Qian Liu
| Snapshot Date: 2025-01-27 13:40 -0500 (Mon, 27 Jan 2025) |
| 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 2025-01-28 11:47 -0500 (Tue, 28 Jan 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | R Under development (unstable) (2025-01-20 r87609) -- "Unsuffered Consequences" | 4659 |
| palomino7 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2025-01-21 r87610 ucrt) -- "Unsuffered Consequences" | 4454 |
| lconway | macOS 12.7.1 Monterey | x86_64 | R Under development (unstable) (2025-01-22 r87618) -- "Unsuffered Consequences" | 4465 |
| kjohnson3 | macOS 13.7.1 Ventura | arm64 | R Under development (unstable) (2025-01-20 r87609) -- "Unsuffered Consequences" | 4419 |
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | R Under development (unstable) (2024-11-24 r87369) -- "Unsuffered Consequences" | 4409 |
| 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 1722/2286 | 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: 2025-01-28 14:27:47 -0000 (Tue, 28 Jan 2025) |
| EndedAt: 2025-01-28 14:30:41 -0000 (Tue, 28 Jan 2025) |
| EllapsedTime: 174.2 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 9.690 0.914 10.640
getCloudData 3.676 0.684 8.589
* 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...
36d6f82625f301_GRCh38.primary_assembly.genome.fa.1.bt2 added
36d6f860cc7d8c_GRCh38.primary_assembly.genome.fa.2.bt2 added
36d6f85bbb1eba_GRCh38.primary_assembly.genome.fa.3.bt2 added
36d6f845583e12_GRCh38.primary_assembly.genome.fa.4.bt2 added
36d6f8224b71ca_GRCh38.primary_assembly.genome.fa.rev.1.bt2 added
36d6f859a7ac08_GRCh38.primary_assembly.genome.fa.rev.2.bt2 added
36d6f82c0b0d44_outfile.txt added
36d6f87dfd1517_GRCh37_to_GRCh38.chain added
36d6f87e6011fa_GRCh37_to_NCBI34.chain added
36d6f822f57b6b_GRCh37_to_NCBI35.chain added
36d6f87c5bef08_GRCh37_to_NCBI36.chain added
36d6f86b3c10d5_GRCh38_to_GRCh37.chain added
36d6f8765fc689_GRCh38_to_NCBI34.chain added
36d6f84c764add_GRCh38_to_NCBI35.chain added
36d6f812cd3ae1_GRCh38_to_NCBI36.chain added
36d6f86d0b7865_NCBI34_to_GRCh37.chain added
36d6f8708d53c9_NCBI34_to_GRCh38.chain added
36d6f873c72bf8_NCBI35_to_GRCh37.chain added
36d6f8b782a1c_NCBI35_to_GRCh38.chain added
36d6f8109ba97e_NCBI36_to_GRCh37.chain added
36d6f8e8b923a_NCBI36_to_GRCh38.chain added
36d6f828cf4918_GRCm38_to_NCBIM36.chain added
36d6f84e60dc60_GRCm38_to_NCBIM37.chain added
36d6f8ee3814c_NCBIM36_to_GRCm38.chain added
36d6f813f32ad0_NCBIM37_to_GRCm38.chain added
36d6f84e48b6ab_1000G_omni2.5.b37.vcf.gz added
36d6f81a8ffdec_1000G_omni2.5.b37.vcf.gz.tbi added
36d6f84b8d926d_Mills_and_1000G_gold_standard.indels.b37.vcf.gz added
36d6f85564fb7_Mills_and_1000G_gold_standard.indels.b37.vcf.gz.tbi added
36d6f87b21b95f_1000G_omni2.5.hg38.vcf.gz added
36d6f8edc7b9c_1000G_omni2.5.hg38.vcf.gz.tbi added
36d6f82b7c42b8_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz added
36d6f85bee36ec_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz.tbi added
36d6f86a979a56_af-only-gnomad.raw.sites.vcf added
36d6f870d480cb_af-only-gnomad.raw.sites.vcf.idx added
36d6f87e39a8b6_Mutect2-exome-panel.vcf.idx added
36d6f8443f465f_Mutect2-WGS-panel-b37.vcf added
36d6f81cdf8e0f_Mutect2-WGS-panel-b37.vcf.idx added
36d6f87c36bdcd_small_exac_common_3.vcf added
36d6f8429f5859_small_exac_common_3.vcf.idx added
36d6f83fd5097a_1000g_pon.hg38.vcf.gz added
36d6f87892acd5_1000g_pon.hg38.vcf.gz.tbi added
36d6f82ddb692e_af-only-gnomad.hg38.vcf.gz added
36d6f83634d003_af-only-gnomad.hg38.vcf.gz.tbi added
36d6f84508f7b2_small_exac_common_3.hg38.vcf.gz added
36d6f840a8a40f_small_exac_common_3.hg38.vcf.gz.tbi added
36d6f823404869_gencode.v41.annotation.gtf added
36d6f835964b7b_gencode.v42.annotation.gtf added
36d6f8346fd007_gencode.vM30.annotation.gtf added
36d6f82eb87285_gencode.vM31.annotation.gtf added
36d6f84631f4f9_gencode.v41.transcripts.fa added
36d6f842fb6242_gencode.v41.transcripts.fa.fai added
36d6f85787bb9d_gencode.v42.transcripts.fa added
36d6f81492d15a_gencode.v42.transcripts.fa.fai added
36d6f851dee38e_gencode.vM30.pc_transcripts.fa added
36d6f86b7ae66d_gencode.vM30.pc_transcripts.fa.fai added
36d6f862db8805_gencode.vM31.pc_transcripts.fa added
36d6f86c6ee17a_gencode.vM31.pc_transcripts.fa.fai added
36d6f8370878db_GRCh38.primary_assembly.genome.fa.1.ht2 added
36d6f86831d7bd_GRCh38.primary_assembly.genome.fa.2.ht2 added
36d6f867909ad9_GRCh38.primary_assembly.genome.fa.3.ht2 added
36d6f845e4f477_GRCh38.primary_assembly.genome.fa.4.ht2 added
36d6f813ae1a75_GRCh38.primary_assembly.genome.fa.5.ht2 added
36d6f8437ed1c5_GRCh38.primary_assembly.genome.fa.6.ht2 added
36d6f8307c8ece_GRCh38.primary_assembly.genome.fa.7.ht2 added
36d6f84829b40_GRCh38.primary_assembly.genome.fa.8.ht2 added
36d6f841b87a7b_GRCh38_full_analysis_set_plus_decoy_hla.fa.fai added
36d6f874bbd52d_GRCh38_full_analysis_set_plus_decoy_hla.fa.amb added
36d6f821622950_GRCh38_full_analysis_set_plus_decoy_hla.fa.ann added
36d6f83def3848_GRCh38_full_analysis_set_plus_decoy_hla.fa.bwt added
36d6f8375b2d86_GRCh38_full_analysis_set_plus_decoy_hla.fa.pac added
36d6f8613732ca_GRCh38_full_analysis_set_plus_decoy_hla.fa.sa added
36d6f83681e51e_GRCh38_full_analysis_set_plus_decoy_hla.fa added
36d6f8653696b5_GRCh38.primary_assembly.genome.fa.fai added
36d6f8176c02ce_GRCh38.primary_assembly.genome.fa.amb added
36d6f87b8adcd0_GRCh38.primary_assembly.genome.fa.ann added
36d6f825df3ac4_GRCh38.primary_assembly.genome.fa.bwt added
36d6f83aac4b37_GRCh38.primary_assembly.genome.fa.pac added
36d6f83121284c_GRCh38.primary_assembly.genome.fa.sa added
36d6f85a4f0acc_GRCh38.primary_assembly.genome.fa added
36d6f86964bdbc_hs37d5.fa.fai added
36d6f877531d45_hs37d5.fa.amb added
36d6f81d4a6d0e_hs37d5.fa.ann added
36d6f840ec7959_hs37d5.fa.bwt added
36d6f8be5ee9f_hs37d5.fa.pac added
36d6f86f29509c_hs37d5.fa.sa added
36d6f82c675fc7_hs37d5.fa added
36d6f86ec176a5_complete_ref_lens.bin added
36d6f85b983216_ctable.bin added
36d6f8636fd8a2_ctg_offsets.bin added
36d6f856f34e62_duplicate_clusters.tsv added
36d6f84328ccef_info.json added
36d6f82954cd19_mphf.bin added
36d6f86aa168d7_pos.bin added
36d6f86a79eb5_pre_indexing.log added
36d6f859d15be7_rank.bin added
36d6f86f240418_ref_indexing.log added
36d6f848601930_refAccumLengths.bin added
36d6f84e8d3114_reflengths.bin added
36d6f810862d68_refseq.bin added
36d6f864f5179_seq.bin added
36d6f85e85e9b_versionInfo.json added
36d6f871bd6032_salmon_index added
36d6f83cd13697_chrLength.txt added
36d6f86b1ef550_chrName.txt added
36d6f89296300_chrNameLength.txt added
36d6f8385c1367_chrStart.txt added
36d6f810fe3014_exonGeTrInfo.tab added
36d6f843d5ae37_exonInfo.tab added
36d6f8697d3bb3_geneInfo.tab added
36d6f86b4d3ae0_Genome added
36d6f82d3a6bf3_genomeParameters.txt added
36d6f860d058f9_Log.out added
36d6f8897a7ee_SA added
36d6f86e26e54d_SAindex added
36d6f86cb64798_sjdbInfo.txt added
36d6f877c0f88a_sjdbList.fromGTF.out.tab added
36d6f81a8e4514_sjdbList.out.tab added
36d6f85b77be3d_transcriptInfo.tab added
36d6f853592aa0_GRCh38.GENCODE.v42_100 added
36d6f87dfe1db6_knownGene_hg38.sql added
36d6f8326b0c9f_knownGene_hg38.txt added
36d6f81681f790_refGene_hg38.sql added
36d6f82752eacf_refGene_hg38.txt added
36d6f81d0c7577_knownGene_mm39.sql added
36d6f81d299645_knownGene_mm39.txt added
36d6f812446b7_refGene_mm39.sql added
36d6f8c30798f_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/RtmpbWZBv9/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
29.147 1.565 34.000
ReUseData.Rcheck/ReUseData-Ex.timings
| name | user | system | elapsed | |
| dataHub-class | 9.690 | 0.914 | 10.640 | |
| dataSearch | 1.729 | 0.032 | 1.765 | |
| dataUpdate | 0 | 0 | 0 | |
| getCloudData | 3.676 | 0.684 | 8.589 | |
| getData | 0.000 | 0.000 | 0.001 | |
| meta_data | 0.001 | 0.001 | 0.001 | |
| recipeHub-class | 0.174 | 0.000 | 0.175 | |
| recipeLoad | 1.986 | 0.095 | 2.089 | |
| recipeMake | 0 | 0 | 0 | |
| recipeSearch | 0.805 | 0.020 | 0.827 | |
| recipeUpdate | 0 | 0 | 0 | |