Qian Liu
| Snapshot Date: 2025-01-20 13:00 -0500 (Mon, 20 Jan 2025) |
| 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 2025-01-23 12:12 -0500 (Thu, 23 Jan 2025).
| 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" | 4746 |
| palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" | 4493 |
| merida1 | macOS 12.7.5 Monterey | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4517 |
| kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4469 |
| taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4394 |
| 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 | | ||||||||
| taishan | Linux (openEuler 24.03 LTS) / 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: 2025-01-21 10:15:25 -0000 (Tue, 21 Jan 2025) |
| EndedAt: 2025-01-21 10:18:02 -0000 (Tue, 21 Jan 2025) |
| EllapsedTime: 157.2 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_1.6.0.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: aarch64-unknown-linux-gnu
* R was compiled by
aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0
GNU Fortran (GCC) 12.3.1 (openEuler 12.3.1-36.oe2403)
* 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 ‘1.6.0’
* 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 8.981 0.422 9.439
getCloudData 3.272 0.252 6.406
* 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-4.4.2/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: 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...
3435b74f7e5f24_GRCh38.primary_assembly.genome.fa.1.bt2 added
3435b71191ca95_GRCh38.primary_assembly.genome.fa.2.bt2 added
3435b723051d46_GRCh38.primary_assembly.genome.fa.3.bt2 added
3435b77aa5d935_GRCh38.primary_assembly.genome.fa.4.bt2 added
3435b7a2edee6_GRCh38.primary_assembly.genome.fa.rev.1.bt2 added
3435b76391505_GRCh38.primary_assembly.genome.fa.rev.2.bt2 added
3435b76be0fcff_outfile.txt added
3435b73349067b_GRCh37_to_GRCh38.chain added
3435b72debb120_GRCh37_to_NCBI34.chain added
3435b717e9e0db_GRCh37_to_NCBI35.chain added
3435b734eb956_GRCh37_to_NCBI36.chain added
3435b7733e16e6_GRCh38_to_GRCh37.chain added
3435b74300d644_GRCh38_to_NCBI34.chain added
3435b74acfe7e_GRCh38_to_NCBI35.chain added
3435b757431132_GRCh38_to_NCBI36.chain added
3435b75bdb83dc_NCBI34_to_GRCh37.chain added
3435b76a83e605_NCBI34_to_GRCh38.chain added
3435b770407dc5_NCBI35_to_GRCh37.chain added
3435b76155a3df_NCBI35_to_GRCh38.chain added
3435b77bd9355_NCBI36_to_GRCh37.chain added
3435b73a72a014_NCBI36_to_GRCh38.chain added
3435b729edfb80_GRCm38_to_NCBIM36.chain added
3435b751586590_GRCm38_to_NCBIM37.chain added
3435b7625d4d0c_NCBIM36_to_GRCm38.chain added
3435b729617fdd_NCBIM37_to_GRCm38.chain added
3435b716da2b31_1000G_omni2.5.b37.vcf.gz added
3435b76cec7631_1000G_omni2.5.b37.vcf.gz.tbi added
3435b75906bbd6_Mills_and_1000G_gold_standard.indels.b37.vcf.gz added
3435b7245190d0_Mills_and_1000G_gold_standard.indels.b37.vcf.gz.tbi added
3435b74b709baf_1000G_omni2.5.hg38.vcf.gz added
3435b734d1e371_1000G_omni2.5.hg38.vcf.gz.tbi added
3435b773cfeff4_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz added
3435b75d026644_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz.tbi added
3435b757d700b7_af-only-gnomad.raw.sites.vcf added
3435b76e75c929_af-only-gnomad.raw.sites.vcf.idx added
3435b76731452a_Mutect2-exome-panel.vcf.idx added
3435b75e1015bc_Mutect2-WGS-panel-b37.vcf added
3435b75a56c629_Mutect2-WGS-panel-b37.vcf.idx added
3435b71a7a4ba6_small_exac_common_3.vcf added
3435b7bfbc6dd_small_exac_common_3.vcf.idx added
3435b77240a704_1000g_pon.hg38.vcf.gz added
3435b71dc904fc_1000g_pon.hg38.vcf.gz.tbi added
3435b77f39ddc3_af-only-gnomad.hg38.vcf.gz added
3435b735417d49_af-only-gnomad.hg38.vcf.gz.tbi added
3435b72276037a_small_exac_common_3.hg38.vcf.gz added
3435b7567ceef5_small_exac_common_3.hg38.vcf.gz.tbi added
3435b7111d0125_gencode.v41.annotation.gtf added
3435b7cf9e97f_gencode.v42.annotation.gtf added
3435b746bd6cba_gencode.vM30.annotation.gtf added
3435b77272a504_gencode.vM31.annotation.gtf added
3435b714b77cd4_gencode.v41.transcripts.fa added
3435b71300cce_gencode.v41.transcripts.fa.fai added
3435b71c60a084_gencode.v42.transcripts.fa added
3435b7660fe264_gencode.v42.transcripts.fa.fai added
3435b7638d59da_gencode.vM30.pc_transcripts.fa added
3435b745c22062_gencode.vM30.pc_transcripts.fa.fai added
3435b77cea0d96_gencode.vM31.pc_transcripts.fa added
3435b75079d00c_gencode.vM31.pc_transcripts.fa.fai added
3435b71ec8dc38_GRCh38.primary_assembly.genome.fa.1.ht2 added
3435b7213b9e66_GRCh38.primary_assembly.genome.fa.2.ht2 added
3435b71bea6bbb_GRCh38.primary_assembly.genome.fa.3.ht2 added
3435b7539abfa9_GRCh38.primary_assembly.genome.fa.4.ht2 added
3435b7150b8e5a_GRCh38.primary_assembly.genome.fa.5.ht2 added
3435b778ecd1ff_GRCh38.primary_assembly.genome.fa.6.ht2 added
3435b72b71c061_GRCh38.primary_assembly.genome.fa.7.ht2 added
3435b73815784_GRCh38.primary_assembly.genome.fa.8.ht2 added
3435b7601e172a_GRCh38_full_analysis_set_plus_decoy_hla.fa.fai added
3435b7981d61d_GRCh38_full_analysis_set_plus_decoy_hla.fa.amb added
3435b75dd81dad_GRCh38_full_analysis_set_plus_decoy_hla.fa.ann added
3435b77a9862d0_GRCh38_full_analysis_set_plus_decoy_hla.fa.bwt added
3435b7157d9cfa_GRCh38_full_analysis_set_plus_decoy_hla.fa.pac added
3435b75018c4b1_GRCh38_full_analysis_set_plus_decoy_hla.fa.sa added
3435b7186167cc_GRCh38_full_analysis_set_plus_decoy_hla.fa added
3435b714b77abd_GRCh38.primary_assembly.genome.fa.fai added
3435b755a41fa_GRCh38.primary_assembly.genome.fa.amb added
3435b73ad76b46_GRCh38.primary_assembly.genome.fa.ann added
3435b76b3469b2_GRCh38.primary_assembly.genome.fa.bwt added
3435b71677431f_GRCh38.primary_assembly.genome.fa.pac added
3435b747d154c5_GRCh38.primary_assembly.genome.fa.sa added
3435b731f1d66c_GRCh38.primary_assembly.genome.fa added
3435b78e9e823_hs37d5.fa.fai added
3435b75c88d199_hs37d5.fa.amb added
3435b73321e33b_hs37d5.fa.ann added
3435b7254a88a8_hs37d5.fa.bwt added
3435b74298b3fe_hs37d5.fa.pac added
3435b716af3d15_hs37d5.fa.sa added
3435b76b0ca90a_hs37d5.fa added
3435b73f82c194_complete_ref_lens.bin added
3435b767290d21_ctable.bin added
3435b79d58542_ctg_offsets.bin added
3435b760be5ffa_duplicate_clusters.tsv added
3435b731378dc_info.json added
3435b75d7044eb_mphf.bin added
3435b775c9ee54_pos.bin added
3435b77c004adc_pre_indexing.log added
3435b78e2054c_rank.bin added
3435b7794b45d8_ref_indexing.log added
3435b75c1e6206_refAccumLengths.bin added
3435b71263db6a_reflengths.bin added
3435b757236385_refseq.bin added
3435b756b6c4d6_seq.bin added
3435b727e17864_versionInfo.json added
3435b7273c2837_salmon_index added
3435b76f182ca2_chrLength.txt added
3435b73c98f322_chrName.txt added
3435b72c966a31_chrNameLength.txt added
3435b729ef97e8_chrStart.txt added
3435b727cd5cd4_exonGeTrInfo.tab added
3435b7430dad51_exonInfo.tab added
3435b771c0ecad_geneInfo.tab added
3435b759bf3341_Genome added
3435b74bf79574_genomeParameters.txt added
3435b74e49be46_Log.out added
3435b7ce1167c_SA added
3435b771421e1c_SAindex added
3435b710e27244_sjdbInfo.txt added
3435b723905391_sjdbList.fromGTF.out.tab added
3435b75c4ec726_sjdbList.out.tab added
3435b7506533d8_transcriptInfo.tab added
3435b7ab960b3_GRCh38.GENCODE.v42_100 added
3435b766244c68_knownGene_hg38.sql added
3435b7312393d2_knownGene_hg38.txt added
3435b7dccd98f_refGene_hg38.sql added
3435b743949154_refGene_hg38.txt added
3435b726ed8227_knownGene_mm39.sql added
3435b79cd246b_knownGene_mm39.txt added
3435b74c7696a0_refGene_mm39.sql added
3435b72038c7ff_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/RtmpifYrTK/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
26.696 1.562 31.519
ReUseData.Rcheck/ReUseData-Ex.timings
| name | user | system | elapsed | |
| dataHub-class | 8.981 | 0.422 | 9.439 | |
| dataSearch | 1.735 | 0.004 | 1.743 | |
| dataUpdate | 0 | 0 | 0 | |
| getCloudData | 3.272 | 0.252 | 6.406 | |
| getData | 0 | 0 | 0 | |
| meta_data | 0.001 | 0.000 | 0.001 | |
| recipeHub-class | 0.164 | 0.012 | 0.179 | |
| recipeLoad | 1.729 | 0.100 | 1.835 | |
| recipeMake | 0.001 | 0.000 | 0.001 | |
| recipeSearch | 0.739 | 0.043 | 0.785 | |
| recipeUpdate | 0 | 0 | 0 | |