Qian Liu
| Snapshot Date: 2024-07-05 14:00 -0400 (Fri, 05 Jul 2024) |
| git_url: https://git.bioconductor.org/packages/ReUseData |
| git_branch: devel |
| git_last_commit: cbe4e73 |
| git_last_commit_date: 2024-04-30 11:46:52 -0400 (Tue, 30 Apr 2024) |
| Back to Multiple platform build/check report for BioC 3.20: simplified long |
|
This page was generated on 2024-07-06 11:39 -0400 (Sat, 06 Jul 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4643 |
| palomino6 | Windows Server 2022 Datacenter | x64 | 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" | 4414 |
| lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4442 |
| kjohnson3 | macOS 13.6.5 Ventura | arm64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4391 |
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 3833 |
| 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 1695/2243 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| ReUseData 1.5.0 (landing page) Qian Liu
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino6 | Windows Server 2022 Datacenter / x64 | ... NOT SUPPORTED ... | ||||||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson3 | macOS 13.6.5 Ventura / arm64 | OK | OK | OK | OK | | ||||||||
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | NA | ERROR | skipped | ||||||||||
|
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: 1.5.0 |
| 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_1.5.0.tar.gz |
| StartedAt: 2024-07-06 02:25:28 -0400 (Sat, 06 Jul 2024) |
| EndedAt: 2024-07-06 02:28:23 -0400 (Sat, 06 Jul 2024) |
| EllapsedTime: 175.3 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_1.5.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/ReUseData.Rcheck’
* using R version 4.4.1 (2024-06-14)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
* running under: Ubuntu 22.04.4 LTS
* using session charset: UTF-8
* checking for file ‘ReUseData/DESCRIPTION’ ... OK
* this is package ‘ReUseData’ version ‘1.5.0’
* 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 6.368 0.272 6.645
* 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 4.4.1 (2024-06-14) -- "Race for Your Life"
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...
cbd02608be0c8_GRCh38.primary_assembly.genome.fa.1.bt2 added
cbd027043d960_GRCh38.primary_assembly.genome.fa.2.bt2 added
cbd0272223934_GRCh38.primary_assembly.genome.fa.3.bt2 added
cbd0214601d20_GRCh38.primary_assembly.genome.fa.4.bt2 added
cbd02662ddb23_GRCh38.primary_assembly.genome.fa.rev.1.bt2 added
cbd02586cf024_GRCh38.primary_assembly.genome.fa.rev.2.bt2 added
cbd021df7529_outfile.txt added
cbd0228d2d6a5_GRCh37_to_GRCh38.chain added
cbd023a15cfc0_GRCh37_to_NCBI34.chain added
cbd0225ba7a1b_GRCh37_to_NCBI35.chain added
cbd022998b199_GRCh37_to_NCBI36.chain added
cbd024690636_GRCh38_to_GRCh37.chain added
cbd02602846b8_GRCh38_to_NCBI34.chain added
cbd0237ddb261_GRCh38_to_NCBI35.chain added
cbd025abb0a2b_GRCh38_to_NCBI36.chain added
cbd02573d5bf8_NCBI34_to_GRCh37.chain added
cbd02486b366c_NCBI34_to_GRCh38.chain added
cbd026cf6832a_NCBI35_to_GRCh37.chain added
cbd0276eaa8a1_NCBI35_to_GRCh38.chain added
cbd021c442eb9_NCBI36_to_GRCh37.chain added
cbd027dc34f37_NCBI36_to_GRCh38.chain added
cbd0225fa01f8_GRCm38_to_NCBIM36.chain added
cbd027d135264_GRCm38_to_NCBIM37.chain added
cbd02121a134d_NCBIM36_to_GRCm38.chain added
cbd025e51832d_NCBIM37_to_GRCm38.chain added
cbd022c7b63f1_1000G_omni2.5.b37.vcf.gz added
cbd0260418ade_1000G_omni2.5.b37.vcf.gz.tbi added
cbd0217f025c2_Mills_and_1000G_gold_standard.indels.b37.vcf.gz added
cbd023ca61469_Mills_and_1000G_gold_standard.indels.b37.vcf.gz.tbi added
cbd022127b52_1000G_omni2.5.hg38.vcf.gz added
cbd0263aab7ba_1000G_omni2.5.hg38.vcf.gz.tbi added
cbd021d31f531_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz added
cbd02725654b2_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz.tbi added
cbd0255ccf0ee_af-only-gnomad.raw.sites.vcf added
cbd0231921251_af-only-gnomad.raw.sites.vcf.idx added
cbd0258842fd5_Mutect2-exome-panel.vcf.idx added
cbd022e39e112_Mutect2-WGS-panel-b37.vcf added
cbd023371877a_Mutect2-WGS-panel-b37.vcf.idx added
cbd02157067a_small_exac_common_3.vcf added
cbd02684fb0d2_small_exac_common_3.vcf.idx added
cbd02592c0195_1000g_pon.hg38.vcf.gz added
cbd022aefb813_1000g_pon.hg38.vcf.gz.tbi added
cbd026cb8b708_af-only-gnomad.hg38.vcf.gz added
cbd023954484d_af-only-gnomad.hg38.vcf.gz.tbi added
cbd0262cd6a74_small_exac_common_3.hg38.vcf.gz added
cbd024773c134_small_exac_common_3.hg38.vcf.gz.tbi added
cbd021091a445_gencode.v41.annotation.gtf added
cbd022b38a0e0_gencode.v42.annotation.gtf added
cbd02346a445e_gencode.vM30.annotation.gtf added
cbd0277c4ce7_gencode.vM31.annotation.gtf added
cbd02477ccf9a_gencode.v41.transcripts.fa added
cbd02322d9395_gencode.v41.transcripts.fa.fai added
cbd022d764edf_gencode.v42.transcripts.fa added
cbd02449021fe_gencode.v42.transcripts.fa.fai added
cbd024447a6e2_gencode.vM30.pc_transcripts.fa added
cbd02bc7d20d_gencode.vM30.pc_transcripts.fa.fai added
cbd02710b85ef_gencode.vM31.pc_transcripts.fa added
cbd02248931c0_gencode.vM31.pc_transcripts.fa.fai added
cbd0223b7f7cf_GRCh38.primary_assembly.genome.fa.1.ht2 added
cbd022db19a58_GRCh38.primary_assembly.genome.fa.2.ht2 added
cbd02269bad12_GRCh38.primary_assembly.genome.fa.3.ht2 added
cbd02762af89_GRCh38.primary_assembly.genome.fa.4.ht2 added
cbd024ae38f8a_GRCh38.primary_assembly.genome.fa.5.ht2 added
cbd0218f201c5_GRCh38.primary_assembly.genome.fa.6.ht2 added
cbd025d2fa078_GRCh38.primary_assembly.genome.fa.7.ht2 added
cbd027c75a1db_GRCh38.primary_assembly.genome.fa.8.ht2 added
cbd027176319a_GRCh38_full_analysis_set_plus_decoy_hla.fa.fai added
cbd02b69818a_GRCh38_full_analysis_set_plus_decoy_hla.fa.amb added
cbd022fe72956_GRCh38_full_analysis_set_plus_decoy_hla.fa.ann added
cbd0272cd3815_GRCh38_full_analysis_set_plus_decoy_hla.fa.bwt added
cbd0273b9325d_GRCh38_full_analysis_set_plus_decoy_hla.fa.pac added
cbd029132aeb_GRCh38_full_analysis_set_plus_decoy_hla.fa.sa added
cbd021dbcf028_GRCh38_full_analysis_set_plus_decoy_hla.fa added
cbd026071e965_GRCh38.primary_assembly.genome.fa.fai added
cbd0242677339_GRCh38.primary_assembly.genome.fa.amb added
cbd028a5a9d_GRCh38.primary_assembly.genome.fa.ann added
cbd0227e5aa99_GRCh38.primary_assembly.genome.fa.bwt added
cbd0252f9177e_GRCh38.primary_assembly.genome.fa.pac added
cbd022bc2fb7d_GRCh38.primary_assembly.genome.fa.sa added
cbd025c4feef7_GRCh38.primary_assembly.genome.fa added
cbd025a756465_hs37d5.fa.fai added
cbd02733fcb17_hs37d5.fa.amb added
cbd02e7d828c_hs37d5.fa.ann added
cbd027ebb345_hs37d5.fa.bwt added
cbd0237cfed15_hs37d5.fa.pac added
cbd0252c5296e_hs37d5.fa.sa added
cbd0213b38552_hs37d5.fa added
cbd0228db7304_complete_ref_lens.bin added
cbd02774e5b2f_ctable.bin added
cbd02376b7d21_ctg_offsets.bin added
cbd02568d0d5d_duplicate_clusters.tsv added
cbd021dea0841_info.json added
cbd023ece2cab_mphf.bin added
cbd0221709ce7_pos.bin added
cbd0236dc0a06_pre_indexing.log added
cbd021bfdcd23_rank.bin added
cbd021de63ec2_ref_indexing.log added
cbd0228523ba1_refAccumLengths.bin added
cbd0227674ead_reflengths.bin added
cbd024dcd6818_refseq.bin added
cbd021b1f73b6_seq.bin added
cbd021b20810a_versionInfo.json added
cbd0256e09304_salmon_index added
cbd0238dc63de_chrLength.txt added
cbd027b926a70_chrName.txt added
cbd021948063d_chrNameLength.txt added
cbd023966be7b_chrStart.txt added
cbd0223781509_exonGeTrInfo.tab added
cbd026c411dbb_exonInfo.tab added
cbd026529b9f9_geneInfo.tab added
cbd027fc80401_Genome added
cbd0246b68221_genomeParameters.txt added
cbd0258698510_Log.out added
cbd02e45868d_SA added
cbd024ea23566_SAindex added
cbd0210397226_sjdbInfo.txt added
cbd02610aaffc_sjdbList.fromGTF.out.tab added
cbd026255bab8_sjdbList.out.tab added
cbd023914e52a_transcriptInfo.tab added
cbd0258590b2b_GRCh38.GENCODE.v42_100 added
cbd0219c137d9_knownGene_hg38.sql added
cbd02fa1f287_knownGene_hg38.txt added
cbd027643136c_refGene_hg38.sql added
cbd02588f6484_refGene_hg38.txt added
cbd0231128f6e_knownGene_mm39.sql added
cbd022d1f1d73_knownGene_mm39.txt added
cbd02748d31a7_refGene_mm39.sql added
cbd024ef8ce31_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/RtmpLiS7Hj/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
20.652 1.303 22.280
ReUseData.Rcheck/ReUseData-Ex.timings
| name | user | system | elapsed | |
| dataHub-class | 6.368 | 0.272 | 6.645 | |
| dataSearch | 1.127 | 0.016 | 1.142 | |
| dataUpdate | 0 | 0 | 0 | |
| getCloudData | 2.775 | 0.072 | 3.562 | |
| getData | 0 | 0 | 0 | |
| meta_data | 0.001 | 0.000 | 0.000 | |
| recipeHub-class | 0.121 | 0.000 | 0.120 | |
| recipeLoad | 1.153 | 0.028 | 1.181 | |
| recipeMake | 0 | 0 | 0 | |
| recipeSearch | 0.518 | 0.004 | 0.521 | |
| recipeUpdate | 0 | 0 | 0 | |