Qian Liu
| Snapshot Date: 2024-12-19 13:00 -0500 (Thu, 19 Dec 2024) |
| 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 2024-12-23 12:04 -0500 (Mon, 23 Dec 2024).
| 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" | 4744 |
| palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" | 4487 |
| merida1 | macOS 12.7.5 Monterey | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4515 |
| kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4467 |
| 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 | | ||||||||
|
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: 2024-12-20 04:43:28 -0500 (Fri, 20 Dec 2024) |
| EndedAt: 2024-12-20 04:46:13 -0500 (Fri, 20 Dec 2024) |
| EllapsedTime: 165.1 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 4.4.2 (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 6.025 0.252 6.28
* 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...
68a082871881b_GRCh38.primary_assembly.genome.fa.1.bt2 added
68a0827a6d460_GRCh38.primary_assembly.genome.fa.2.bt2 added
68a086d6a9158_GRCh38.primary_assembly.genome.fa.3.bt2 added
68a081636a5d4_GRCh38.primary_assembly.genome.fa.4.bt2 added
68a08700f464f_GRCh38.primary_assembly.genome.fa.rev.1.bt2 added
68a08827f139_GRCh38.primary_assembly.genome.fa.rev.2.bt2 added
68a08de43e02_outfile.txt added
68a085cd7163_GRCh37_to_GRCh38.chain added
68a085539938c_GRCh37_to_NCBI34.chain added
68a08566f995c_GRCh37_to_NCBI35.chain added
68a0838f8a5a6_GRCh37_to_NCBI36.chain added
68a083507ea99_GRCh38_to_GRCh37.chain added
68a0858402e13_GRCh38_to_NCBI34.chain added
68a0844dcb8fc_GRCh38_to_NCBI35.chain added
68a0888fb398_GRCh38_to_NCBI36.chain added
68a08554fe2ca_NCBI34_to_GRCh37.chain added
68a085bb78b7a_NCBI34_to_GRCh38.chain added
68a084f32a450_NCBI35_to_GRCh37.chain added
68a087a16eeee_NCBI35_to_GRCh38.chain added
68a0831538d37_NCBI36_to_GRCh37.chain added
68a086e1f582e_NCBI36_to_GRCh38.chain added
68a0861aa4f97_GRCm38_to_NCBIM36.chain added
68a08f66d19b_GRCm38_to_NCBIM37.chain added
68a081e326fba_NCBIM36_to_GRCm38.chain added
68a086acc8f42_NCBIM37_to_GRCm38.chain added
68a0838bf8eb_1000G_omni2.5.b37.vcf.gz added
68a08e51df54_1000G_omni2.5.b37.vcf.gz.tbi added
68a0841952716_Mills_and_1000G_gold_standard.indels.b37.vcf.gz added
68a08dfbe6c3_Mills_and_1000G_gold_standard.indels.b37.vcf.gz.tbi added
68a081bc710e4_1000G_omni2.5.hg38.vcf.gz added
68a0863ba1727_1000G_omni2.5.hg38.vcf.gz.tbi added
68a08366d6ede_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz added
68a08436de544_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz.tbi added
68a085124a87f_af-only-gnomad.raw.sites.vcf added
68a084ca414b3_af-only-gnomad.raw.sites.vcf.idx added
68a08337d2b94_Mutect2-exome-panel.vcf.idx added
68a08594c99b8_Mutect2-WGS-panel-b37.vcf added
68a085a8852b5_Mutect2-WGS-panel-b37.vcf.idx added
68a08394a9cf7_small_exac_common_3.vcf added
68a082e862d45_small_exac_common_3.vcf.idx added
68a0830f7ec12_1000g_pon.hg38.vcf.gz added
68a087243429d_1000g_pon.hg38.vcf.gz.tbi added
68a08638e17de_af-only-gnomad.hg38.vcf.gz added
68a089381a25_af-only-gnomad.hg38.vcf.gz.tbi added
68a08371ffb99_small_exac_common_3.hg38.vcf.gz added
68a086c1dcb76_small_exac_common_3.hg38.vcf.gz.tbi added
68a085e87fcf0_gencode.v41.annotation.gtf added
68a0812d78714_gencode.v42.annotation.gtf added
68a083b506fc6_gencode.vM30.annotation.gtf added
68a08589eebde_gencode.vM31.annotation.gtf added
68a08442b144b_gencode.v41.transcripts.fa added
68a08296fc7f4_gencode.v41.transcripts.fa.fai added
68a083a493b75_gencode.v42.transcripts.fa added
68a085391e5e7_gencode.v42.transcripts.fa.fai added
68a0847a237af_gencode.vM30.pc_transcripts.fa added
68a082515cab7_gencode.vM30.pc_transcripts.fa.fai added
68a08571dded2_gencode.vM31.pc_transcripts.fa added
68a0855f41703_gencode.vM31.pc_transcripts.fa.fai added
68a0866aaf1cd_GRCh38.primary_assembly.genome.fa.1.ht2 added
68a086519c595_GRCh38.primary_assembly.genome.fa.2.ht2 added
68a0871bb27e8_GRCh38.primary_assembly.genome.fa.3.ht2 added
68a084a6508f4_GRCh38.primary_assembly.genome.fa.4.ht2 added
68a081b873473_GRCh38.primary_assembly.genome.fa.5.ht2 added
68a0835290d2c_GRCh38.primary_assembly.genome.fa.6.ht2 added
68a081b89b174_GRCh38.primary_assembly.genome.fa.7.ht2 added
68a08682b4926_GRCh38.primary_assembly.genome.fa.8.ht2 added
68a0868a638c0_GRCh38_full_analysis_set_plus_decoy_hla.fa.fai added
68a0874d64b2c_GRCh38_full_analysis_set_plus_decoy_hla.fa.amb added
68a0842b39bdc_GRCh38_full_analysis_set_plus_decoy_hla.fa.ann added
68a0821f0d5b7_GRCh38_full_analysis_set_plus_decoy_hla.fa.bwt added
68a08235c7871_GRCh38_full_analysis_set_plus_decoy_hla.fa.pac added
68a0873ab87ee_GRCh38_full_analysis_set_plus_decoy_hla.fa.sa added
68a0814341855_GRCh38_full_analysis_set_plus_decoy_hla.fa added
68a086ea904f_GRCh38.primary_assembly.genome.fa.fai added
68a087ce3a213_GRCh38.primary_assembly.genome.fa.amb added
68a084b5413ee_GRCh38.primary_assembly.genome.fa.ann added
68a0873085bc5_GRCh38.primary_assembly.genome.fa.bwt added
68a085b6b9f03_GRCh38.primary_assembly.genome.fa.pac added
68a085e2b9b02_GRCh38.primary_assembly.genome.fa.sa added
68a082e58cb8c_GRCh38.primary_assembly.genome.fa added
68a08340a8ae1_hs37d5.fa.fai added
68a082256af4e_hs37d5.fa.amb added
68a0857c89380_hs37d5.fa.ann added
68a086e53c656_hs37d5.fa.bwt added
68a0875e89535_hs37d5.fa.pac added
68a081f6acb2f_hs37d5.fa.sa added
68a081369910d_hs37d5.fa added
68a084d067407_complete_ref_lens.bin added
68a08755ee233_ctable.bin added
68a087a1482da_ctg_offsets.bin added
68a083220399c_duplicate_clusters.tsv added
68a08671a0a1b_info.json added
68a0844798bcf_mphf.bin added
68a084da76e0f_pos.bin added
68a081c431747_pre_indexing.log added
68a0860033d43_rank.bin added
68a0835d2b736_ref_indexing.log added
68a084e95008_refAccumLengths.bin added
68a0854d9886f_reflengths.bin added
68a0878865312_refseq.bin added
68a0826da25bf_seq.bin added
68a08783600e1_versionInfo.json added
68a086c31db00_salmon_index added
68a083b0e3e14_chrLength.txt added
68a087f209130_chrName.txt added
68a0869157d13_chrNameLength.txt added
68a086625203_chrStart.txt added
68a087228ecf6_exonGeTrInfo.tab added
68a0844811c17_exonInfo.tab added
68a08648ded05_geneInfo.tab added
68a082081b882_Genome added
68a08788ba6f8_genomeParameters.txt added
68a086e49c53_Log.out added
68a08784a4c02_SA added
68a0866df6d4f_SAindex added
68a087ccd3188_sjdbInfo.txt added
68a0817b51732_sjdbList.fromGTF.out.tab added
68a087a48fe5c_sjdbList.out.tab added
68a0849d3a58f_transcriptInfo.tab added
68a08d13f965_GRCh38.GENCODE.v42_100 added
68a08745d8137_knownGene_hg38.sql added
68a087bf3df2b_knownGene_hg38.txt added
68a08742e0380_refGene_hg38.sql added
68a0838d70d06_refGene_hg38.txt added
68a08499b4d3b_knownGene_mm39.sql added
68a0810711ac7_knownGene_mm39.txt added
68a0818da4a49_refGene_mm39.sql added
68a087f6e0471_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/RtmpJ1hOoU/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
18.863 1.579 20.752
ReUseData.Rcheck/ReUseData-Ex.timings
| name | user | system | elapsed | |
| dataHub-class | 6.025 | 0.252 | 6.280 | |
| dataSearch | 1.118 | 0.029 | 1.147 | |
| dataUpdate | 0 | 0 | 0 | |
| getCloudData | 2.503 | 0.092 | 3.320 | |
| getData | 0 | 0 | 0 | |
| meta_data | 0.000 | 0.000 | 0.001 | |
| recipeHub-class | 0.127 | 0.012 | 0.141 | |
| recipeLoad | 1.306 | 0.034 | 1.341 | |
| recipeMake | 0 | 0 | 0 | |
| recipeSearch | 0.601 | 0.005 | 0.608 | |
| recipeUpdate | 0 | 0 | 0 | |