Qian Liu
| Snapshot Date: 2025-03-26 13:40 -0400 (Wed, 26 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 2025-03-27 11:46 -0400 (Thu, 27 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" | 4783 |
| palomino7 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2025-03-01 r87860 ucrt) -- "Unsuffered Consequences" | 4552 |
| lconway | macOS 12.7.1 Monterey | x86_64 | R Under development (unstable) (2025-03-02 r87868) -- "Unsuffered Consequences" | 4581 |
| kjohnson3 | macOS 13.7.1 Ventura | arm64 | R Under development (unstable) (2025-03-02 r87868) -- "Unsuffered Consequences" | 4533 |
| kunpeng2 | Linux (openEuler 24.03 LTS) | aarch64 | R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" | 4463 |
| 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 1741/2315 | 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. |
| Package: ReUseData |
| Version: 1.7.0 |
| Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:ReUseData.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings ReUseData_1.7.0.tar.gz |
| StartedAt: 2025-03-26 21:05:02 -0400 (Wed, 26 Mar 2025) |
| EndedAt: 2025-03-26 21:05:53 -0400 (Wed, 26 Mar 2025) |
| EllapsedTime: 50.6 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: ReUseData.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:ReUseData.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings ReUseData_1.7.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/ReUseData.Rcheck’
* using R Under development (unstable) (2025-03-02 r87868)
* using platform: aarch64-apple-darwin20
* R was compiled by
Apple clang version 14.0.0 (clang-1400.0.29.202)
GNU Fortran (GCC) 14.2.0
* running under: macOS Ventura 13.7.1
* 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 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
* 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
‘/Users/biocbuild/bbs-3.21-bioc/meat/ReUseData.Rcheck/00check.log’
for details.
ReUseData.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL ReUseData ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/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) (2025-03-02 r87868) -- "Unsuffered Consequences"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin20
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...
14bd7ab193f7_GRCh38.primary_assembly.genome.fa.1.bt2 added
14bd20697c0f_GRCh38.primary_assembly.genome.fa.2.bt2 added
14bd6d4fcd68_GRCh38.primary_assembly.genome.fa.3.bt2 added
14bd12369ee9_GRCh38.primary_assembly.genome.fa.4.bt2 added
14bd3ffadc56_GRCh38.primary_assembly.genome.fa.rev.1.bt2 added
14bd6e97b2ea_GRCh38.primary_assembly.genome.fa.rev.2.bt2 added
14bd2963595f_outfile.txt added
14bd39808133_GRCh37_to_GRCh38.chain added
14bd23a258c3_GRCh37_to_NCBI34.chain added
14bd77717c7b_GRCh37_to_NCBI35.chain added
14bd3ba3ac80_GRCh37_to_NCBI36.chain added
14bd76922616_GRCh38_to_GRCh37.chain added
14bd7502ab2a_GRCh38_to_NCBI34.chain added
14bd2338e6a_GRCh38_to_NCBI35.chain added
14bd6cad247_GRCh38_to_NCBI36.chain added
14bd6db336cc_NCBI34_to_GRCh37.chain added
14bd10d2c358_NCBI34_to_GRCh38.chain added
14bd7d16cf08_NCBI35_to_GRCh37.chain added
14bd64725660_NCBI35_to_GRCh38.chain added
14bde84ec25_NCBI36_to_GRCh37.chain added
14bd38ab7895_NCBI36_to_GRCh38.chain added
14bd1799b44_GRCm38_to_NCBIM36.chain added
14bd56c08e1d_GRCm38_to_NCBIM37.chain added
14bd7bb23e69_NCBIM36_to_GRCm38.chain added
14bd731f9ef0_NCBIM37_to_GRCm38.chain added
14bd20fbd99c_1000G_omni2.5.b37.vcf.gz added
14bd768ba1ae_1000G_omni2.5.b37.vcf.gz.tbi added
14bd4923e34f_Mills_and_1000G_gold_standard.indels.b37.vcf.gz added
14bd53207d0c_Mills_and_1000G_gold_standard.indels.b37.vcf.gz.tbi added
14bd79f1c976_1000G_omni2.5.hg38.vcf.gz added
14bd70e1a085_1000G_omni2.5.hg38.vcf.gz.tbi added
14bd6cf1b5a8_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz added
14bd70cd6078_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz.tbi added
14bd3b78a023_af-only-gnomad.raw.sites.vcf added
14bd6c597855_af-only-gnomad.raw.sites.vcf.idx added
14bd65eb4c05_Mutect2-exome-panel.vcf.idx added
14bd3acc1089_Mutect2-WGS-panel-b37.vcf added
14bd2b51b087_Mutect2-WGS-panel-b37.vcf.idx added
14bd1c8549_small_exac_common_3.vcf added
14bd50727bad_small_exac_common_3.vcf.idx added
14bdc15c41e_1000g_pon.hg38.vcf.gz added
14bd68fe93c4_1000g_pon.hg38.vcf.gz.tbi added
14bd21975eb6_af-only-gnomad.hg38.vcf.gz added
14bd58cb0ff4_af-only-gnomad.hg38.vcf.gz.tbi added
14bd7b8489b6_small_exac_common_3.hg38.vcf.gz added
14bd3a6d4b14_small_exac_common_3.hg38.vcf.gz.tbi added
14bd5d5c2c03_gencode.v41.annotation.gtf added
14bd4e4da8d7_gencode.v42.annotation.gtf added
14bd4c87e36a_gencode.vM30.annotation.gtf added
14bd6d636b66_gencode.vM31.annotation.gtf added
14bd1a202da5_gencode.v41.transcripts.fa added
14bd3694b909_gencode.v41.transcripts.fa.fai added
14bd5e0019dd_gencode.v42.transcripts.fa added
14bd58a22c61_gencode.v42.transcripts.fa.fai added
14bd7f0fc1bc_gencode.vM30.pc_transcripts.fa added
14bd63785ecf_gencode.vM30.pc_transcripts.fa.fai added
14bd73989b0d_gencode.vM31.pc_transcripts.fa added
14bd27ebadc5_gencode.vM31.pc_transcripts.fa.fai added
14bd61dd74fc_GRCh38.primary_assembly.genome.fa.1.ht2 added
14bd122b7e96_GRCh38.primary_assembly.genome.fa.2.ht2 added
14bd6583b32b_GRCh38.primary_assembly.genome.fa.3.ht2 added
14bd2968001e_GRCh38.primary_assembly.genome.fa.4.ht2 added
14bd6adfc6ce_GRCh38.primary_assembly.genome.fa.5.ht2 added
14bd9753533_GRCh38.primary_assembly.genome.fa.6.ht2 added
14bd6df7ac1e_GRCh38.primary_assembly.genome.fa.7.ht2 added
14bd1f451df9_GRCh38.primary_assembly.genome.fa.8.ht2 added
14bd72b2d678_GRCh38_full_analysis_set_plus_decoy_hla.fa.fai added
14bd3b1e9b1c_GRCh38_full_analysis_set_plus_decoy_hla.fa.amb added
14bd56596996_GRCh38_full_analysis_set_plus_decoy_hla.fa.ann added
14bd8232324_GRCh38_full_analysis_set_plus_decoy_hla.fa.bwt added
14bd3ad814a8_GRCh38_full_analysis_set_plus_decoy_hla.fa.pac added
14bd40343fc6_GRCh38_full_analysis_set_plus_decoy_hla.fa.sa added
14bd26470118_GRCh38_full_analysis_set_plus_decoy_hla.fa added
14bd7f98e249_GRCh38.primary_assembly.genome.fa.fai added
14bde306811_GRCh38.primary_assembly.genome.fa.amb added
14bdc003b5e_GRCh38.primary_assembly.genome.fa.ann added
14bd63399e79_GRCh38.primary_assembly.genome.fa.bwt added
14bd5bd34cd3_GRCh38.primary_assembly.genome.fa.pac added
14bdd58dfbe_GRCh38.primary_assembly.genome.fa.sa added
14bd45c939ca_GRCh38.primary_assembly.genome.fa added
14bd1df12091_hs37d5.fa.fai added
14bd41911ef2_hs37d5.fa.amb added
14bd1e86c37f_hs37d5.fa.ann added
14bd218cd681_hs37d5.fa.bwt added
14bd2556c05c_hs37d5.fa.pac added
14bd626eeb2a_hs37d5.fa.sa added
14bd601144e2_hs37d5.fa added
14bddc182b4_complete_ref_lens.bin added
14bd1b6bfe7a_ctable.bin added
14bd4f1009a6_ctg_offsets.bin added
14bd25e999d7_duplicate_clusters.tsv added
14bdb7305b3_info.json added
14bd2c7b30a4_mphf.bin added
14bd4bb675cc_pos.bin added
14bd37efcae9_pre_indexing.log added
14bd5ff2a3af_rank.bin added
14bd32d8675f_ref_indexing.log added
14bd1d6aa80d_refAccumLengths.bin added
14bd453efc91_reflengths.bin added
14bd2a37b71b_refseq.bin added
14bd2fd66344_seq.bin added
14bd240f1de5_versionInfo.json added
14bd5c73b7e1_salmon_index added
14bd312d4432_chrLength.txt added
14bd12d847d7_chrName.txt added
14bd35547deb_chrNameLength.txt added
14bd3e16eaa7_chrStart.txt added
14bd528799c9_exonGeTrInfo.tab added
14bd44818573_exonInfo.tab added
14bd13606428_geneInfo.tab added
14bd1d4f8808_Genome added
14bd506bd440_genomeParameters.txt added
14bd573bdeff_Log.out added
14bd1bad6417_SA added
14bd14863033_SAindex added
14bd75c66ecb_sjdbInfo.txt added
14bd36940dd5_sjdbList.fromGTF.out.tab added
14bd321836f1_sjdbList.out.tab added
14bd53bf21e8_transcriptInfo.tab added
14bd294b314c_GRCh38.GENCODE.v42_100 added
14bd79189c2_knownGene_hg38.sql added
14bd63eb236f_knownGene_hg38.txt added
14bd62637fa8_refGene_hg38.sql added
14bd7252210e_refGene_hg38.txt added
14bd6df858c4_knownGene_mm39.sql added
14bd4b8be443_knownGene_mm39.txt added
14bd4d371174_refGene_mm39.sql added
14bd5a5afe46_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:
/var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpDw0Exb/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
7.341 1.082 9.108
ReUseData.Rcheck/ReUseData-Ex.timings
| name | user | system | elapsed | |
| dataHub-class | 1.888 | 0.224 | 2.117 | |
| dataSearch | 0.322 | 0.015 | 0.337 | |
| dataUpdate | 0 | 0 | 0 | |
| getCloudData | 0.848 | 0.051 | 1.587 | |
| getData | 0 | 0 | 0 | |
| meta_data | 0 | 0 | 0 | |
| recipeHub-class | 0.036 | 0.004 | 0.040 | |
| recipeLoad | 0.377 | 0.029 | 0.408 | |
| recipeMake | 0 | 0 | 0 | |
| recipeSearch | 0.161 | 0.013 | 0.176 | |
| recipeUpdate | 0 | 0 | 0 | |