Qian Liu
| Snapshot Date: 2024-12-23 13:40 -0500 (Mon, 23 Dec 2024) |
| 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 2024-12-24 11:47 -0500 (Tue, 24 Dec 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | R Under development (unstable) (2024-10-21 r87258) -- "Unsuffered Consequences" | 4754 |
| palomino7 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2024-10-26 r87273 ucrt) -- "Unsuffered Consequences" | 4472 |
| lconway | macOS 12.7.1 Monterey | x86_64 | R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" | 4426 |
| kjohnson3 | macOS 13.7.1 Ventura | arm64 | R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" | 4381 |
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | R Under development (unstable) (2024-11-24 r87369) -- "Unsuffered Consequences" | 4373 |
| 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 1714/2274 | 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. - See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host. |
| Package: ReUseData |
| Version: 1.7.0 |
| 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_1.7.0.tar.gz |
| StartedAt: 2024-12-24 10:22:59 -0000 (Tue, 24 Dec 2024) |
| EndedAt: 2024-12-24 10:25:48 -0000 (Tue, 24 Dec 2024) |
| EllapsedTime: 168.2 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_1.7.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/ReUseData.Rcheck’
* using R Under development (unstable) (2024-11-24 r87369)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0
GNU Fortran (GCC) 14.2.0
* running under: openEuler 24.03 (LTS)
* 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 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 9.550 0.463 10.047
getCloudData 3.773 0.096 6.355
* 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-3.21-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-4.5.0-devel_2024-11-24/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 Under development (unstable) (2024-11-24 r87369) -- "Unsuffered Consequences"
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...
1d3843481b2c2e_GRCh38.primary_assembly.genome.fa.1.bt2 added
1d384318a41032_GRCh38.primary_assembly.genome.fa.2.bt2 added
1d384376420ae4_GRCh38.primary_assembly.genome.fa.3.bt2 added
1d38437cea45c9_GRCh38.primary_assembly.genome.fa.4.bt2 added
1d384333783426_GRCh38.primary_assembly.genome.fa.rev.1.bt2 added
1d384310e12d8e_GRCh38.primary_assembly.genome.fa.rev.2.bt2 added
1d38432fce40c8_outfile.txt added
1d384332d0d413_GRCh37_to_GRCh38.chain added
1d38433b01185_GRCh37_to_NCBI34.chain added
1d38436e284d3_GRCh37_to_NCBI35.chain added
1d3843d580b1a_GRCh37_to_NCBI36.chain added
1d384367991721_GRCh38_to_GRCh37.chain added
1d384370665e0_GRCh38_to_NCBI34.chain added
1d384312c2b547_GRCh38_to_NCBI35.chain added
1d38435b098c3e_GRCh38_to_NCBI36.chain added
1d38431650ef60_NCBI34_to_GRCh37.chain added
1d38433941af22_NCBI34_to_GRCh38.chain added
1d38435f990f9a_NCBI35_to_GRCh37.chain added
1d38436dc72233_NCBI35_to_GRCh38.chain added
1d3843787f759e_NCBI36_to_GRCh37.chain added
1d3843322a78c3_NCBI36_to_GRCh38.chain added
1d384363d797db_GRCm38_to_NCBIM36.chain added
1d3843f221beb_GRCm38_to_NCBIM37.chain added
1d3843de764ca_NCBIM36_to_GRCm38.chain added
1d3843498f638c_NCBIM37_to_GRCm38.chain added
1d38435b5b0f50_1000G_omni2.5.b37.vcf.gz added
1d38435d6b3b8e_1000G_omni2.5.b37.vcf.gz.tbi added
1d3843501a0ee2_Mills_and_1000G_gold_standard.indels.b37.vcf.gz added
1d38431b801733_Mills_and_1000G_gold_standard.indels.b37.vcf.gz.tbi added
1d38436113d491_1000G_omni2.5.hg38.vcf.gz added
1d38434d72de70_1000G_omni2.5.hg38.vcf.gz.tbi added
1d3843639b4361_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz added
1d384379b7e4c3_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz.tbi added
1d384343b4e954_af-only-gnomad.raw.sites.vcf added
1d38436085892b_af-only-gnomad.raw.sites.vcf.idx added
1d38432d3018ea_Mutect2-exome-panel.vcf.idx added
1d3843549616e3_Mutect2-WGS-panel-b37.vcf added
1d38431053c9f3_Mutect2-WGS-panel-b37.vcf.idx added
1d38436000ecfd_small_exac_common_3.vcf added
1d384358462868_small_exac_common_3.vcf.idx added
1d384317364ec6_1000g_pon.hg38.vcf.gz added
1d38436d58f817_1000g_pon.hg38.vcf.gz.tbi added
1d38433fdf3f89_af-only-gnomad.hg38.vcf.gz added
1d38431e3cb4a7_af-only-gnomad.hg38.vcf.gz.tbi added
1d38431bad5e_small_exac_common_3.hg38.vcf.gz added
1d38431ae8cbc7_small_exac_common_3.hg38.vcf.gz.tbi added
1d3843348da407_gencode.v41.annotation.gtf added
1d3843395d5c81_gencode.v42.annotation.gtf added
1d38437a81db61_gencode.vM30.annotation.gtf added
1d38432254c63a_gencode.vM31.annotation.gtf added
1d384331dcd21f_gencode.v41.transcripts.fa added
1d38432cac5424_gencode.v41.transcripts.fa.fai added
1d384362c5e16_gencode.v42.transcripts.fa added
1d384340feee0a_gencode.v42.transcripts.fa.fai added
1d38433a93b8ee_gencode.vM30.pc_transcripts.fa added
1d38434fbbc1a2_gencode.vM30.pc_transcripts.fa.fai added
1d38431c59fd5a_gencode.vM31.pc_transcripts.fa added
1d384317fef47d_gencode.vM31.pc_transcripts.fa.fai added
1d38431fd5d084_GRCh38.primary_assembly.genome.fa.1.ht2 added
1d384337da148e_GRCh38.primary_assembly.genome.fa.2.ht2 added
1d38437912c90e_GRCh38.primary_assembly.genome.fa.3.ht2 added
1d38436d48aef5_GRCh38.primary_assembly.genome.fa.4.ht2 added
1d38431b7557ef_GRCh38.primary_assembly.genome.fa.5.ht2 added
1d384372caadd2_GRCh38.primary_assembly.genome.fa.6.ht2 added
1d384330fd9849_GRCh38.primary_assembly.genome.fa.7.ht2 added
1d38437bfae11a_GRCh38.primary_assembly.genome.fa.8.ht2 added
1d38431ffac6bc_GRCh38_full_analysis_set_plus_decoy_hla.fa.fai added
1d3843593af2c_GRCh38_full_analysis_set_plus_decoy_hla.fa.amb added
1d3843c4eab0e_GRCh38_full_analysis_set_plus_decoy_hla.fa.ann added
1d38437ffbb3b9_GRCh38_full_analysis_set_plus_decoy_hla.fa.bwt added
1d38435dd9d794_GRCh38_full_analysis_set_plus_decoy_hla.fa.pac added
1d38432384f9d4_GRCh38_full_analysis_set_plus_decoy_hla.fa.sa added
1d38436d54abd0_GRCh38_full_analysis_set_plus_decoy_hla.fa added
1d38431db9171d_GRCh38.primary_assembly.genome.fa.fai added
1d384341c1ae7b_GRCh38.primary_assembly.genome.fa.amb added
1d38436d70592f_GRCh38.primary_assembly.genome.fa.ann added
1d384338a1e2e4_GRCh38.primary_assembly.genome.fa.bwt added
1d3843764f5283_GRCh38.primary_assembly.genome.fa.pac added
1d384326cdb5b0_GRCh38.primary_assembly.genome.fa.sa added
1d38433323be45_GRCh38.primary_assembly.genome.fa added
1d384318a418bd_hs37d5.fa.fai added
1d384358aa87cf_hs37d5.fa.amb added
1d38435fd0126a_hs37d5.fa.ann added
1d38431ed076d3_hs37d5.fa.bwt added
1d384319a975da_hs37d5.fa.pac added
1d38431a63cb58_hs37d5.fa.sa added
1d38436e8c3875_hs37d5.fa added
1d384336037334_complete_ref_lens.bin added
1d38433262bfd5_ctable.bin added
1d3843e6208fa_ctg_offsets.bin added
1d38436ddd87c2_duplicate_clusters.tsv added
1d38432b7588e4_info.json added
1d38437baab7ef_mphf.bin added
1d3843952dfb2_pos.bin added
1d38431e4036b6_pre_indexing.log added
1d38432ca85038_rank.bin added
1d384354dc0cc_ref_indexing.log added
1d38433e3afd72_refAccumLengths.bin added
1d3843323bff65_reflengths.bin added
1d3843119c6bda_refseq.bin added
1d38433e36b12b_seq.bin added
1d38431015d6f9_versionInfo.json added
1d3843352165af_salmon_index added
1d38432b8b5cfb_chrLength.txt added
1d38432dceee17_chrName.txt added
1d384376e3142a_chrNameLength.txt added
1d384318fbb62a_chrStart.txt added
1d38436670d0fb_exonGeTrInfo.tab added
1d38436d3266ad_exonInfo.tab added
1d38433fc96bda_geneInfo.tab added
1d384319948f41_Genome added
1d38435d67f6b_genomeParameters.txt added
1d38431873f3aa_Log.out added
1d38437964a1ab_SA added
1d384324a6f63e_SAindex added
1d3843321d6984_sjdbInfo.txt added
1d384313c86d03_sjdbList.fromGTF.out.tab added
1d384313332eb4_sjdbList.out.tab added
1d38436820dcb8_transcriptInfo.tab added
1d3843462b2cd9_GRCh38.GENCODE.v42_100 added
1d3843219537ae_knownGene_hg38.sql added
1d384355fe647b_knownGene_hg38.txt added
1d384371a0b5bd_refGene_hg38.sql added
1d38431d3fef9d_refGene_hg38.txt added
1d38435f51442d_knownGene_mm39.sql added
1d3843fe0ec73_knownGene_mm39.txt added
1d384349e83fd5_refGene_mm39.sql added
1d3843649f04f9_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/RtmpglPr30/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
29.893 2.067 34.921
ReUseData.Rcheck/ReUseData-Ex.timings
| name | user | system | elapsed | |
| dataHub-class | 9.550 | 0.463 | 10.047 | |
| dataSearch | 1.695 | 0.020 | 1.718 | |
| dataUpdate | 0 | 0 | 0 | |
| getCloudData | 3.773 | 0.096 | 6.355 | |
| getData | 0 | 0 | 0 | |
| meta_data | 0.001 | 0.000 | 0.001 | |
| recipeHub-class | 0.176 | 0.012 | 0.195 | |
| recipeLoad | 1.891 | 0.048 | 1.959 | |
| recipeMake | 0 | 0 | 0 | |
| recipeSearch | 0.797 | 0.008 | 0.806 | |
| recipeUpdate | 0 | 0 | 0 | |