Qian Liu
| Snapshot Date: 2025-09-19 13:45 -0400 (Fri, 19 Sep 2025) |
| git_url: https://git.bioconductor.org/packages/ReUseData |
| git_branch: devel |
| git_last_commit: c5927b9 |
| git_last_commit_date: 2025-04-15 13:01:44 -0400 (Tue, 15 Apr 2025) |
| Back to Multiple platform build/check report for BioC 3.22: simplified long |
|
This page was generated on 2025-09-20 12:05 -0400 (Sat, 20 Sep 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" | 4814 |
| lconway | macOS 12.7.1 Monterey | x86_64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4603 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4547 |
| taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4553 |
| 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 1751/2333 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| ReUseData 1.9.0 (landing page) Qian Liu
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson3 | macOS 13.7.7 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: 1.9.0 |
| 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_1.9.0.tar.gz |
| StartedAt: 2025-09-19 23:26:42 -0400 (Fri, 19 Sep 2025) |
| EndedAt: 2025-09-19 23:29:14 -0400 (Fri, 19 Sep 2025) |
| EllapsedTime: 151.7 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_1.9.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.22-bioc/meat/ReUseData.Rcheck’
* using R version 4.5.1 Patched (2025-09-10 r88807)
* using platform: x86_64-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 Monterey 12.7.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘ReUseData/DESCRIPTION’ ... OK
* this is package ‘ReUseData’ version ‘1.9.0’
* 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
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
dataHub-class 7.475 0.878 8.485
getCloudData 2.730 0.157 7.311
* 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-3.22-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-x86_64/Resources/library’ * installing *source* package ‘ReUseData’ ... ** this is package ‘ReUseData’ version ‘1.9.0’ ** 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 version 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-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...
6cc3729de7dc_GRCh38.primary_assembly.genome.fa.1.bt2 added
6cc35ce1574d_GRCh38.primary_assembly.genome.fa.2.bt2 added
6cc34e2aafde_GRCh38.primary_assembly.genome.fa.3.bt2 added
6cc354803fe9_GRCh38.primary_assembly.genome.fa.4.bt2 added
6cc32fe40556_GRCh38.primary_assembly.genome.fa.rev.1.bt2 added
6cc3231a69aa_GRCh38.primary_assembly.genome.fa.rev.2.bt2 added
6cc31b0f29e7_outfile.txt added
6cc3880a92_GRCh37_to_GRCh38.chain added
6cc3636df783_GRCh37_to_NCBI34.chain added
6cc34894ec74_GRCh37_to_NCBI35.chain added
6cc3292fd8e6_GRCh37_to_NCBI36.chain added
6cc3448f92a_GRCh38_to_GRCh37.chain added
6cc352de3698_GRCh38_to_NCBI34.chain added
6cc37ad25fa8_GRCh38_to_NCBI35.chain added
6cc39864d97_GRCh38_to_NCBI36.chain added
6cc3504ff963_NCBI34_to_GRCh37.chain added
6cc3327dfbc6_NCBI34_to_GRCh38.chain added
6cc36d1c9e0f_NCBI35_to_GRCh37.chain added
6cc371cd22bf_NCBI35_to_GRCh38.chain added
6cc352a463f7_NCBI36_to_GRCh37.chain added
6cc3269f1784_NCBI36_to_GRCh38.chain added
6cc316c0eeeb_GRCm38_to_NCBIM36.chain added
6cc3548591f8_GRCm38_to_NCBIM37.chain added
6cc3d325c22_NCBIM36_to_GRCm38.chain added
6cc3653ec2f2_NCBIM37_to_GRCm38.chain added
6cc37b70d1cb_1000G_omni2.5.b37.vcf.gz added
6cc32bdda5bd_1000G_omni2.5.b37.vcf.gz.tbi added
6cc364ac31ca_Mills_and_1000G_gold_standard.indels.b37.vcf.gz added
6cc364f8f868_Mills_and_1000G_gold_standard.indels.b37.vcf.gz.tbi added
6cc3157ca7a2_1000G_omni2.5.hg38.vcf.gz added
6cc32ae187b3_1000G_omni2.5.hg38.vcf.gz.tbi added
6cc33c940ec3_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz added
6cc31c554347_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz.tbi added
6cc321b3f8d9_af-only-gnomad.raw.sites.vcf added
6cc32e967fd8_af-only-gnomad.raw.sites.vcf.idx added
6cc31aa355cd_Mutect2-exome-panel.vcf.idx added
6cc359561364_Mutect2-WGS-panel-b37.vcf added
6cc32213380e_Mutect2-WGS-panel-b37.vcf.idx added
6cc31bc5309c_small_exac_common_3.vcf added
6cc32efa6002_small_exac_common_3.vcf.idx added
6cc337b53b66_1000g_pon.hg38.vcf.gz added
6cc35b4ec21c_1000g_pon.hg38.vcf.gz.tbi added
6cc3fa9eb19_af-only-gnomad.hg38.vcf.gz added
6cc35c89be57_af-only-gnomad.hg38.vcf.gz.tbi added
6cc3572f7137_small_exac_common_3.hg38.vcf.gz added
6cc36bb1fe98_small_exac_common_3.hg38.vcf.gz.tbi added
6cc372c1e464_gencode.v41.annotation.gtf added
6cc317799c18_gencode.v42.annotation.gtf added
6cc330f6f7b2_gencode.vM30.annotation.gtf added
6cc325ffe03b_gencode.vM31.annotation.gtf added
6cc341da54fa_gencode.v41.transcripts.fa added
6cc365010adc_gencode.v41.transcripts.fa.fai added
6cc327702552_gencode.v42.transcripts.fa added
6cc333a23eb8_gencode.v42.transcripts.fa.fai added
6cc360c3bc83_gencode.vM30.pc_transcripts.fa added
6cc3528d6e16_gencode.vM30.pc_transcripts.fa.fai added
6cc3433690b1_gencode.vM31.pc_transcripts.fa added
6cc3335576f0_gencode.vM31.pc_transcripts.fa.fai added
6cc32ff3a0e4_GRCh38.primary_assembly.genome.fa.1.ht2 added
6cc323c7f154_GRCh38.primary_assembly.genome.fa.2.ht2 added
6cc31bb4d426_GRCh38.primary_assembly.genome.fa.3.ht2 added
6cc37cd418ff_GRCh38.primary_assembly.genome.fa.4.ht2 added
6cc348b54d5f_GRCh38.primary_assembly.genome.fa.5.ht2 added
6cc376eabd43_GRCh38.primary_assembly.genome.fa.6.ht2 added
6cc32d2fb6b3_GRCh38.primary_assembly.genome.fa.7.ht2 added
6cc31783b8f2_GRCh38.primary_assembly.genome.fa.8.ht2 added
6cc348e323ed_GRCh38_full_analysis_set_plus_decoy_hla.fa.fai added
6cc3384bc1fd_GRCh38_full_analysis_set_plus_decoy_hla.fa.amb added
6cc375ace5ea_GRCh38_full_analysis_set_plus_decoy_hla.fa.ann added
6cc32a2aa201_GRCh38_full_analysis_set_plus_decoy_hla.fa.bwt added
6cc354f20547_GRCh38_full_analysis_set_plus_decoy_hla.fa.pac added
6cc35d38a3e2_GRCh38_full_analysis_set_plus_decoy_hla.fa.sa added
6cc3318f7a3e_GRCh38_full_analysis_set_plus_decoy_hla.fa added
6cc342a295dd_GRCh38.primary_assembly.genome.fa.fai added
6cc3401d0258_GRCh38.primary_assembly.genome.fa.amb added
6cc33085004a_GRCh38.primary_assembly.genome.fa.ann added
6cc36bd61328_GRCh38.primary_assembly.genome.fa.bwt added
6cc33383de67_GRCh38.primary_assembly.genome.fa.pac added
6cc3167e569d_GRCh38.primary_assembly.genome.fa.sa added
6cc3406868f4_GRCh38.primary_assembly.genome.fa added
6cc36c28c35_hs37d5.fa.fai added
6cc34e82ef0a_hs37d5.fa.amb added
6cc3761ba1ca_hs37d5.fa.ann added
6cc3101b115a_hs37d5.fa.bwt added
6cc3611033f8_hs37d5.fa.pac added
6cc36ec41090_hs37d5.fa.sa added
6cc3a1b96c0_hs37d5.fa added
6cc319461c6f_complete_ref_lens.bin added
6cc349f4c85f_ctable.bin added
6cc3658efae7_ctg_offsets.bin added
6cc3dfa87c8_duplicate_clusters.tsv added
6cc33ae862a3_info.json added
6cc36ea3d98b_mphf.bin added
6cc3471f6d6c_pos.bin added
6cc36048f1ee_pre_indexing.log added
6cc3550371a4_rank.bin added
6cc35519f196_ref_indexing.log added
6cc31a43da80_refAccumLengths.bin added
6cc35cbe16f8_reflengths.bin added
6cc343d62359_refseq.bin added
6cc31faacada_seq.bin added
6cc35ebbe74_versionInfo.json added
6cc33824b4b5_salmon_index added
6cc371d3f3de_chrLength.txt added
6cc3122fae34_chrName.txt added
6cc37855e13f_chrNameLength.txt added
6cc34e372cd1_chrStart.txt added
6cc385f7575_exonGeTrInfo.tab added
6cc33318589e_exonInfo.tab added
6cc33620747_geneInfo.tab added
6cc318cbc80d_Genome added
6cc36abada32_genomeParameters.txt added
6cc3114b3f5c_Log.out added
6cc3632cb9e2_SA added
6cc3d5fd74c_SAindex added
6cc3f2fc570_sjdbInfo.txt added
6cc394b43da_sjdbList.fromGTF.out.tab added
6cc32c53a1fa_sjdbList.out.tab added
6cc326af3ad2_transcriptInfo.tab added
6cc33a3ec4d5_GRCh38.GENCODE.v42_100 added
6cc36eec99d2_knownGene_hg38.sql added
6cc36f66e2e2_knownGene_hg38.txt added
6cc34bb99c91_refGene_hg38.sql added
6cc36d61a6e_refGene_hg38.txt added
6cc352612f43_knownGene_mm39.sql added
6cc36a6601f5_knownGene_mm39.txt added
6cc34f0ab265_refGene_mm39.sql added
6cc347462d6d_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:
/tmp/Rtmp1kGdxq/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
22.308 2.422 25.854
ReUseData.Rcheck/ReUseData-Ex.timings
| name | user | system | elapsed | |
| dataHub-class | 7.475 | 0.878 | 8.485 | |
| dataSearch | 1.402 | 0.060 | 1.475 | |
| dataUpdate | 0.000 | 0.001 | 0.001 | |
| getCloudData | 2.730 | 0.157 | 7.311 | |
| getData | 0.001 | 0.000 | 0.001 | |
| meta_data | 0.001 | 0.000 | 0.001 | |
| recipeHub-class | 0.150 | 0.016 | 0.168 | |
| recipeLoad | 1.576 | 0.100 | 1.689 | |
| recipeMake | 0.000 | 0.000 | 0.001 | |
| recipeSearch | 0.657 | 0.045 | 0.709 | |
| recipeUpdate | 0.000 | 0.000 | 0.001 | |