Qian Liu
| Snapshot Date: 2025-01-23 13:40 -0500 (Thu, 23 Jan 2025) |
| git_url: https://git.bioconductor.org/packages/ReUseData |
| git_branch: devel |
| git_last_commit: 85fc756 |
| git_last_commit_date: 2024-10-29 11:17:22 -0500 (Tue, 29 Oct 2024) |
| Back to Multiple platform build/check report for BioC 3.21: simplified long |
|
This page was generated on 2025-01-24 11:41 -0500 (Fri, 24 Jan 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | R Under development (unstable) (2025-01-20 r87609) -- "Unsuffered Consequences" | 4609 |
| palomino7 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2025-01-21 r87610 ucrt) -- "Unsuffered Consequences" | 4393 |
| lconway | macOS 12.7.1 Monterey | x86_64 | R Under development (unstable) (2025-01-20 r87609) -- "Unsuffered Consequences" | 3839 |
| kjohnson3 | macOS 13.7.1 Ventura | arm64 | R Under development (unstable) (2025-01-20 r87609) -- "Unsuffered Consequences" | 3835 |
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | R Under development (unstable) (2024-11-24 r87369) -- "Unsuffered Consequences" | 4408 |
| 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 1722/2286 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| ReUseData 1.7.0 (landing page) Qian Liu
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino7 | Windows Server 2022 Datacenter / x64 | ... NOT SUPPORTED ... | ||||||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson3 | macOS 13.7.1 Ventura / arm64 | OK | OK | OK | OK | | ||||||||
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / 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: 1.7.0 |
| Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:ReUseData.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings ReUseData_1.7.0.tar.gz |
| StartedAt: 2025-01-23 20:06:40 -0500 (Thu, 23 Jan 2025) |
| EndedAt: 2025-01-23 20:09:16 -0500 (Thu, 23 Jan 2025) |
| EllapsedTime: 156.3 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: ReUseData.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:ReUseData.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings ReUseData_1.7.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/ReUseData.Rcheck’
* using R Under development (unstable) (2025-01-20 r87609)
* using platform: x86_64-apple-darwin20
* R was compiled by
Apple clang version 14.0.0 (clang-1400.0.29.202)
GNU Fortran (GCC) 14.2.0
* running under: macOS Monterey 12.7.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘ReUseData/DESCRIPTION’ ... OK
* this is package ‘ReUseData’ version ‘1.7.0’
* 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 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 7.951 1.017 9.701
* 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 running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: 1 NOTE
See
‘/Users/biocbuild/bbs-3.21-bioc/meat/ReUseData.Rcheck/00check.log’
for details.
ReUseData.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL ReUseData ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library’ * installing *source* package ‘ReUseData’ ... ** this is package ‘ReUseData’ version ‘1.7.0’ ** 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 Under development (unstable) (2025-01-20 r87609) -- "Unsuffered Consequences"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20
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...
9a4f59725894_GRCh38.primary_assembly.genome.fa.1.bt2 added
9a4f62158a6c_GRCh38.primary_assembly.genome.fa.2.bt2 added
9a4f7432eac2_GRCh38.primary_assembly.genome.fa.3.bt2 added
9a4f3ad2a227_GRCh38.primary_assembly.genome.fa.4.bt2 added
9a4f5a93cc9c_GRCh38.primary_assembly.genome.fa.rev.1.bt2 added
9a4f1d5e4439_GRCh38.primary_assembly.genome.fa.rev.2.bt2 added
9a4f17d1093f_outfile.txt added
9a4f1cb61350_GRCh37_to_GRCh38.chain added
9a4f75adf7e9_GRCh37_to_NCBI34.chain added
9a4f706f1e5a_GRCh37_to_NCBI35.chain added
9a4ff31e061_GRCh37_to_NCBI36.chain added
9a4f13820812_GRCh38_to_GRCh37.chain added
9a4f3ddfdfbf_GRCh38_to_NCBI34.chain added
9a4f34da9455_GRCh38_to_NCBI35.chain added
9a4f7a40738e_GRCh38_to_NCBI36.chain added
9a4f1d62ae56_NCBI34_to_GRCh37.chain added
9a4f39a39f2c_NCBI34_to_GRCh38.chain added
9a4f25271f44_NCBI35_to_GRCh37.chain added
9a4f2b75bc6a_NCBI35_to_GRCh38.chain added
9a4f3ea4e970_NCBI36_to_GRCh37.chain added
9a4f3cd9d831_NCBI36_to_GRCh38.chain added
9a4f200982d_GRCm38_to_NCBIM36.chain added
9a4f7506b361_GRCm38_to_NCBIM37.chain added
9a4faeae14d_NCBIM36_to_GRCm38.chain added
9a4f426d8bd4_NCBIM37_to_GRCm38.chain added
9a4f25f72d5e_1000G_omni2.5.b37.vcf.gz added
9a4f6c389cb_1000G_omni2.5.b37.vcf.gz.tbi added
9a4ff8b71e5_Mills_and_1000G_gold_standard.indels.b37.vcf.gz added
9a4fbe2795c_Mills_and_1000G_gold_standard.indels.b37.vcf.gz.tbi added
9a4f418d8d1c_1000G_omni2.5.hg38.vcf.gz added
9a4f342b4ae3_1000G_omni2.5.hg38.vcf.gz.tbi added
9a4f64197d7_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz added
9a4f3c57a776_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz.tbi added
9a4f1eb352ed_af-only-gnomad.raw.sites.vcf added
9a4ff09555a_af-only-gnomad.raw.sites.vcf.idx added
9a4f2dc28f6c_Mutect2-exome-panel.vcf.idx added
9a4f405612ec_Mutect2-WGS-panel-b37.vcf added
9a4f52f464f3_Mutect2-WGS-panel-b37.vcf.idx added
9a4f2b0fb811_small_exac_common_3.vcf added
9a4f14fd7a2d_small_exac_common_3.vcf.idx added
9a4fd602b1f_1000g_pon.hg38.vcf.gz added
9a4f24af0715_1000g_pon.hg38.vcf.gz.tbi added
9a4f5efa0683_af-only-gnomad.hg38.vcf.gz added
9a4f70c1b32b_af-only-gnomad.hg38.vcf.gz.tbi added
9a4f3cda05e2_small_exac_common_3.hg38.vcf.gz added
9a4fdb857a4_small_exac_common_3.hg38.vcf.gz.tbi added
9a4f4181d705_gencode.v41.annotation.gtf added
9a4f334baadc_gencode.v42.annotation.gtf added
9a4f2cbe6bd3_gencode.vM30.annotation.gtf added
9a4f9990098_gencode.vM31.annotation.gtf added
9a4f1bf60014_gencode.v41.transcripts.fa added
9a4f337f2f63_gencode.v41.transcripts.fa.fai added
9a4f630026fe_gencode.v42.transcripts.fa added
9a4f1f002079_gencode.v42.transcripts.fa.fai added
9a4f4153f7d5_gencode.vM30.pc_transcripts.fa added
9a4f6fb3e274_gencode.vM30.pc_transcripts.fa.fai added
9a4fad866f7_gencode.vM31.pc_transcripts.fa added
9a4f54fe7b1_gencode.vM31.pc_transcripts.fa.fai added
9a4f40f41830_GRCh38.primary_assembly.genome.fa.1.ht2 added
9a4f596018a0_GRCh38.primary_assembly.genome.fa.2.ht2 added
9a4f33f0de37_GRCh38.primary_assembly.genome.fa.3.ht2 added
9a4fa8d0785_GRCh38.primary_assembly.genome.fa.4.ht2 added
9a4f30e8b22c_GRCh38.primary_assembly.genome.fa.5.ht2 added
9a4f7d097fc9_GRCh38.primary_assembly.genome.fa.6.ht2 added
9a4f7aa4a540_GRCh38.primary_assembly.genome.fa.7.ht2 added
9a4f4f5d4ba7_GRCh38.primary_assembly.genome.fa.8.ht2 added
9a4f7611e9a5_GRCh38_full_analysis_set_plus_decoy_hla.fa.fai added
9a4f12028c32_GRCh38_full_analysis_set_plus_decoy_hla.fa.amb added
9a4f65422fda_GRCh38_full_analysis_set_plus_decoy_hla.fa.ann added
9a4f5c53c525_GRCh38_full_analysis_set_plus_decoy_hla.fa.bwt added
9a4f7fb42f7d_GRCh38_full_analysis_set_plus_decoy_hla.fa.pac added
9a4fe99f90b_GRCh38_full_analysis_set_plus_decoy_hla.fa.sa added
9a4f1ead48aa_GRCh38_full_analysis_set_plus_decoy_hla.fa added
9a4f27da0a2_GRCh38.primary_assembly.genome.fa.fai added
9a4f5bcecf5_GRCh38.primary_assembly.genome.fa.amb added
9a4f3668cbc4_GRCh38.primary_assembly.genome.fa.ann added
9a4f1a19ccc4_GRCh38.primary_assembly.genome.fa.bwt added
9a4f13d2653f_GRCh38.primary_assembly.genome.fa.pac added
9a4f59f51543_GRCh38.primary_assembly.genome.fa.sa added
9a4f69470fd8_GRCh38.primary_assembly.genome.fa added
9a4f386163e7_hs37d5.fa.fai added
9a4f1e5ef9c_hs37d5.fa.amb added
9a4f1ed5ebbd_hs37d5.fa.ann added
9a4f6e67d51b_hs37d5.fa.bwt added
9a4f62d8183d_hs37d5.fa.pac added
9a4f591f7f7d_hs37d5.fa.sa added
9a4f22eb1541_hs37d5.fa added
9a4f77c0704f_complete_ref_lens.bin added
9a4f7b0d8ff4_ctable.bin added
9a4f37661b49_ctg_offsets.bin added
9a4f10897209_duplicate_clusters.tsv added
9a4f2f9db55a_info.json added
9a4f1aed4022_mphf.bin added
9a4f4e0d85fd_pos.bin added
9a4f59d7cd13_pre_indexing.log added
9a4f66d8c879_rank.bin added
9a4f2251b4af_ref_indexing.log added
9a4f222d5ec3_refAccumLengths.bin added
9a4f50a865bc_reflengths.bin added
9a4f5faf4302_refseq.bin added
9a4f6b586961_seq.bin added
9a4f796e9655_versionInfo.json added
9a4f4b4fe4bb_salmon_index added
9a4f6a31d79d_chrLength.txt added
9a4f6e42bae2_chrName.txt added
9a4f5efb83fb_chrNameLength.txt added
9a4f52960474_chrStart.txt added
9a4f76fe8607_exonGeTrInfo.tab added
9a4f40117299_exonInfo.tab added
9a4f397abbab_geneInfo.tab added
9a4f28b6f508_Genome added
9a4f390f51a_genomeParameters.txt added
9a4f21cb7fca_Log.out added
9a4f3732b81b_SA added
9a4f62d510ec_SAindex added
9a4f124a28a5_sjdbInfo.txt added
9a4f42b27204_sjdbList.fromGTF.out.tab added
9a4f515b86d1_sjdbList.out.tab added
9a4f4ff02d11_transcriptInfo.tab added
9a4f211ee017_GRCh38.GENCODE.v42_100 added
9a4f720a16fd_knownGene_hg38.sql added
9a4f746b7688_knownGene_hg38.txt added
9a4f3b33166e_refGene_hg38.sql added
9a4f1705ae1f_refGene_hg38.txt added
9a4f75ea8107_knownGene_mm39.sql added
9a4f76bd2f0b_knownGene_mm39.txt added
9a4f7e5bb813_refGene_mm39.sql added
9a4f37922834_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/Rtmp5wT1Kv/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
23.273 3.038 27.457
ReUseData.Rcheck/ReUseData-Ex.timings
| name | user | system | elapsed | |
| dataHub-class | 7.951 | 1.017 | 9.701 | |
| dataSearch | 1.457 | 0.066 | 1.539 | |
| dataUpdate | 0.000 | 0.000 | 0.001 | |
| getCloudData | 3.011 | 0.178 | 3.883 | |
| getData | 0.000 | 0.000 | 0.001 | |
| meta_data | 0.001 | 0.000 | 0.002 | |
| recipeHub-class | 0.155 | 0.014 | 0.172 | |
| recipeLoad | 1.691 | 0.112 | 1.827 | |
| recipeMake | 0.000 | 0.001 | 0.001 | |
| recipeSearch | 0.726 | 0.048 | 0.782 | |
| recipeUpdate | 0.000 | 0.000 | 0.001 | |