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 12:02 -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. |
| Package: ReUseData |
| Version: 1.6.0 |
| Command: /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:ReUseData.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings ReUseData_1.6.0.tar.gz |
| StartedAt: 2024-11-20 08:21:10 -0500 (Wed, 20 Nov 2024) |
| EndedAt: 2024-11-20 08:23:54 -0500 (Wed, 20 Nov 2024) |
| EllapsedTime: 163.6 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: ReUseData.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:ReUseData.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings ReUseData_1.6.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/meat/ReUseData.Rcheck’
* using R version 4.4.2 (2024-10-31)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0
GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0
* running under: Ubuntu 24.04.1 LTS
* using session charset: UTF-8
* 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
* 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 re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE
Status: 1 NOTE
See
‘/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/meat/ReUseData.Rcheck/00check.log’
for details.
ReUseData.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD INSTALL ReUseData ### ############################################################################## ############################################################################## * installing to library ‘/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/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: x86_64-pc-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...
1abdce6793ca95_GRCh38.primary_assembly.genome.fa.1.bt2 added
1abdce2fbad613_GRCh38.primary_assembly.genome.fa.2.bt2 added
1abdce522abaf3_GRCh38.primary_assembly.genome.fa.3.bt2 added
1abdce19dda811_GRCh38.primary_assembly.genome.fa.4.bt2 added
1abdceed2d163_GRCh38.primary_assembly.genome.fa.rev.1.bt2 added
1abdce7784b0b1_GRCh38.primary_assembly.genome.fa.rev.2.bt2 added
1abdce7f018b69_outfile.txt added
1abdce160cdb35_GRCh37_to_GRCh38.chain added
1abdce60bb2256_GRCh37_to_NCBI34.chain added
1abdce73295eb1_GRCh37_to_NCBI35.chain added
1abdce3602cbb6_GRCh37_to_NCBI36.chain added
1abdce384c510b_GRCh38_to_GRCh37.chain added
1abdce7069d174_GRCh38_to_NCBI34.chain added
1abdce5fd31e4d_GRCh38_to_NCBI35.chain added
1abdce23dee072_GRCh38_to_NCBI36.chain added
1abdce3c5ec529_NCBI34_to_GRCh37.chain added
1abdce28ad2fd8_NCBI34_to_GRCh38.chain added
1abdcee2648b6_NCBI35_to_GRCh37.chain added
1abdce732c6078_NCBI35_to_GRCh38.chain added
1abdce215411d7_NCBI36_to_GRCh37.chain added
1abdce7afdefde_NCBI36_to_GRCh38.chain added
1abdce3d9e987f_GRCm38_to_NCBIM36.chain added
1abdce7213d243_GRCm38_to_NCBIM37.chain added
1abdce63cadf98_NCBIM36_to_GRCm38.chain added
1abdce1246bb28_NCBIM37_to_GRCm38.chain added
1abdce69fb267c_1000G_omni2.5.b37.vcf.gz added
1abdce2feaa3f4_1000G_omni2.5.b37.vcf.gz.tbi added
1abdce4be3271f_Mills_and_1000G_gold_standard.indels.b37.vcf.gz added
1abdce7c29b040_Mills_and_1000G_gold_standard.indels.b37.vcf.gz.tbi added
1abdceb48f974_1000G_omni2.5.hg38.vcf.gz added
1abdce4da30856_1000G_omni2.5.hg38.vcf.gz.tbi added
1abdce63bd7ad5_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz added
1abdce3b03cf87_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz.tbi added
1abdce1fcdc34a_af-only-gnomad.raw.sites.vcf added
1abdce7d9b22e6_af-only-gnomad.raw.sites.vcf.idx added
1abdce49d6a0ea_Mutect2-exome-panel.vcf.idx added
1abdce175273fb_Mutect2-WGS-panel-b37.vcf added
1abdce7c9cae50_Mutect2-WGS-panel-b37.vcf.idx added
1abdce5fe37c1f_small_exac_common_3.vcf added
1abdce780d9652_small_exac_common_3.vcf.idx added
1abdce6fc60d01_1000g_pon.hg38.vcf.gz added
1abdce15e647d5_1000g_pon.hg38.vcf.gz.tbi added
1abdce3059e75d_af-only-gnomad.hg38.vcf.gz added
1abdce602fde75_af-only-gnomad.hg38.vcf.gz.tbi added
1abdce75b96623_small_exac_common_3.hg38.vcf.gz added
1abdce5438c7cf_small_exac_common_3.hg38.vcf.gz.tbi added
1abdce1c8ea39e_gencode.v41.annotation.gtf added
1abdce1e6695fb_gencode.v42.annotation.gtf added
1abdce625f1085_gencode.vM30.annotation.gtf added
1abdcefbb0416_gencode.vM31.annotation.gtf added
1abdce3fbaa7d3_gencode.v41.transcripts.fa added
1abdce5d5d0063_gencode.v41.transcripts.fa.fai added
1abdce4d599c95_gencode.v42.transcripts.fa added
1abdce31ce7a16_gencode.v42.transcripts.fa.fai added
1abdce4127dffc_gencode.vM30.pc_transcripts.fa added
1abdce5fa057bd_gencode.vM30.pc_transcripts.fa.fai added
1abdce1bc9a092_gencode.vM31.pc_transcripts.fa added
1abdce711283f0_gencode.vM31.pc_transcripts.fa.fai added
1abdce2b837edc_GRCh38.primary_assembly.genome.fa.1.ht2 added
1abdce17f350d2_GRCh38.primary_assembly.genome.fa.2.ht2 added
1abdce7c5b7d64_GRCh38.primary_assembly.genome.fa.3.ht2 added
1abdce79268733_GRCh38.primary_assembly.genome.fa.4.ht2 added
1abdce7bb0cba7_GRCh38.primary_assembly.genome.fa.5.ht2 added
1abdce375f4ceb_GRCh38.primary_assembly.genome.fa.6.ht2 added
1abdce18f44a7d_GRCh38.primary_assembly.genome.fa.7.ht2 added
1abdce794bee8e_GRCh38.primary_assembly.genome.fa.8.ht2 added
1abdce135edd5_GRCh38_full_analysis_set_plus_decoy_hla.fa.fai added
1abdce3046be78_GRCh38_full_analysis_set_plus_decoy_hla.fa.amb added
1abdce75e89cde_GRCh38_full_analysis_set_plus_decoy_hla.fa.ann added
1abdce611969f4_GRCh38_full_analysis_set_plus_decoy_hla.fa.bwt added
1abdce285454ca_GRCh38_full_analysis_set_plus_decoy_hla.fa.pac added
1abdce65aea9df_GRCh38_full_analysis_set_plus_decoy_hla.fa.sa added
1abdce76ffb1ca_GRCh38_full_analysis_set_plus_decoy_hla.fa added
1abdce58ae3c27_GRCh38.primary_assembly.genome.fa.fai added
1abdce45de8854_GRCh38.primary_assembly.genome.fa.amb added
1abdce6cb917ed_GRCh38.primary_assembly.genome.fa.ann added
1abdce2ce703f6_GRCh38.primary_assembly.genome.fa.bwt added
1abdce626d2bf2_GRCh38.primary_assembly.genome.fa.pac added
1abdceb1fade8_GRCh38.primary_assembly.genome.fa.sa added
1abdcef46147b_GRCh38.primary_assembly.genome.fa added
1abdce72283008_hs37d5.fa.fai added
1abdce4ada55bb_hs37d5.fa.amb added
1abdce6ca314df_hs37d5.fa.ann added
1abdce3f81cc9d_hs37d5.fa.bwt added
1abdce7ca8cfd1_hs37d5.fa.pac added
1abdce2dcaf4db_hs37d5.fa.sa added
1abdce1f22245a_hs37d5.fa added
1abdce18727064_complete_ref_lens.bin added
1abdce1edd78cb_ctable.bin added
1abdce4aa5a336_ctg_offsets.bin added
1abdce3065c136_duplicate_clusters.tsv added
1abdce1b38f62f_info.json added
1abdce43cc2a69_mphf.bin added
1abdce2c168cde_pos.bin added
1abdce5298431a_pre_indexing.log added
1abdce5cc074e6_rank.bin added
1abdce25627b6c_ref_indexing.log added
1abdce53ce30ef_refAccumLengths.bin added
1abdced07335f_reflengths.bin added
1abdce1b4b184a_refseq.bin added
1abdce34e79ae3_seq.bin added
1abdce355b8829_versionInfo.json added
1abdcef9c229_salmon_index added
1abdce2be74cad_chrLength.txt added
1abdcee09c451_chrName.txt added
1abdce46d84a7d_chrNameLength.txt added
1abdce18a0649a_chrStart.txt added
1abdce3af0c847_exonGeTrInfo.tab added
1abdce2945766f_exonInfo.tab added
1abdce23c01283_geneInfo.tab added
1abdce4a36dcc3_Genome added
1abdce1b6da677_genomeParameters.txt added
1abdce6e9a683e_Log.out added
1abdce36d9f1a2_SA added
1abdce5aef7314_SAindex added
1abdce6b433810_sjdbInfo.txt added
1abdce64a4e67d_sjdbList.fromGTF.out.tab added
1abdce7a11976e_sjdbList.out.tab added
1abdce3b5a874_transcriptInfo.tab added
1abdce3825f48_GRCh38.GENCODE.v42_100 added
1abdce44b73aa4_knownGene_hg38.sql added
1abdce341b69aa_knownGene_hg38.txt added
1abdce1ebb5577_refGene_hg38.sql added
1abdce883650e_refGene_hg38.txt added
1abdce6031f688_knownGene_mm39.sql added
1abdce71539891_knownGene_mm39.txt added
1abdce6543d9f4_refGene_mm39.sql added
1abdce59471f4_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/RtmpVbGBMY/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
14.361 1.537 19.022
ReUseData.Rcheck/ReUseData-Ex.timings
| name | user | system | elapsed | |
| dataHub-class | 4.009 | 0.238 | 4.440 | |
| dataSearch | 0.791 | 0.008 | 0.921 | |
| dataUpdate | 0.001 | 0.000 | 0.001 | |
| getCloudData | 2.704 | 0.027 | 3.786 | |
| getData | 0 | 0 | 0 | |
| meta_data | 0.000 | 0.001 | 0.000 | |
| recipeHub-class | 0.498 | 0.001 | 0.510 | |
| recipeLoad | 1.484 | 0.056 | 1.809 | |
| recipeMake | 0 | 0 | 0 | |
| recipeSearch | 0.395 | 0.012 | 0.414 | |
| recipeUpdate | 0 | 0 | 0 | |