Qian Liu
| Snapshot Date: 2024-09-11 14:00 -0400 (Wed, 11 Sep 2024) |
| git_url: https://git.bioconductor.org/packages/ReUseData |
| git_branch: devel |
| git_last_commit: cbe4e73 |
| git_last_commit_date: 2024-04-30 11:46:52 -0400 (Tue, 30 Apr 2024) |
| Back to Multiple platform build/check report for BioC 3.20: simplified long |
|
This page was generated on 2024-09-12 11:41 -0400 (Thu, 12 Sep 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4713 |
| teran2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4444 |
| palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" | 4450 |
| lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4483 |
| kjohnson3 | macOS 13.6.5 Ventura | arm64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4430 |
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4428 |
| 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 1707/2258 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| ReUseData 1.5.0 (landing page) Qian Liu
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| teran2 | 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 | | ||||||||
| kjohnson3 | macOS 13.6.5 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. |
| Package: ReUseData |
| Version: 1.5.0 |
| 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_1.5.0.tar.gz |
| StartedAt: 2024-09-12 02:17:45 -0400 (Thu, 12 Sep 2024) |
| EndedAt: 2024-09-12 02:20:33 -0400 (Thu, 12 Sep 2024) |
| EllapsedTime: 168.2 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_1.5.0.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: x86_64-pc-linux-gnu
* R was compiled by
gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
* running under: Ubuntu 22.04.5 LTS
* using session charset: UTF-8
* checking for file ‘ReUseData/DESCRIPTION’ ... OK
* this is package ‘ReUseData’ version ‘1.5.0’
* 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 5.981 0.356 6.34
* 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
‘/home/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 ‘/home/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 4.4.1 (2024-06-14) -- "Race for Your Life"
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...
5b311643060cb_GRCh38.primary_assembly.genome.fa.1.bt2 added
5b31171280cc2_GRCh38.primary_assembly.genome.fa.2.bt2 added
5b31138f1296b_GRCh38.primary_assembly.genome.fa.3.bt2 added
5b31131f42ea0_GRCh38.primary_assembly.genome.fa.4.bt2 added
5b31124f6c01d_GRCh38.primary_assembly.genome.fa.rev.1.bt2 added
5b3112f73cb89_GRCh38.primary_assembly.genome.fa.rev.2.bt2 added
5b3112257c1d4_outfile.txt added
5b311282d9fdb_GRCh37_to_GRCh38.chain added
5b3113d9a66f6_GRCh37_to_NCBI34.chain added
5b3114be773a0_GRCh37_to_NCBI35.chain added
5b31140583f6d_GRCh37_to_NCBI36.chain added
5b3112387eb69_GRCh38_to_GRCh37.chain added
5b3116412ebae_GRCh38_to_NCBI34.chain added
5b3117db9d2b3_GRCh38_to_NCBI35.chain added
5b3116ddb6762_GRCh38_to_NCBI36.chain added
5b3111f8f92c7_NCBI34_to_GRCh37.chain added
5b3114dea5d5d_NCBI34_to_GRCh38.chain added
5b3113e97510e_NCBI35_to_GRCh37.chain added
5b31123b2024c_NCBI35_to_GRCh38.chain added
5b31120eaf996_NCBI36_to_GRCh37.chain added
5b31116ee6019_NCBI36_to_GRCh38.chain added
5b3114efbde24_GRCm38_to_NCBIM36.chain added
5b31123dff4a7_GRCm38_to_NCBIM37.chain added
5b311cd7cc73_NCBIM36_to_GRCm38.chain added
5b3114248210a_NCBIM37_to_GRCm38.chain added
5b3117a054828_1000G_omni2.5.b37.vcf.gz added
5b3114793db2f_1000G_omni2.5.b37.vcf.gz.tbi added
5b31158c2d083_Mills_and_1000G_gold_standard.indels.b37.vcf.gz added
5b311c4228d9_Mills_and_1000G_gold_standard.indels.b37.vcf.gz.tbi added
5b3114d02bea0_1000G_omni2.5.hg38.vcf.gz added
5b31157db73c7_1000G_omni2.5.hg38.vcf.gz.tbi added
5b311707289a4_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz added
5b3113e2acb63_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz.tbi added
5b31110cc9d32_af-only-gnomad.raw.sites.vcf added
5b3112266b844_af-only-gnomad.raw.sites.vcf.idx added
5b31163218b80_Mutect2-exome-panel.vcf.idx added
5b311404068bb_Mutect2-WGS-panel-b37.vcf added
5b31144be7a18_Mutect2-WGS-panel-b37.vcf.idx added
5b311b4f2b5b_small_exac_common_3.vcf added
5b3117ddacfb1_small_exac_common_3.vcf.idx added
5b31110a5edb8_1000g_pon.hg38.vcf.gz added
5b3114ba76ac9_1000g_pon.hg38.vcf.gz.tbi added
5b3112162bb1a_af-only-gnomad.hg38.vcf.gz added
5b31174b8d967_af-only-gnomad.hg38.vcf.gz.tbi added
5b31149613d7c_small_exac_common_3.hg38.vcf.gz added
5b311f3e227d_small_exac_common_3.hg38.vcf.gz.tbi added
5b31114486c2e_gencode.v41.annotation.gtf added
5b311174b9ad9_gencode.v42.annotation.gtf added
5b3114dd5738b_gencode.vM30.annotation.gtf added
5b31137fa6e7a_gencode.vM31.annotation.gtf added
5b3113836946f_gencode.v41.transcripts.fa added
5b31164c3d3a4_gencode.v41.transcripts.fa.fai added
5b3116f64c9e_gencode.v42.transcripts.fa added
5b3115c168916_gencode.v42.transcripts.fa.fai added
5b311719ba018_gencode.vM30.pc_transcripts.fa added
5b311493e6da8_gencode.vM30.pc_transcripts.fa.fai added
5b311561bd13e_gencode.vM31.pc_transcripts.fa added
5b311392f7b47_gencode.vM31.pc_transcripts.fa.fai added
5b31122013e2c_GRCh38.primary_assembly.genome.fa.1.ht2 added
5b311625dfa17_GRCh38.primary_assembly.genome.fa.2.ht2 added
5b31163239e8_GRCh38.primary_assembly.genome.fa.3.ht2 added
5b31179dcb1f3_GRCh38.primary_assembly.genome.fa.4.ht2 added
5b31152d083bb_GRCh38.primary_assembly.genome.fa.5.ht2 added
5b311445d054b_GRCh38.primary_assembly.genome.fa.6.ht2 added
5b311aa94f25_GRCh38.primary_assembly.genome.fa.7.ht2 added
5b31175373c00_GRCh38.primary_assembly.genome.fa.8.ht2 added
5b311277e90cb_GRCh38_full_analysis_set_plus_decoy_hla.fa.fai added
5b3114ae9b7e0_GRCh38_full_analysis_set_plus_decoy_hla.fa.amb added
5b31139f5b618_GRCh38_full_analysis_set_plus_decoy_hla.fa.ann added
5b31132cdbc26_GRCh38_full_analysis_set_plus_decoy_hla.fa.bwt added
5b31148c48791_GRCh38_full_analysis_set_plus_decoy_hla.fa.pac added
5b3114a9ba3d1_GRCh38_full_analysis_set_plus_decoy_hla.fa.sa added
5b3117e7526ef_GRCh38_full_analysis_set_plus_decoy_hla.fa added
5b3116a2742ab_GRCh38.primary_assembly.genome.fa.fai added
5b3113f547d38_GRCh38.primary_assembly.genome.fa.amb added
5b31147d6646c_GRCh38.primary_assembly.genome.fa.ann added
5b31179656528_GRCh38.primary_assembly.genome.fa.bwt added
5b311539ce966_GRCh38.primary_assembly.genome.fa.pac added
5b3115f21ff45_GRCh38.primary_assembly.genome.fa.sa added
5b311473ad8b3_GRCh38.primary_assembly.genome.fa added
5b311b9757e0_hs37d5.fa.fai added
5b311175893b5_hs37d5.fa.amb added
5b3112bfeac58_hs37d5.fa.ann added
5b311128da47e_hs37d5.fa.bwt added
5b311736f1ccb_hs37d5.fa.pac added
5b3111d9a4c70_hs37d5.fa.sa added
5b3115bcc1226_hs37d5.fa added
5b311498aee0a_complete_ref_lens.bin added
5b31156c9c7b7_ctable.bin added
5b3117dcd5052_ctg_offsets.bin added
5b3112be8e821_duplicate_clusters.tsv added
5b3115cfc019f_info.json added
5b31177aa0245_mphf.bin added
5b3117eb96bdd_pos.bin added
5b311215906ea_pre_indexing.log added
5b311253516a_rank.bin added
5b31173f0a7dd_ref_indexing.log added
5b31148d797b5_refAccumLengths.bin added
5b3114d3d094a_reflengths.bin added
5b3112de65df5_refseq.bin added
5b3117ba553dc_seq.bin added
5b311160190db_versionInfo.json added
5b311788201c6_salmon_index added
5b3117a1a7acb_chrLength.txt added
5b31128d387_chrName.txt added
5b31137d67efe_chrNameLength.txt added
5b31141f0df37_chrStart.txt added
5b311798e38af_exonGeTrInfo.tab added
5b311b736864_exonInfo.tab added
5b3112112de7d_geneInfo.tab added
5b31140c91163_Genome added
5b311170ac044_genomeParameters.txt added
5b311386b7232_Log.out added
5b3116cc7bdbb_SA added
5b311299864c2_SAindex added
5b3112bda8efd_sjdbInfo.txt added
5b311a620a2b_sjdbList.fromGTF.out.tab added
5b31156476e9_sjdbList.out.tab added
5b31175657d07_transcriptInfo.tab added
5b311612bd1e2_GRCh38.GENCODE.v42_100 added
5b311331c73b_knownGene_hg38.sql added
5b311214e6529_knownGene_hg38.txt added
5b3113e27d382_refGene_hg38.sql added
5b3117adbc981_refGene_hg38.txt added
5b3112007d106_knownGene_mm39.sql added
5b3115f80da6c_knownGene_mm39.txt added
5b3117d2f1aeb_refGene_mm39.sql added
5b31113f878e3_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/Rtmp0nfKA1/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
19.194 1.376 21.254
ReUseData.Rcheck/ReUseData-Ex.timings
| name | user | system | elapsed | |
| dataHub-class | 5.981 | 0.356 | 6.340 | |
| dataSearch | 1.136 | 0.048 | 1.184 | |
| dataUpdate | 0.000 | 0.000 | 0.001 | |
| getCloudData | 2.675 | 0.106 | 3.545 | |
| getData | 0 | 0 | 0 | |
| meta_data | 0.001 | 0.000 | 0.000 | |
| recipeHub-class | 0.13 | 0.00 | 0.13 | |
| recipeLoad | 1.229 | 0.016 | 1.246 | |
| recipeMake | 0.001 | 0.000 | 0.000 | |
| recipeSearch | 0.518 | 0.004 | 0.522 | |
| recipeUpdate | 0.001 | 0.000 | 0.000 | |