Qian Liu
| Snapshot Date: 2024-07-03 14:00 -0400 (Wed, 03 Jul 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 2024-07-04 11:45 -0400 (Thu, 04 Jul 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" | 4411 |
| palomino6 | Windows Server 2022 Datacenter | x64 | 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" | 4413 |
| lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4395 |
| kjohnson3 | macOS 13.6.5 Ventura | arm64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4390 |
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4407 |
| 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 1695/2243 | 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 | | ||||||||
| palomino6 | 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. - See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host. |
| Package: ReUseData |
| Version: 1.5.0 |
| 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_1.5.0.tar.gz |
| StartedAt: 2024-07-04 08:33:00 -0000 (Thu, 04 Jul 2024) |
| EndedAt: 2024-07-04 08:35:46 -0000 (Thu, 04 Jul 2024) |
| EllapsedTime: 166.3 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_1.5.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/ReUseData.Rcheck’
* using R version 4.4.0 (2024-04-24)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
gcc (GCC) 12.2.1 20220819 (openEuler 12.2.1-14)
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 ‘1.5.0’
* 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 9.040 0.307 9.379
getCloudData 3.574 0.276 6.358
* 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-4.4.0/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 4.4.0 (2024-04-24) -- "Puppy Cup"
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...
61f9f334a480e_GRCh38.primary_assembly.genome.fa.1.bt2 added
61f9ffe30d62_GRCh38.primary_assembly.genome.fa.2.bt2 added
61f9f4dfdaa49_GRCh38.primary_assembly.genome.fa.3.bt2 added
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61f9f4a491f50_GRCh38.primary_assembly.genome.fa.rev.1.bt2 added
61f9f75d32038_GRCh38.primary_assembly.genome.fa.rev.2.bt2 added
61f9f39c132e1_outfile.txt added
61f9f68b58433_GRCh37_to_GRCh38.chain added
61f9f3a6d765c_GRCh37_to_NCBI34.chain added
61f9f5660b4b0_GRCh37_to_NCBI35.chain added
61f9f4b4da989_GRCh37_to_NCBI36.chain added
61f9f5f6f63ab_GRCh38_to_GRCh37.chain added
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61f9f39961c58_NCBI34_to_GRCh37.chain added
61f9f1d1714cd_NCBI34_to_GRCh38.chain added
61f9f6dc41f80_NCBI35_to_GRCh37.chain added
61f9f349e6f6b_NCBI35_to_GRCh38.chain added
61f9f7b680479_NCBI36_to_GRCh37.chain added
61f9f74dd47_NCBI36_to_GRCh38.chain added
61f9f462f3ebd_GRCm38_to_NCBIM36.chain added
61f9f5e8d782c_GRCm38_to_NCBIM37.chain added
61f9f259ea2f9_NCBIM36_to_GRCm38.chain added
61f9f1f60f9ac_NCBIM37_to_GRCm38.chain added
61f9f79a98218_1000G_omni2.5.b37.vcf.gz added
61f9f7a42286d_1000G_omni2.5.b37.vcf.gz.tbi added
61f9f213137db_Mills_and_1000G_gold_standard.indels.b37.vcf.gz added
61f9f6990360d_Mills_and_1000G_gold_standard.indels.b37.vcf.gz.tbi added
61f9f5736e206_1000G_omni2.5.hg38.vcf.gz added
61f9f6cb78fb1_1000G_omni2.5.hg38.vcf.gz.tbi added
61f9f1cda7e1b_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz added
61f9f6719ef68_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz.tbi added
61f9f3ab539fa_af-only-gnomad.raw.sites.vcf added
61f9f48d82e0a_af-only-gnomad.raw.sites.vcf.idx added
61f9f31630eb8_Mutect2-exome-panel.vcf.idx added
61f9f30885a32_Mutect2-WGS-panel-b37.vcf added
61f9f29960ec_Mutect2-WGS-panel-b37.vcf.idx added
61f9f1a1892eb_small_exac_common_3.vcf added
61f9f6af5d08e_small_exac_common_3.vcf.idx added
61f9f58fa159c_1000g_pon.hg38.vcf.gz added
61f9f65663c74_1000g_pon.hg38.vcf.gz.tbi added
61f9f4a65343a_af-only-gnomad.hg38.vcf.gz added
61f9f7732137f_af-only-gnomad.hg38.vcf.gz.tbi added
61f9f21b7ed70_small_exac_common_3.hg38.vcf.gz added
61f9f3a2b2d25_small_exac_common_3.hg38.vcf.gz.tbi added
61f9f30c82fd8_gencode.v41.annotation.gtf added
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61f9f27ef4ca5_gencode.vM30.annotation.gtf added
61f9f65669f43_gencode.vM31.annotation.gtf added
61f9f3a3706b7_gencode.v41.transcripts.fa added
61f9f286429ec_gencode.v41.transcripts.fa.fai added
61f9f2b95de00_gencode.v42.transcripts.fa added
61f9f18c47ee4_gencode.v42.transcripts.fa.fai added
61f9f4e02cce6_gencode.vM30.pc_transcripts.fa added
61f9f4af6d7ad_gencode.vM30.pc_transcripts.fa.fai added
61f9f126e00fc_gencode.vM31.pc_transcripts.fa added
61f9f4844f553_gencode.vM31.pc_transcripts.fa.fai added
61f9f6c280f88_GRCh38.primary_assembly.genome.fa.1.ht2 added
61f9f7bfe3709_GRCh38.primary_assembly.genome.fa.2.ht2 added
61f9f1f7bd75a_GRCh38.primary_assembly.genome.fa.3.ht2 added
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61f9f695c6c2_GRCh38.primary_assembly.genome.fa.6.ht2 added
61f9f1394d933_GRCh38.primary_assembly.genome.fa.7.ht2 added
61f9f61b0e32f_GRCh38.primary_assembly.genome.fa.8.ht2 added
61f9f37f8d57b_GRCh38_full_analysis_set_plus_decoy_hla.fa.fai added
61f9f441d3366_GRCh38_full_analysis_set_plus_decoy_hla.fa.amb added
61f9f644a441b_GRCh38_full_analysis_set_plus_decoy_hla.fa.ann added
61f9f52116866_GRCh38_full_analysis_set_plus_decoy_hla.fa.bwt added
61f9f2f1303f4_GRCh38_full_analysis_set_plus_decoy_hla.fa.pac added
61f9f3d4459b7_GRCh38_full_analysis_set_plus_decoy_hla.fa.sa added
61f9f3777a4db_GRCh38_full_analysis_set_plus_decoy_hla.fa added
61f9f7978382e_GRCh38.primary_assembly.genome.fa.fai added
61f9f34766d37_GRCh38.primary_assembly.genome.fa.amb added
61f9f592f924b_GRCh38.primary_assembly.genome.fa.ann added
61f9f33a36553_GRCh38.primary_assembly.genome.fa.bwt added
61f9f653e9d0f_GRCh38.primary_assembly.genome.fa.pac added
61f9f17fe9489_GRCh38.primary_assembly.genome.fa.sa added
61f9f5b92b1f9_GRCh38.primary_assembly.genome.fa added
61f9f4aa53c52_hs37d5.fa.fai added
61f9f52359b41_hs37d5.fa.amb added
61f9f3f6dbe5_hs37d5.fa.ann added
61f9f763b1a53_hs37d5.fa.bwt added
61f9f6afa1a25_hs37d5.fa.pac added
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61f9f7966522b_duplicate_clusters.tsv added
61f9f39ba7579_info.json added
61f9f639a0c1_mphf.bin added
61f9f123f074f_pos.bin added
61f9f40503c3b_pre_indexing.log added
61f9f19ce79f4_rank.bin added
61f9f73efea7e_ref_indexing.log added
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61f9f583a2e99_refseq.bin added
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61f9fcfeb14f_versionInfo.json added
61f9f157e8851_salmon_index added
61f9f1d21ef8_chrLength.txt added
61f9f676e97d_chrName.txt added
61f9f49f4f588_chrNameLength.txt added
61f9f5b01b143_chrStart.txt added
61f9f3a1a4ed1_exonGeTrInfo.tab added
61f9f2f339297_exonInfo.tab added
61f9f730045cd_geneInfo.tab added
61f9f15ad00ca_Genome added
61f9f79d8cee9_genomeParameters.txt added
61f9f4535e10e_Log.out added
61f9f19a3dcaf_SA added
61f9f7013e93c_SAindex added
61f9f302ffb33_sjdbInfo.txt added
61f9f6b9d857b_sjdbList.fromGTF.out.tab added
61f9f3145db3c_sjdbList.out.tab added
61f9f2d981654_transcriptInfo.tab added
61f9f5dc239a_GRCh38.GENCODE.v42_100 added
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61f9f26fe687f_knownGene_hg38.txt added
61f9f3f969913_refGene_hg38.sql added
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61f9f393d6fcf_knownGene_mm39.sql added
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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/Rtmpwo9UYW/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
29.350 2.034 32.953
ReUseData.Rcheck/ReUseData-Ex.timings
| name | user | system | elapsed | |
| dataHub-class | 9.040 | 0.307 | 9.379 | |
| dataSearch | 1.646 | 0.032 | 1.682 | |
| dataUpdate | 0.000 | 0.000 | 0.001 | |
| getCloudData | 3.574 | 0.276 | 6.358 | |
| getData | 0.000 | 0.000 | 0.001 | |
| meta_data | 0.001 | 0.000 | 0.001 | |
| recipeHub-class | 0.182 | 0.000 | 0.184 | |
| recipeLoad | 1.965 | 0.067 | 2.481 | |
| recipeMake | 0 | 0 | 0 | |
| recipeSearch | 0.840 | 0.032 | 0.874 | |
| recipeUpdate | 0 | 0 | 0 | |