Qian Liu
| Snapshot Date: 2025-03-21 13:40 -0400 (Fri, 21 Mar 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 -0400 (Tue, 29 Oct 2024) |
| Back to Multiple platform build/check report for BioC 3.21: simplified long |
|
This page was generated on 2025-03-22 11:47 -0400 (Sat, 22 Mar 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | R Under development (unstable) (2025-03-13 r87965) -- "Unsuffered Consequences" | 4777 |
| palomino7 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2025-03-01 r87860 ucrt) -- "Unsuffered Consequences" | 4547 |
| lconway | macOS 12.7.1 Monterey | x86_64 | R Under development (unstable) (2025-03-02 r87868) -- "Unsuffered Consequences" | 4576 |
| kjohnson3 | macOS 13.7.1 Ventura | arm64 | R Under development (unstable) (2025-03-02 r87868) -- "Unsuffered Consequences" | 4528 |
| kunpeng2 | Linux (openEuler 24.03 LTS) | aarch64 | R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" | 4458 |
| 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 1740/2313 | 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 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: 1.7.0 |
| 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: 2025-03-22 10:19:31 -0000 (Sat, 22 Mar 2025) |
| EndedAt: 2025-03-22 10:22:22 -0000 (Sat, 22 Mar 2025) |
| EllapsedTime: 171.1 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) (2025-02-19 r87757)
* 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-SP1)
* 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 8.973 0.767 9.776
getCloudData 3.480 0.240 8.028
* 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-devel_2025-02-19/site-library’ * installing *source* package ‘ReUseData’ ... ** this is package ‘ReUseData’ version ‘1.7.0’ ** 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) (2025-02-19 r87757) -- "Unsuffered Consequences"
Copyright (C) 2025 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...
180cab3a0426e5_GRCh38.primary_assembly.genome.fa.1.bt2 added
180cab43510a65_GRCh38.primary_assembly.genome.fa.2.bt2 added
180cab11f5c8f4_GRCh38.primary_assembly.genome.fa.3.bt2 added
180cab3acfdfb_GRCh38.primary_assembly.genome.fa.4.bt2 added
180cab7afc176_GRCh38.primary_assembly.genome.fa.rev.1.bt2 added
180cab7100329a_GRCh38.primary_assembly.genome.fa.rev.2.bt2 added
180cab178830a_outfile.txt added
180cab1e0ff7_GRCh37_to_GRCh38.chain added
180cab71632ac3_GRCh37_to_NCBI34.chain added
180cab7de27966_GRCh37_to_NCBI35.chain added
180cab1dd6a5c2_GRCh37_to_NCBI36.chain added
180cab58b7f7fe_GRCh38_to_GRCh37.chain added
180cab7d41fa67_GRCh38_to_NCBI34.chain added
180cab54056915_GRCh38_to_NCBI35.chain added
180cab5c030252_GRCh38_to_NCBI36.chain added
180caba7ea26f_NCBI34_to_GRCh37.chain added
180cab26bccae3_NCBI34_to_GRCh38.chain added
180cab32fea687_NCBI35_to_GRCh37.chain added
180cab2a4e97f0_NCBI35_to_GRCh38.chain added
180cab37fc83f7_NCBI36_to_GRCh37.chain added
180cab74ed6a4e_NCBI36_to_GRCh38.chain added
180cab4f727b0a_GRCm38_to_NCBIM36.chain added
180cabbe3b7e5_GRCm38_to_NCBIM37.chain added
180cab39e6be5a_NCBIM36_to_GRCm38.chain added
180cab9af335e_NCBIM37_to_GRCm38.chain added
180cab1c0b8390_1000G_omni2.5.b37.vcf.gz added
180cab30f07f6d_1000G_omni2.5.b37.vcf.gz.tbi added
180cab398b69d4_Mills_and_1000G_gold_standard.indels.b37.vcf.gz added
180cab259105eb_Mills_and_1000G_gold_standard.indels.b37.vcf.gz.tbi added
180cab25716e60_1000G_omni2.5.hg38.vcf.gz added
180cab5598e7c_1000G_omni2.5.hg38.vcf.gz.tbi added
180cab5f952cd0_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz added
180cab68c278c5_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz.tbi added
180cab174f5771_af-only-gnomad.raw.sites.vcf added
180cab63422acc_af-only-gnomad.raw.sites.vcf.idx added
180cab70723a3b_Mutect2-exome-panel.vcf.idx added
180cab84f8a0b_Mutect2-WGS-panel-b37.vcf added
180cab64baadd6_Mutect2-WGS-panel-b37.vcf.idx added
180cab70904a33_small_exac_common_3.vcf added
180cab79b2b4ce_small_exac_common_3.vcf.idx added
180cab629d273c_1000g_pon.hg38.vcf.gz added
180cabe66eff5_1000g_pon.hg38.vcf.gz.tbi added
180cab526aaccc_af-only-gnomad.hg38.vcf.gz added
180cab5fdf21a3_af-only-gnomad.hg38.vcf.gz.tbi added
180cab626c590a_small_exac_common_3.hg38.vcf.gz added
180cab2e6daf1e_small_exac_common_3.hg38.vcf.gz.tbi added
180cab6a5dc412_gencode.v41.annotation.gtf added
180cab92923ee_gencode.v42.annotation.gtf added
180cab616c55a6_gencode.vM30.annotation.gtf added
180cab14ac5c03_gencode.vM31.annotation.gtf added
180cab4125a7e5_gencode.v41.transcripts.fa added
180cab5659bff4_gencode.v41.transcripts.fa.fai added
180cab641ed70d_gencode.v42.transcripts.fa added
180cab4d095fca_gencode.v42.transcripts.fa.fai added
180cab10407e4e_gencode.vM30.pc_transcripts.fa added
180cab6dce0a6b_gencode.vM30.pc_transcripts.fa.fai added
180cab6914e35a_gencode.vM31.pc_transcripts.fa added
180cab4130fdbb_gencode.vM31.pc_transcripts.fa.fai added
180cab2759743f_GRCh38.primary_assembly.genome.fa.1.ht2 added
180cabea5e945_GRCh38.primary_assembly.genome.fa.2.ht2 added
180cab66a26c1c_GRCh38.primary_assembly.genome.fa.3.ht2 added
180cab2cb302bb_GRCh38.primary_assembly.genome.fa.4.ht2 added
180cab6e3b1615_GRCh38.primary_assembly.genome.fa.5.ht2 added
180cab4f64e4e1_GRCh38.primary_assembly.genome.fa.6.ht2 added
180cab44025a2c_GRCh38.primary_assembly.genome.fa.7.ht2 added
180cab517d40e1_GRCh38.primary_assembly.genome.fa.8.ht2 added
180cab3fd71f1d_GRCh38_full_analysis_set_plus_decoy_hla.fa.fai added
180cab4c51e438_GRCh38_full_analysis_set_plus_decoy_hla.fa.amb added
180cab3637eeb7_GRCh38_full_analysis_set_plus_decoy_hla.fa.ann added
180cab30676950_GRCh38_full_analysis_set_plus_decoy_hla.fa.bwt added
180cab46049906_GRCh38_full_analysis_set_plus_decoy_hla.fa.pac added
180cab18d515f3_GRCh38_full_analysis_set_plus_decoy_hla.fa.sa added
180cab3ece5945_GRCh38_full_analysis_set_plus_decoy_hla.fa added
180cab186f45d3_GRCh38.primary_assembly.genome.fa.fai added
180cab78b43796_GRCh38.primary_assembly.genome.fa.amb added
180cab213ab24f_GRCh38.primary_assembly.genome.fa.ann added
180cab46dcf4f1_GRCh38.primary_assembly.genome.fa.bwt added
180cab6311fba9_GRCh38.primary_assembly.genome.fa.pac added
180cab2a63d63d_GRCh38.primary_assembly.genome.fa.sa added
180cab28494a97_GRCh38.primary_assembly.genome.fa added
180cab77be57ac_hs37d5.fa.fai added
180cab6b897e22_hs37d5.fa.amb added
180cab7ea30a8b_hs37d5.fa.ann added
180cab5bdd2eb9_hs37d5.fa.bwt added
180cab3892ddec_hs37d5.fa.pac added
180cabee388d9_hs37d5.fa.sa added
180cab49ab3924_hs37d5.fa added
180cab21a7c146_complete_ref_lens.bin added
180cab50148695_ctable.bin added
180cab7104ad63_ctg_offsets.bin added
180cab304daa8b_duplicate_clusters.tsv added
180cab36b6f2b1_info.json added
180cab1db7b01e_mphf.bin added
180cab1e88c0a1_pos.bin added
180cab61bd792_pre_indexing.log added
180cab61ba0a4b_rank.bin added
180cab70060182_ref_indexing.log added
180cab45f2f6af_refAccumLengths.bin added
180cab2e0bee83_reflengths.bin added
180cab263df03a_refseq.bin added
180cab765a5fff_seq.bin added
180cab74108789_versionInfo.json added
180cab3f13062d_salmon_index added
180cab3528b944_chrLength.txt added
180cabc7fcd5c_chrName.txt added
180cab37c73dc4_chrNameLength.txt added
180cab56636b94_chrStart.txt added
180cab535cc24e_exonGeTrInfo.tab added
180cab1ad9396d_exonInfo.tab added
180cabc741d1_geneInfo.tab added
180cab7ba60ce5_Genome added
180cab12979119_genomeParameters.txt added
180cab6c50bff4_Log.out added
180cab7a491771_SA added
180cab6e74bfd2_SAindex added
180cab24e39de0_sjdbInfo.txt added
180cab92ca04a_sjdbList.fromGTF.out.tab added
180cab381ff8f6_sjdbList.out.tab added
180cab468b5f27_transcriptInfo.tab added
180cab594126df_GRCh38.GENCODE.v42_100 added
180cab2924a659_knownGene_hg38.sql added
180cab76d909b2_knownGene_hg38.txt added
180cabff81990_refGene_hg38.sql added
180cab46dc5677_refGene_hg38.txt added
180cab1561ca53_knownGene_mm39.sql added
180cab1613f123_knownGene_mm39.txt added
180cab289660c2_refGene_mm39.sql added
180cab567cbd6_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/RtmpCcq1r0/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
30.169 2.247 34.912
ReUseData.Rcheck/ReUseData-Ex.timings
| name | user | system | elapsed | |
| dataHub-class | 8.973 | 0.767 | 9.776 | |
| dataSearch | 1.631 | 0.040 | 1.675 | |
| dataUpdate | 0 | 0 | 0 | |
| getCloudData | 3.480 | 0.240 | 8.028 | |
| getData | 0 | 0 | 0 | |
| meta_data | 0.000 | 0.000 | 0.001 | |
| recipeHub-class | 0.185 | 0.008 | 0.196 | |
| recipeLoad | 1.882 | 0.131 | 2.022 | |
| recipeMake | 0 | 0 | 0 | |
| recipeSearch | 0.806 | 0.052 | 0.860 | |
| recipeUpdate | 0.000 | 0.000 | 0.001 | |