Qian Liu
| Snapshot Date: 2024-11-19 13:40 -0500 (Tue, 19 Nov 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 2024-11-20 12:08 -0500 (Wed, 20 Nov 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| teran2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4481 |
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4479 |
| palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" | 4359 |
| lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4539 |
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 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
| teran2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | | ||||||||
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | ||||||||||
| palomino8 | Windows Server 2022 Datacenter / x64 | ... NOT SUPPORTED ... | ||||||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | 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. - See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host. |
| Package: ReUseData |
| Version: 1.6.0 |
| Command: /home/biocbuild/R/R/bin/R CMD check --install=check:ReUseData.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings ReUseData_1.6.0.tar.gz |
| StartedAt: 2024-11-20 11:35:03 -0000 (Wed, 20 Nov 2024) |
| EndedAt: 2024-11-20 11:38:01 -0000 (Wed, 20 Nov 2024) |
| EllapsedTime: 177.3 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: ReUseData.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/R/R/bin/R CMD check --install=check:ReUseData.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings ReUseData_1.6.0.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: aarch64-unknown-linux-gnu
* R was compiled by
gcc (GCC) 12.2.1 20220819 (openEuler 12.2.1-14)
GNU Fortran (GCC) 10.3.1
* running under: openEuler 22.03 (LTS-SP1)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* 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 9.632 0.558 10.232
getCloudData 3.690 0.145 9.230
* 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
‘/home/biocbuild/bbs-3.20-bioc/meat/ReUseData.Rcheck/00check.log’
for details.
ReUseData.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R/bin/R CMD INSTALL ReUseData ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/R/R-4.4.1/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: aarch64-unknown-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...
1e1bbf2da89f19_GRCh38.primary_assembly.genome.fa.1.bt2 added
1e1bbf4e6ef663_GRCh38.primary_assembly.genome.fa.2.bt2 added
1e1bbf352a53fd_GRCh38.primary_assembly.genome.fa.3.bt2 added
1e1bbfaecc5a6_GRCh38.primary_assembly.genome.fa.4.bt2 added
1e1bbf73dfc0e4_GRCh38.primary_assembly.genome.fa.rev.1.bt2 added
1e1bbf37ca2356_GRCh38.primary_assembly.genome.fa.rev.2.bt2 added
1e1bbf7935aed6_outfile.txt added
1e1bbf258e700a_GRCh37_to_GRCh38.chain added
1e1bbf60ef30d7_GRCh37_to_NCBI34.chain added
1e1bbf51563723_GRCh37_to_NCBI35.chain added
1e1bbf32c04dc3_GRCh37_to_NCBI36.chain added
1e1bbf561d2981_GRCh38_to_GRCh37.chain added
1e1bbf4b6a562b_GRCh38_to_NCBI34.chain added
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1e1bbf6d715bf4_GRCh38_to_NCBI36.chain added
1e1bbf20f0a543_NCBI34_to_GRCh37.chain added
1e1bbf72b77cce_NCBI34_to_GRCh38.chain added
1e1bbf41833cd_NCBI35_to_GRCh37.chain added
1e1bbfc7b6f29_NCBI35_to_GRCh38.chain added
1e1bbf58eb9a4e_NCBI36_to_GRCh37.chain added
1e1bbf66cbcfd1_NCBI36_to_GRCh38.chain added
1e1bbf1bb0d016_GRCm38_to_NCBIM36.chain added
1e1bbf1b613633_GRCm38_to_NCBIM37.chain added
1e1bbf3e82a2c8_NCBIM36_to_GRCm38.chain added
1e1bbf780a5c8d_NCBIM37_to_GRCm38.chain added
1e1bbf23ba6a4b_1000G_omni2.5.b37.vcf.gz added
1e1bbf6ecee5b4_1000G_omni2.5.b37.vcf.gz.tbi added
1e1bbf32e2a44_Mills_and_1000G_gold_standard.indels.b37.vcf.gz added
1e1bbf6acf4a70_Mills_and_1000G_gold_standard.indels.b37.vcf.gz.tbi added
1e1bbf36568340_1000G_omni2.5.hg38.vcf.gz added
1e1bbf41d3ca67_1000G_omni2.5.hg38.vcf.gz.tbi added
1e1bbf1877e98a_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz added
1e1bbf4c579a4_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz.tbi added
1e1bbf76fe1e64_af-only-gnomad.raw.sites.vcf added
1e1bbf2364af30_af-only-gnomad.raw.sites.vcf.idx added
1e1bbf78a53a88_Mutect2-exome-panel.vcf.idx added
1e1bbf2ec841ba_Mutect2-WGS-panel-b37.vcf added
1e1bbf1c9a5e06_Mutect2-WGS-panel-b37.vcf.idx added
1e1bbf1e33aa92_small_exac_common_3.vcf added
1e1bbffb77291_small_exac_common_3.vcf.idx added
1e1bbf6df09529_1000g_pon.hg38.vcf.gz added
1e1bbf50f3f855_1000g_pon.hg38.vcf.gz.tbi added
1e1bbf65d49c13_af-only-gnomad.hg38.vcf.gz added
1e1bbf395aeb55_af-only-gnomad.hg38.vcf.gz.tbi added
1e1bbf6d17e700_small_exac_common_3.hg38.vcf.gz added
1e1bbf5345f807_small_exac_common_3.hg38.vcf.gz.tbi added
1e1bbf5a4b9098_gencode.v41.annotation.gtf added
1e1bbf5fcf63ce_gencode.v42.annotation.gtf added
1e1bbf575e2bd4_gencode.vM30.annotation.gtf added
1e1bbf66c6ffc1_gencode.vM31.annotation.gtf added
1e1bbf38bafe1d_gencode.v41.transcripts.fa added
1e1bbf3e29fba5_gencode.v41.transcripts.fa.fai added
1e1bbf277cfd7_gencode.v42.transcripts.fa added
1e1bbf541c3450_gencode.v42.transcripts.fa.fai added
1e1bbf7cac9e6d_gencode.vM30.pc_transcripts.fa added
1e1bbf7a822c65_gencode.vM30.pc_transcripts.fa.fai added
1e1bbf77d69e9b_gencode.vM31.pc_transcripts.fa added
1e1bbf6b7b8421_gencode.vM31.pc_transcripts.fa.fai added
1e1bbf7db056a9_GRCh38.primary_assembly.genome.fa.1.ht2 added
1e1bbf62a5e90c_GRCh38.primary_assembly.genome.fa.2.ht2 added
1e1bbf21d20762_GRCh38.primary_assembly.genome.fa.3.ht2 added
1e1bbf3f842110_GRCh38.primary_assembly.genome.fa.4.ht2 added
1e1bbf7b1dd296_GRCh38.primary_assembly.genome.fa.5.ht2 added
1e1bbf26978106_GRCh38.primary_assembly.genome.fa.6.ht2 added
1e1bbf36823f74_GRCh38.primary_assembly.genome.fa.7.ht2 added
1e1bbf1e8281c6_GRCh38.primary_assembly.genome.fa.8.ht2 added
1e1bbf1f3cbb8e_GRCh38_full_analysis_set_plus_decoy_hla.fa.fai added
1e1bbf654a812e_GRCh38_full_analysis_set_plus_decoy_hla.fa.amb added
1e1bbf3b1cdfcd_GRCh38_full_analysis_set_plus_decoy_hla.fa.ann added
1e1bbf3d706620_GRCh38_full_analysis_set_plus_decoy_hla.fa.bwt added
1e1bbf7501f3bf_GRCh38_full_analysis_set_plus_decoy_hla.fa.pac added
1e1bbf290d74f6_GRCh38_full_analysis_set_plus_decoy_hla.fa.sa added
1e1bbfe645e75_GRCh38_full_analysis_set_plus_decoy_hla.fa added
1e1bbf5ad68fd2_GRCh38.primary_assembly.genome.fa.fai added
1e1bbf6268604b_GRCh38.primary_assembly.genome.fa.amb added
1e1bbf7b7c4575_GRCh38.primary_assembly.genome.fa.ann added
1e1bbf2e1c87d9_GRCh38.primary_assembly.genome.fa.bwt added
1e1bbf3cb3f0e3_GRCh38.primary_assembly.genome.fa.pac added
1e1bbf5b4ba943_GRCh38.primary_assembly.genome.fa.sa added
1e1bbf57ab3ad_GRCh38.primary_assembly.genome.fa added
1e1bbf237af0a5_hs37d5.fa.fai added
1e1bbf1406a760_hs37d5.fa.amb added
1e1bbf43a4af53_hs37d5.fa.ann added
1e1bbf25f2c07c_hs37d5.fa.bwt added
1e1bbf6822dbb1_hs37d5.fa.pac added
1e1bbf40514dc0_hs37d5.fa.sa added
1e1bbf2074ece1_hs37d5.fa added
1e1bbf5ff97a4c_complete_ref_lens.bin added
1e1bbf2bccd1e2_ctable.bin added
1e1bbf1e25438a_ctg_offsets.bin added
1e1bbf429f6358_duplicate_clusters.tsv added
1e1bbf4d9ed944_info.json added
1e1bbf5da9649a_mphf.bin added
1e1bbf3dbd35ee_pos.bin added
1e1bbf74365a4a_pre_indexing.log added
1e1bbf142ba40e_rank.bin added
1e1bbf5c3fb7b5_ref_indexing.log added
1e1bbf137315d8_refAccumLengths.bin added
1e1bbf7976253c_reflengths.bin added
1e1bbf175c9782_refseq.bin added
1e1bbf50e37bf8_seq.bin added
1e1bbf6e7818fc_versionInfo.json added
1e1bbf406a0c78_salmon_index added
1e1bbf5f47da6d_chrLength.txt added
1e1bbf494ea8ce_chrName.txt added
1e1bbf22d26cc4_chrNameLength.txt added
1e1bbf5ac41fe2_chrStart.txt added
1e1bbf776b30a8_exonGeTrInfo.tab added
1e1bbf5f865da7_exonInfo.tab added
1e1bbf360fc925_geneInfo.tab added
1e1bbf7ce5e455_Genome added
1e1bbf3014e4c_genomeParameters.txt added
1e1bbf4a167086_Log.out added
1e1bbf408a93a8_SA added
1e1bbf28f40ec9_SAindex added
1e1bbf32394c37_sjdbInfo.txt added
1e1bbfdbe169_sjdbList.fromGTF.out.tab added
1e1bbf4968fbaa_sjdbList.out.tab added
1e1bbf1232c683_transcriptInfo.tab added
1e1bbf2ca8b34b_GRCh38.GENCODE.v42_100 added
1e1bbf678e3f35_knownGene_hg38.sql added
1e1bbf54d229dc_knownGene_hg38.txt added
1e1bbf7a478c8f_refGene_hg38.sql added
1e1bbf4537a3cf_refGene_hg38.txt added
1e1bbf128f5fca_knownGene_mm39.sql added
1e1bbf6e7de6d9_knownGene_mm39.txt added
1e1bbf596347de_refGene_mm39.sql added
1e1bbf6ecf177f_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/tmp/RtmpehC9Ki/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
29.546 1.517 36.180
ReUseData.Rcheck/ReUseData-Ex.timings
| name | user | system | elapsed | |
| dataHub-class | 9.632 | 0.558 | 10.232 | |
| dataSearch | 1.825 | 0.020 | 1.850 | |
| dataUpdate | 0 | 0 | 0 | |
| getCloudData | 3.690 | 0.145 | 9.230 | |
| getData | 0 | 0 | 0 | |
| meta_data | 0.001 | 0.000 | 0.000 | |
| recipeHub-class | 0.176 | 0.003 | 0.181 | |
| recipeLoad | 1.870 | 0.095 | 1.976 | |
| recipeMake | 0 | 0 | 0 | |
| recipeSearch | 0.797 | 0.027 | 0.827 | |
| recipeUpdate | 0 | 0 | 0 | |