Qian Liu
| Snapshot Date: 2023-11-01 14:05:06 -0400 (Wed, 01 Nov 2023) |
| git_url: https://git.bioconductor.org/packages/ReUseData |
| git_branch: RELEASE_3_18 |
| git_last_commit: 4abc363 |
| git_last_commit_date: 2023-10-24 11:46:21 -0400 (Tue, 24 Oct 2023) |
| Back to Multiple platform build/check report for BioC 3.18: simplified long |
|
This page was generated on 2023-11-02 11:41:10 -0400 (Thu, 02 Nov 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 22.04.2 LTS) | x86_64 | 4.3.1 (2023-06-16) -- "Beagle Scouts" | 4729 |
| palomino4 | Windows Server 2022 Datacenter | x64 | 4.3.1 (2023-06-16 ucrt) -- "Beagle Scouts" | 4463 |
| lconway | macOS 12.6.5 Monterey | x86_64 | 4.3.1 Patched (2023-06-17 r84564) -- "Beagle Scouts" | 4478 |
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | 4.3.1 (2023-06-16) -- "Beagle Scouts" | 4464 |
| 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 1725/2266 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| ReUseData 1.2.0 (landing page) Qian Liu
| nebbiolo2 | Linux (Ubuntu 22.04.2 LTS) / x86_64 | OK | ERROR | skipped | |||||||||
| palomino4 | Windows Server 2022 Datacenter / x64 | ... NOT SUPPORTED ... | ||||||||||||
| lconway | macOS 12.6.5 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson1 | macOS 13.6.1 Ventura / arm64 | see weekly results here | ||||||||||||
| 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: 1.2.0 |
| Command: /home/biocbuild/R/R-4.3.1/bin/R CMD check --install=check:ReUseData.install-out.txt --library=/home/biocbuild/R/R-4.3.1/site-library --no-vignettes --timings ReUseData_1.2.0.tar.gz |
| StartedAt: 2023-11-02 13:39:22 -0000 (Thu, 02 Nov 2023) |
| EndedAt: 2023-11-02 13:42:45 -0000 (Thu, 02 Nov 2023) |
| EllapsedTime: 203.5 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: ReUseData.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/R/R-4.3.1/bin/R CMD check --install=check:ReUseData.install-out.txt --library=/home/biocbuild/R/R-4.3.1/site-library --no-vignettes --timings ReUseData_1.2.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.18-bioc/meat/ReUseData.Rcheck’
* using R version 4.3.1 (2023-06-16)
* using platform: aarch64-unknown-linux-gnu (64-bit)
* R was compiled by
gcc (GCC) 10.3.1
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 ‘1.2.0’
* 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 R 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
dataUpdate 15.984 0.977 17.621
getCloudData 10.817 0.382 14.467
dataHub-class 9.912 0.359 10.301
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’
OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... 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-3.18-bioc/meat/ReUseData.Rcheck/00check.log’
for details.
ReUseData.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R-4.3.1/bin/R CMD INSTALL ReUseData ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/R/R-4.3.1/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 4.3.1 (2023-06-16) -- "Beagle Scouts"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: aarch64-unknown-linux-gnu (64-bit)
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...
1f80de2b2e5ce7_GRCh38.primary_assembly.genome.fa.1.bt2 added
1f80de4701ae30_GRCh38.primary_assembly.genome.fa.2.bt2 added
1f80de35bb1a57_GRCh38.primary_assembly.genome.fa.3.bt2 added
1f80de19ef0758_GRCh38.primary_assembly.genome.fa.4.bt2 added
1f80de18eab56a_GRCh38.primary_assembly.genome.fa.rev.1.bt2 added
1f80de1a28b7b6_GRCh38.primary_assembly.genome.fa.rev.2.bt2 added
1f80de51a54e13_outfile.txt added
1f80de495c0923_GRCh37_to_GRCh38.chain added
1f80de4e69190e_GRCh37_to_NCBI34.chain added
1f80de523bee54_GRCh37_to_NCBI35.chain added
1f80de46ae6f6b_GRCh37_to_NCBI36.chain added
1f80de676d0828_GRCh38_to_GRCh37.chain added
1f80de651abcb4_GRCh38_to_NCBI34.chain added
1f80de6afbfda9_GRCh38_to_NCBI35.chain added
1f80de4088f26c_GRCh38_to_NCBI36.chain added
1f80de7afb18c8_NCBI34_to_GRCh37.chain added
1f80de73a7f2dd_NCBI34_to_GRCh38.chain added
1f80de74f80b81_NCBI35_to_GRCh37.chain added
1f80de23cab342_NCBI35_to_GRCh38.chain added
1f80de27a69488_NCBI36_to_GRCh37.chain added
1f80de159967bd_NCBI36_to_GRCh38.chain added
1f80de3f9bbde7_GRCm38_to_NCBIM36.chain added
1f80de3abcc463_GRCm38_to_NCBIM37.chain added
1f80de7198d620_NCBIM36_to_GRCm38.chain added
1f80de4a43feb4_NCBIM37_to_GRCm38.chain added
1f80de454d1c0d_1000G_omni2.5.b37.vcf.gz added
1f80deffdee52_1000G_omni2.5.b37.vcf.gz.tbi added
1f80de32741614_Mills_and_1000G_gold_standard.indels.b37.vcf.gz added
1f80de16a2b3a6_Mills_and_1000G_gold_standard.indels.b37.vcf.gz.tbi added
1f80de2083cfc3_1000G_omni2.5.hg38.vcf.gz added
1f80de3b375cdc_1000G_omni2.5.hg38.vcf.gz.tbi added
1f80de41d1108d_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz added
1f80de67857df3_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz.tbi added
1f80de70f27734_af-only-gnomad.raw.sites.vcf added
1f80de5bc017e5_af-only-gnomad.raw.sites.vcf.idx added
1f80de70335d_Mutect2-exome-panel.vcf.idx added
1f80deb1b2eea_Mutect2-WGS-panel-b37.vcf added
1f80de2d6565f9_Mutect2-WGS-panel-b37.vcf.idx added
1f80de49cc3c81_small_exac_common_3.vcf added
1f80de598447f8_small_exac_common_3.vcf.idx added
1f80de7fa1544d_1000g_pon.hg38.vcf.gz added
1f80de107aabec_1000g_pon.hg38.vcf.gz.tbi added
1f80de40f15020_af-only-gnomad.hg38.vcf.gz added
1f80de64bc1101_af-only-gnomad.hg38.vcf.gz.tbi added
1f80de7b76a995_small_exac_common_3.hg38.vcf.gz added
1f80de17a428c_small_exac_common_3.hg38.vcf.gz.tbi added
1f80de5fb729c9_gencode.v41.annotation.gtf added
1f80de6f1e9c72_gencode.v42.annotation.gtf added
1f80de76724e0d_gencode.vM30.annotation.gtf added
1f80de381dd0b_gencode.vM31.annotation.gtf added
1f80de16c530fa_gencode.v41.transcripts.fa added
1f80dec0bb5cb_gencode.v41.transcripts.fa.fai added
1f80de431d9af2_gencode.v42.transcripts.fa added
1f80de5181f55d_gencode.v42.transcripts.fa.fai added
1f80de7da48beb_gencode.vM30.pc_transcripts.fa added
1f80ded6199a7_gencode.vM30.pc_transcripts.fa.fai added
1f80de16cf116a_gencode.vM31.pc_transcripts.fa added
1f80deda27a3d_gencode.vM31.pc_transcripts.fa.fai added
1f80de3fd5afbb_GRCh38.primary_assembly.genome.fa.1.ht2 added
1f80de2d71c510_GRCh38.primary_assembly.genome.fa.2.ht2 added
1f80de2e264a01_GRCh38.primary_assembly.genome.fa.3.ht2 added
1f80de7b0d0c98_GRCh38.primary_assembly.genome.fa.4.ht2 added
1f80de6f42d59e_GRCh38.primary_assembly.genome.fa.5.ht2 added
1f80de15abc7f4_GRCh38.primary_assembly.genome.fa.6.ht2 added
1f80de6bff83cc_GRCh38.primary_assembly.genome.fa.7.ht2 added
1f80de4b02ed83_GRCh38.primary_assembly.genome.fa.8.ht2 added
1f80de161bfb52_GRCh38_full_analysis_set_plus_decoy_hla.fa.fai added
1f80de771ab2b6_GRCh38_full_analysis_set_plus_decoy_hla.fa.amb added
1f80de7868537c_GRCh38_full_analysis_set_plus_decoy_hla.fa.ann added
1f80de5fe837d3_GRCh38_full_analysis_set_plus_decoy_hla.fa.bwt added
1f80de509efaae_GRCh38_full_analysis_set_plus_decoy_hla.fa.pac added
1f80de7809a7c9_GRCh38_full_analysis_set_plus_decoy_hla.fa.sa added
1f80de7062e3bf_GRCh38_full_analysis_set_plus_decoy_hla.fa added
1f80de11904ace_GRCh38.primary_assembly.genome.fa.fai added
1f80de5cc5b8ca_GRCh38.primary_assembly.genome.fa.amb added
1f80de6bd98d54_GRCh38.primary_assembly.genome.fa.ann added
1f80de130a8d5a_GRCh38.primary_assembly.genome.fa.bwt added
1f80de3c7ce293_GRCh38.primary_assembly.genome.fa.pac added
1f80de5af829c6_GRCh38.primary_assembly.genome.fa.sa added
1f80de97cdb67_GRCh38.primary_assembly.genome.fa added
1f80de3ffebf9e_hs37d5.fa.fai added
1f80de71bd5ac0_hs37d5.fa.amb added
1f80de15889132_hs37d5.fa.ann added
1f80de31c5a91_hs37d5.fa.bwt added
1f80de433f501d_hs37d5.fa.pac added
1f80de132d1d1e_hs37d5.fa.sa added
1f80de107df438_hs37d5.fa added
1f80de5a0e6187_complete_ref_lens.bin added
1f80de20cf975b_ctable.bin added
1f80de5053a3f3_ctg_offsets.bin added
1f80de7802698_duplicate_clusters.tsv added
1f80de4ef5e15c_info.json added
1f80de4b60b08b_mphf.bin added
1f80de76c2fc36_pos.bin added
1f80de64a1a951_pre_indexing.log added
1f80de37603457_rank.bin added
1f80de41c5e9b9_ref_indexing.log added
1f80de7abda4a3_refAccumLengths.bin added
1f80de2e7ae70d_reflengths.bin added
1f80de3a2e3d36_refseq.bin added
1f80de5aa5dc76_seq.bin added
1f80de7f19e1bb_versionInfo.json added
1f80de3237e4ff_salmon_index added
1f80de4b08c035_chrLength.txt added
1f80de10aa2c89_chrName.txt added
1f80deefd9dca_chrNameLength.txt added
1f80de36e24d89_chrStart.txt added
1f80de23b4b9e3_exonGeTrInfo.tab added
1f80de4b7a805d_exonInfo.tab added
1f80de11da774f_geneInfo.tab added
1f80de2d31954b_Genome added
1f80deb793ffc_genomeParameters.txt added
1f80de397d20f_Log.out added
1f80de42ba267d_SA added
1f80dee959a8d_SAindex added
1f80de46d7222c_sjdbInfo.txt added
1f80de55e7439b_sjdbList.fromGTF.out.tab added
1f80de1f138ec5_sjdbList.out.tab added
1f80de20e583b3_transcriptInfo.tab added
1f80de76b6daf7_GRCh38.GENCODE.v42_100 added
1f80de6f6732b8_knownGene_hg38.sql added
1f80de2865aa4b_knownGene_hg38.txt added
1f80de45acbc53_refGene_hg38.sql added
1f80de3ac7e344_refGene_hg38.txt added
1f80de1f28a681_knownGene_mm39.sql added
1f80de2a4e65a4_knownGene_mm39.txt added
1f80de7228179b_refGene_mm39.sql added
1f80de60ee903b_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/RtmpDcfE9w/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 ]
>
> proc.time()
user system elapsed
29.607 1.510 32.622
ReUseData.Rcheck/ReUseData-Ex.timings
| name | user | system | elapsed | |
| dataHub-class | 9.912 | 0.359 | 10.301 | |
| dataSearch | 1.704 | 0.031 | 1.740 | |
| dataUpdate | 15.984 | 0.977 | 17.621 | |
| getCloudData | 10.817 | 0.382 | 14.467 | |
| getData | 3.435 | 0.159 | 3.601 | |
| meta_data | 0.004 | 0.000 | 0.004 | |
| recipeHub-class | 0.273 | 0.000 | 0.273 | |
| recipeLoad | 1.601 | 0.035 | 1.642 | |
| recipeMake | 3.208 | 0.164 | 3.397 | |
| recipeSearch | 0.870 | 0.024 | 0.895 | |
| recipeUpdate | 0 | 0 | 0 | |