Qian Liu
| Snapshot Date: 2025-03-31 13:00 -0400 (Mon, 31 Mar 2025) |
| 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 -0400 (Tue, 29 Oct 2024) |
| Back to Multiple platform build/check report for BioC 3.20: simplified long |
|
This page was generated on 2025-04-02 19:29 -0400 (Wed, 02 Apr 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.3 (2025-02-28) -- "Trophy Case" | 4764 |
| palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.3 (2025-02-28 ucrt) -- "Trophy Case" | 4495 |
| merida1 | macOS 12.7.5 Monterey | x86_64 | 4.4.3 (2025-02-28) -- "Trophy Case" | 4522 |
| kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.3 (2025-02-28) -- "Trophy Case" | 4449 |
| taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.4.3 (2025-02-28) -- "Trophy Case" | 4426 |
| 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
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino8 | Windows Server 2022 Datacenter / x64 | ... NOT SUPPORTED ... | ||||||||||||
| merida1 | macOS 12.7.5 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | OK | OK | OK | | ||||||||
| taishan | 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. |
| 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: 2025-04-01 01:28:54 -0400 (Tue, 01 Apr 2025) |
| EndedAt: 2025-04-01 01:31:37 -0400 (Tue, 01 Apr 2025) |
| EllapsedTime: 163.2 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_1.6.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/ReUseData.Rcheck’
* using R version 4.4.3 (2025-02-28)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.2 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
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
dataHub-class 5.695 0.254 5.953
* 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 4.4.3 (2025-02-28) -- "Trophy Case"
Copyright (C) 2025 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...
27e03b1da46271_GRCh38.primary_assembly.genome.fa.1.bt2 added
27e03b4ab67074_GRCh38.primary_assembly.genome.fa.2.bt2 added
27e03b7bf08faf_GRCh38.primary_assembly.genome.fa.3.bt2 added
27e03b6e8650b9_GRCh38.primary_assembly.genome.fa.4.bt2 added
27e03b1054cece_GRCh38.primary_assembly.genome.fa.rev.1.bt2 added
27e03b7b08c059_GRCh38.primary_assembly.genome.fa.rev.2.bt2 added
27e03b4e4d3f1b_outfile.txt added
27e03b85a3d33_GRCh37_to_GRCh38.chain added
27e03b71c93bec_GRCh37_to_NCBI34.chain added
27e03b26d54a7c_GRCh37_to_NCBI35.chain added
27e03b7e38cfc5_GRCh37_to_NCBI36.chain added
27e03bcd79ce1_GRCh38_to_GRCh37.chain added
27e03b19660294_GRCh38_to_NCBI34.chain added
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27e03b9dc9bc8_GRCh38_to_NCBI36.chain added
27e03b32b41897_NCBI34_to_GRCh37.chain added
27e03b3d311400_NCBI34_to_GRCh38.chain added
27e03b2b5a54d5_NCBI35_to_GRCh37.chain added
27e03b535cdea6_NCBI35_to_GRCh38.chain added
27e03b3a5a597_NCBI36_to_GRCh37.chain added
27e03bdf2fa2f_NCBI36_to_GRCh38.chain added
27e03b4fc419a5_GRCm38_to_NCBIM36.chain added
27e03b448338a9_GRCm38_to_NCBIM37.chain added
27e03b24e94ab0_NCBIM36_to_GRCm38.chain added
27e03b3280f271_NCBIM37_to_GRCm38.chain added
27e03b29d22aaa_1000G_omni2.5.b37.vcf.gz added
27e03b7f67459b_1000G_omni2.5.b37.vcf.gz.tbi added
27e03b53cce119_Mills_and_1000G_gold_standard.indels.b37.vcf.gz added
27e03b5d952175_Mills_and_1000G_gold_standard.indels.b37.vcf.gz.tbi added
27e03b54fe6341_1000G_omni2.5.hg38.vcf.gz added
27e03bb2d1887_1000G_omni2.5.hg38.vcf.gz.tbi added
27e03b7b3983e6_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz added
27e03b1fb4d3b6_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz.tbi added
27e03b71da836_af-only-gnomad.raw.sites.vcf added
27e03b69bfd4a0_af-only-gnomad.raw.sites.vcf.idx added
27e03b3009a284_Mutect2-exome-panel.vcf.idx added
27e03b2266890_Mutect2-WGS-panel-b37.vcf added
27e03b380d13bb_Mutect2-WGS-panel-b37.vcf.idx added
27e03b3863dfb8_small_exac_common_3.vcf added
27e03b73efa47c_small_exac_common_3.vcf.idx added
27e03b5ee25e37_1000g_pon.hg38.vcf.gz added
27e03b369caf7d_1000g_pon.hg38.vcf.gz.tbi added
27e03bc7415d_af-only-gnomad.hg38.vcf.gz added
27e03b784860cb_af-only-gnomad.hg38.vcf.gz.tbi added
27e03b2261c03_small_exac_common_3.hg38.vcf.gz added
27e03baa3dd26_small_exac_common_3.hg38.vcf.gz.tbi added
27e03b2afc7962_gencode.v41.annotation.gtf added
27e03b3f573003_gencode.v42.annotation.gtf added
27e03b35fe31fb_gencode.vM30.annotation.gtf added
27e03b7e595809_gencode.vM31.annotation.gtf added
27e03b42fcd59a_gencode.v41.transcripts.fa added
27e03b43f12c2a_gencode.v41.transcripts.fa.fai added
27e03b4e1d71ae_gencode.v42.transcripts.fa added
27e03b7800e43_gencode.v42.transcripts.fa.fai added
27e03b68da76da_gencode.vM30.pc_transcripts.fa added
27e03b9e641f_gencode.vM30.pc_transcripts.fa.fai added
27e03b315238ed_gencode.vM31.pc_transcripts.fa added
27e03b6841bc75_gencode.vM31.pc_transcripts.fa.fai added
27e03b546b4538_GRCh38.primary_assembly.genome.fa.1.ht2 added
27e03bee75a63_GRCh38.primary_assembly.genome.fa.2.ht2 added
27e03b3d401fb6_GRCh38.primary_assembly.genome.fa.3.ht2 added
27e03b5f985dc0_GRCh38.primary_assembly.genome.fa.4.ht2 added
27e03ba20de49_GRCh38.primary_assembly.genome.fa.5.ht2 added
27e03b5cf4f36c_GRCh38.primary_assembly.genome.fa.6.ht2 added
27e03b66b605f6_GRCh38.primary_assembly.genome.fa.7.ht2 added
27e03b73e0b2e9_GRCh38.primary_assembly.genome.fa.8.ht2 added
27e03bcfe95f1_GRCh38_full_analysis_set_plus_decoy_hla.fa.fai added
27e03b68dc6e86_GRCh38_full_analysis_set_plus_decoy_hla.fa.amb added
27e03b2bedc6a4_GRCh38_full_analysis_set_plus_decoy_hla.fa.ann added
27e03b456275a9_GRCh38_full_analysis_set_plus_decoy_hla.fa.bwt added
27e03b5ccc1303_GRCh38_full_analysis_set_plus_decoy_hla.fa.pac added
27e03bad024db_GRCh38_full_analysis_set_plus_decoy_hla.fa.sa added
27e03b7bff2526_GRCh38_full_analysis_set_plus_decoy_hla.fa added
27e03b5d935460_GRCh38.primary_assembly.genome.fa.fai added
27e03b31885a7_GRCh38.primary_assembly.genome.fa.amb added
27e03b7e25412a_GRCh38.primary_assembly.genome.fa.ann added
27e03b68373186_GRCh38.primary_assembly.genome.fa.bwt added
27e03b2e14ff09_GRCh38.primary_assembly.genome.fa.pac added
27e03b3d7c712d_GRCh38.primary_assembly.genome.fa.sa added
27e03b1e356381_GRCh38.primary_assembly.genome.fa added
27e03b2c6e5712_hs37d5.fa.fai added
27e03b7946c8_hs37d5.fa.amb added
27e03b62268fab_hs37d5.fa.ann added
27e03b7a8bc8c1_hs37d5.fa.bwt added
27e03b7f9550b_hs37d5.fa.pac added
27e03b4b010685_hs37d5.fa.sa added
27e03b7b2a2ce0_hs37d5.fa added
27e03b394b8df9_complete_ref_lens.bin added
27e03b3342c2fa_ctable.bin added
27e03b4f957219_ctg_offsets.bin added
27e03b4832e85c_duplicate_clusters.tsv added
27e03b7082e2b1_info.json added
27e03b2f2dcfd9_mphf.bin added
27e03b5253c6a5_pos.bin added
27e03b4d77d61d_pre_indexing.log added
27e03b15e3d5cf_rank.bin added
27e03b4634798f_ref_indexing.log added
27e03b5a766c0e_refAccumLengths.bin added
27e03b7ec04456_reflengths.bin added
27e03b72224033_refseq.bin added
27e03b1fd8e1b7_seq.bin added
27e03b5b8c5759_versionInfo.json added
27e03b7cf2650f_salmon_index added
27e03b1bd806de_chrLength.txt added
27e03b391fabb9_chrName.txt added
27e03baeab6_chrNameLength.txt added
27e03b19fd4808_chrStart.txt added
27e03b2156dd40_exonGeTrInfo.tab added
27e03b2e1fe9bf_exonInfo.tab added
27e03b5779b935_geneInfo.tab added
27e03b3f8c40c1_Genome added
27e03b5a8e40d2_genomeParameters.txt added
27e03b57f2fffd_Log.out added
27e03b21b2d06d_SA added
27e03b551a0993_SAindex added
27e03b5fec5509_sjdbInfo.txt added
27e03b6cb3d6f2_sjdbList.fromGTF.out.tab added
27e03b50443673_sjdbList.out.tab added
27e03b1937e302_transcriptInfo.tab added
27e03b1ff699ed_GRCh38.GENCODE.v42_100 added
27e03b1fd9a88c_knownGene_hg38.sql added
27e03b616acb5e_knownGene_hg38.txt added
27e03b10797c9e_refGene_hg38.sql added
27e03b4f077865_refGene_hg38.txt added
27e03b33be9203_knownGene_mm39.sql added
27e03b5df152bb_knownGene_mm39.txt added
27e03b64eb4e35_refGene_mm39.sql added
27e03b79f30b92_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/bbs-3.20-bioc/tmpdir/Rtmptf1zcW/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
18.961 1.121 20.386
ReUseData.Rcheck/ReUseData-Ex.timings
| name | user | system | elapsed | |
| dataHub-class | 5.695 | 0.254 | 5.953 | |
| dataSearch | 1.086 | 0.011 | 1.098 | |
| dataUpdate | 0.001 | 0.000 | 0.000 | |
| getCloudData | 2.583 | 0.122 | 3.469 | |
| getData | 0 | 0 | 0 | |
| meta_data | 0.001 | 0.000 | 0.000 | |
| recipeHub-class | 0.135 | 0.005 | 0.140 | |
| recipeLoad | 1.265 | 0.060 | 1.326 | |
| recipeMake | 0 | 0 | 0 | |
| recipeSearch | 0.536 | 0.016 | 0.552 | |
| recipeUpdate | 0.000 | 0.001 | 0.000 | |