome.fa.1.bt2 added
2c20b862e79eaa_GRCh38.primary_assembly.genome.fa.2.bt2 added
2c20b822455b87_GRCh38.primary_assembly.genome.fa.3.bt2 added
2c20b87830f16c_GRCh38.primary_assembly.genome.fa.4.bt2 added
2c20b8414d0077_GRCh38.primary_assembly.genome.fa.rev.1.bt2 added
2c20b82814f5f8_GRCh38.primary_assembly.genome.fa.rev.2.bt2 added
2c20b84ded0356_outfile.txt added
2c20b8568b4296_GRCh37_to_GRCh38.chain added
2c20b87221e86e_GRCh37_to_NCBI34.chain added
2c20b84f5094fc_GRCh37_to_NCBI35.chain added
2c20b85ba23cce_GRCh37_to_NCBI36.chain added
2c20b8451580a7_GRCh38_to_GRCh37.chain added
2c20b858a60c45_GRCh38_to_NCBI34.chain added
2c20b835cb0806_GRCh38_to_NCBI35.chain added
2c20b81b9e9ad3_GRCh38_to_NCBI36.chain added
2c20b84279863_NCBI34_to_GRCh37.chain added
2c20b8605769b_NCBI34_to_GRCh38.chain added
2c20b88d5490c_NCBI35_to_GRCh37.chain added
2c20b85da02a9_NCBI35_to_GRCh38.chain added
2c20b840646a24_NCBI36_to_GRCh37.chain added
2c20b856d564cd_NCBI36_to_GRCh38.chain added
2c20b8775245e9_GRCm38_to_NCBIM36.chain added
2c20b865f06ede_GRCm38_to_NCBIM37.chain added
2c20b83b8a8ed9_NCBIM36_to_GRCm38.chain added
2c20b83e09158e_NCBIM37_to_GRCm38.chain added
2c20b85882053a_1000G_omni2.5.b37.vcf.gz added
2c20b81d0afbc2_1000G_omni2.5.b37.vcf.gz.tbi added
2c20b8788c9fcf_Mills_and_1000G_gold_standard.indels.b37.vcf.gz added
2c20b81c714dec_Mills_and_1000G_gold_standard.indels.b37.vcf.gz.tbi added
2c20b8229a0f4f_1000G_omni2.5.hg38.vcf.gz added
2c20b85ae60ae1_1000G_omni2.5.hg38.vcf.gz.tbi added
2c20b8d778f5a_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz added
2c20b8581adf9_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz.tbi added
2c20b87d2b6668_af-only-gnomad.raw.sites.vcf added
2c20b85a880c6_af-only-gnomad.raw.sites.vcf.idx added
2c20b846ceae70_Mutect2-exome-panel.vcf.idx added
2c20b825405c61_Mutect2-WGS-panel-b37.vcf added
2c20b85395841c_Mutect2-WGS-panel-b37.vcf.idx added
2c20b81d59f107_small_exac_common_3.vcf added
2c20b8176244cf_small_exac_common_3.vcf.idx added
2c20b822e61918_1000g_pon.hg38.vcf.gz added
2c20b878fc2dd5_1000g_pon.hg38.vcf.gz.tbi added
2c20b85c77c576_af-only-gnomad.hg38.vcf.gz added
2c20b87b8c255d_af-only-gnomad.hg38.vcf.gz.tbi added
2c20b82ec735db_small_exac_common_3.hg38.vcf.gz added
2c20b878166049_small_exac_common_3.hg38.vcf.gz.tbi added
2c20b87fb3bdc1_gencode.v41.annotation.gtf added
2c20b834ccac77_gencode.v42.annotation.gtf added
2c20b8eba955_gencode.vM30.annotation.gtf added
2c20b858dc06a_gencode.vM31.annotation.gtf added
2c20b87531169b_gencode.v41.transcripts.fa added
2c20b857c10e23_gencode.v41.transcripts.fa.fai added
2c20b87ce00653_gencode.v42.transcripts.fa added
2c20b85b218579_gencode.v42.transcripts.fa.fai added
2c20b8134b9cfc_gencode.vM30.pc_transcripts.fa added
2c20b83ae91be1_gencode.vM30.pc_transcripts.fa.fai added
2c20b833a38ab4_gencode.vM31.pc_transcripts.fa added
2c20b8305698be_gencode.vM31.pc_transcripts.fa.fai added
2c20b83375bbb0_GRCh38.primary_assembly.genome.fa.1.ht2 added
2c20b85014d8a0_GRCh38.primary_assembly.genome.fa.2.ht2 added
2c20b852f0a80d_GRCh38.primary_assembly.genome.fa.3.ht2 added
2c20b8e5bc691_GRCh38.primary_assembly.genome.fa.4.ht2 added
2c20b85d8c67fa_GRCh38.primary_assembly.genome.fa.5.ht2 added
2c20b858725607_GRCh38.primary_assembly.genome.fa.6.ht2 added
2c20b8b872cfa_GRCh38.primary_assembly.genome.fa.7.ht2 added
2c20b86334e8c0_GRCh38.primary_assembly.genome.fa.8.ht2 added
2c20b81f410477_GRCh38_full_analysis_set_plus_decoy_hla.fa.fai added
2c20b830c7895b_GRCh38_full_analysis_set_plus_decoy_hla.fa.amb added
2c20b836ca6cdd_GRCh38_full_analysis_set_plus_decoy_hla.fa.ann added
2c20b83c9af57e_GRCh38_full_analysis_set_plus_decoy_hla.fa.bwt added
2c20b84829ce2a_GRCh38_full_analysis_set_plus_decoy_hla.fa.pac added
2c20b859b085f5_GRCh38_full_analysis_set_plus_decoy_hla.fa.sa added
2c20b835972353_GRCh38_full_analysis_set_plus_decoy_hla.fa added
2c20b824a193a1_GRCh38.primary_assembly.genome.fa.fai added
2c20b8553cab53_GRCh38.primary_assembly.genome.fa.amb added
2c20b8645e592f_GRCh38.primary_assembly.genome.fa.ann added
2c20b81cb7f3ea_GRCh38.primary_assembly.genome.fa.bwt added
2c20b854f06914_GRCh38.primary_assembly.genome.fa.pac added
2c20b8192b05a6_GRCh38.primary_assembly.genome.fa.sa added
2c20b81da39d40_GRCh38.primary_assembly.genome.fa added
2c20b85a7e297e_hs37d5.fa.fai added
2c20b8e5c1c41_hs37d5.fa.amb added
2c20b87564ab63_hs37d5.fa.ann added
2c20b8575e2fd1_hs37d5.fa.bwt added
2c20b8697da1bb_hs37d5.fa.pac added
2c20b88b0485f_hs37d5.fa.sa added
2c20b812474bb2_hs37d5.fa added
2c20b81d212c6f_complete_ref_lens.bin added
2c20b83906e11d_ctable.bin added
2c20b845bd0762_ctg_offsets.bin added
2c20b86d36050f_duplicate_clusters.tsv added
2c20b8bf7892b_info.json added
2c20b85418cdf4_mphf.bin added
2c20b84ac26d0a_pos.bin added
2c20b86469df32_pre_indexing.log added
2c20b85f9ffaee_rank.bin added
2c20b82df755ca_ref_indexing.log added
2c20b83aae3a9_refAccumLengths.bin added
2c20b810678449_reflengths.bin added
2c20b864c1c2a7_refseq.bin added
2c20b84045d928_seq.bin added
2c20b858915273_versionInfo.json added
2c20b83e72489d_salmon_index added
2c20b875dcfc7b_chrLength.txt added
2c20b87d32e614_chrName.txt added
2c20b813aef3f0_chrNameLength.txt added
2c20b85a3b55aa_chrStart.txt added
2c20b819ead9ff_exonGeTrInfo.tab added
2c20b8689f5d04_exonInfo.tab added
2c20b873665b50_geneInfo.tab added
2c20b8378e773f_Genome added
2c20b8431d8682_genomeParameters.txt added
2c20b81c27792_Log.out added
2c20b82cf322a2_SA added
2c20b81a7bb653_SAindex added
2c20b86b40194d_sjdbInfo.txt added
2c20b835a36b01_sjdbList.fromGTF.out.tab added
2c20b82cc30205_sjdbList.out.tab added
2c20b886145bc_transcriptInfo.tab added
2c20b86eaa4c1e_GRCh38.GENCODE.v42_100 added
2c20b872800967_knownGene_hg38.sql added
2c20b875974acb_knownGene_hg38.txt added
2c20b87aa1d549_refGene_hg38.sql added
2c20b84698d75b_refGene_hg38.txt added
2c20b84059b7d5_knownGene_mm39.sql added
2c20b85f0bb47b_knownGene_mm39.txt added
2c20b82638d249_refGene_mm39.sql added
2c20b86e510da0_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/RtmpBWYDmM/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
19.181 1.269 20.690
ReUseData.Rcheck/ReUseData-Ex.timings
| name | user | system | elapsed | |
| dataHub-class | 5.863 | 0.276 | 6.142 | |
| dataSearch | 1.115 | 0.023 | 1.137 | |
| dataUpdate | 0 | 0 | 0 | |
| getCloudData | 2.667 | 0.121 | 3.608 | |
| getData | 0 | 0 | 0 | |
| meta_data | 0.001 | 0.000 | 0.000 | |
| recipeHub-class | 0.125 | 0.002 | 0.128 | |
| recipeLoad | 1.327 | 0.052 | 1.380 | |
| recipeMake | 0 | 0 | 0 | |
| recipeSearch | 0.537 | 0.022 | 0.559 | |
| recipeUpdate | 0 | 0 | 0 | |