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 11:44 -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. |
| 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: 2025-03-21 23:30:51 -0400 (Fri, 21 Mar 2025) |
| EndedAt: 2025-03-21 23:33:26 -0400 (Fri, 21 Mar 2025) |
| EllapsedTime: 154.9 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: 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 ‘1.7.0’
* 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
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
dataHub-class 7.243 0.872 8.222
getCloudData 2.657 0.154 6.544
* 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-x86_64/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: 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...
ef405d664790_GRCh38.primary_assembly.genome.fa.1.bt2 added
ef4065e46ed7_GRCh38.primary_assembly.genome.fa.2.bt2 added
ef4078291983_GRCh38.primary_assembly.genome.fa.3.bt2 added
ef40524a2516_GRCh38.primary_assembly.genome.fa.4.bt2 added
ef401c8f18f_GRCh38.primary_assembly.genome.fa.rev.1.bt2 added
ef402f6ae433_GRCh38.primary_assembly.genome.fa.rev.2.bt2 added
ef4012abe897_outfile.txt added
ef4054331b14_GRCh37_to_GRCh38.chain added
ef406736e93b_GRCh37_to_NCBI34.chain added
ef40460a556d_GRCh37_to_NCBI35.chain added
ef40506e8b07_GRCh37_to_NCBI36.chain added
ef40969a1d2_GRCh38_to_GRCh37.chain added
ef4075fee6d1_GRCh38_to_NCBI34.chain added
ef4031e3dfdc_GRCh38_to_NCBI35.chain added
ef40677dfe1a_GRCh38_to_NCBI36.chain added
ef40b5920b_NCBI34_to_GRCh37.chain added
ef401087108a_NCBI34_to_GRCh38.chain added
ef40134edc80_NCBI35_to_GRCh37.chain added
ef401e6e6167_NCBI35_to_GRCh38.chain added
ef4060bcc0cc_NCBI36_to_GRCh37.chain added
ef40815c2b2_NCBI36_to_GRCh38.chain added
ef404ca13843_GRCm38_to_NCBIM36.chain added
ef406c74de02_GRCm38_to_NCBIM37.chain added
ef406c9b8cee_NCBIM36_to_GRCm38.chain added
ef40584194f6_NCBIM37_to_GRCm38.chain added
ef40399acfbe_1000G_omni2.5.b37.vcf.gz added
ef4062bce07d_1000G_omni2.5.b37.vcf.gz.tbi added
ef405e36612f_Mills_and_1000G_gold_standard.indels.b37.vcf.gz added
ef40442684fb_Mills_and_1000G_gold_standard.indels.b37.vcf.gz.tbi added
ef403ce49db1_1000G_omni2.5.hg38.vcf.gz added
ef40452ceeb2_1000G_omni2.5.hg38.vcf.gz.tbi added
ef408eb0b99_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz added
ef407f466e61_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz.tbi added
ef4068f8e38e_af-only-gnomad.raw.sites.vcf added
ef402c23b579_af-only-gnomad.raw.sites.vcf.idx added
ef405c5f3192_Mutect2-exome-panel.vcf.idx added
ef406daf979e_Mutect2-WGS-panel-b37.vcf added
ef40230b3e54_Mutect2-WGS-panel-b37.vcf.idx added
ef4037290ec5_small_exac_common_3.vcf added
ef406888c3cd_small_exac_common_3.vcf.idx added
ef406aeefd58_1000g_pon.hg38.vcf.gz added
ef40703ad340_1000g_pon.hg38.vcf.gz.tbi added
ef4026034850_af-only-gnomad.hg38.vcf.gz added
ef4021808faf_af-only-gnomad.hg38.vcf.gz.tbi added
ef407f593b57_small_exac_common_3.hg38.vcf.gz added
ef403b470e12_small_exac_common_3.hg38.vcf.gz.tbi added
ef4035ecde25_gencode.v41.annotation.gtf added
ef4051ec6acb_gencode.v42.annotation.gtf added
ef4078575f71_gencode.vM30.annotation.gtf added
ef40303b3170_gencode.vM31.annotation.gtf added
ef407e2ac8cc_gencode.v41.transcripts.fa added
ef402ae509ca_gencode.v41.transcripts.fa.fai added
ef4022e5c2c6_gencode.v42.transcripts.fa added
ef401a566710_gencode.v42.transcripts.fa.fai added
ef401e8858f2_gencode.vM30.pc_transcripts.fa added
ef409878787_gencode.vM30.pc_transcripts.fa.fai added
ef4020d2b4f4_gencode.vM31.pc_transcripts.fa added
ef4069661001_gencode.vM31.pc_transcripts.fa.fai added
ef402ba4e7b6_GRCh38.primary_assembly.genome.fa.1.ht2 added
ef405768741c_GRCh38.primary_assembly.genome.fa.2.ht2 added
ef40a9f0719_GRCh38.primary_assembly.genome.fa.3.ht2 added
ef404e8affc1_GRCh38.primary_assembly.genome.fa.4.ht2 added
ef4079d0030_GRCh38.primary_assembly.genome.fa.5.ht2 added
ef4054775337_GRCh38.primary_assembly.genome.fa.6.ht2 added
ef4065f86b33_GRCh38.primary_assembly.genome.fa.7.ht2 added
ef4018461592_GRCh38.primary_assembly.genome.fa.8.ht2 added
ef40213230b1_GRCh38_full_analysis_set_plus_decoy_hla.fa.fai added
ef40661ac57d_GRCh38_full_analysis_set_plus_decoy_hla.fa.amb added
ef40679bc5e9_GRCh38_full_analysis_set_plus_decoy_hla.fa.ann added
ef4023de7923_GRCh38_full_analysis_set_plus_decoy_hla.fa.bwt added
ef4062e2fb3a_GRCh38_full_analysis_set_plus_decoy_hla.fa.pac added
ef4023dbcf8e_GRCh38_full_analysis_set_plus_decoy_hla.fa.sa added
ef4034178606_GRCh38_full_analysis_set_plus_decoy_hla.fa added
ef4074600ea1_GRCh38.primary_assembly.genome.fa.fai added
ef404e60a7b7_GRCh38.primary_assembly.genome.fa.amb added
ef402ba30794_GRCh38.primary_assembly.genome.fa.ann added
ef405c469bed_GRCh38.primary_assembly.genome.fa.bwt added
ef401fa713ef_GRCh38.primary_assembly.genome.fa.pac added
ef40120dc025_GRCh38.primary_assembly.genome.fa.sa added
ef4044c1c665_GRCh38.primary_assembly.genome.fa added
ef40dc83427_hs37d5.fa.fai added
ef4052d7f382_hs37d5.fa.amb added
ef405fb4064b_hs37d5.fa.ann added
ef4024095703_hs37d5.fa.bwt added
ef40612f9870_hs37d5.fa.pac added
ef407bc112e8_hs37d5.fa.sa added
ef4040c07cd1_hs37d5.fa added
ef401d429e8d_complete_ref_lens.bin added
ef40b749fd_ctable.bin added
ef4015a8169_ctg_offsets.bin added
ef405ce61530_duplicate_clusters.tsv added
ef4057931f6_info.json added
ef4057bf1048_mphf.bin added
ef4040c613f9_pos.bin added
ef40c4961a8_pre_indexing.log added
ef4025aa62e5_rank.bin added
ef405542bbb4_ref_indexing.log added
ef4010315227_refAccumLengths.bin added
ef40160886bf_reflengths.bin added
ef409c670e6_refseq.bin added
ef40431e110d_seq.bin added
ef406af18ee7_versionInfo.json added
ef4018dd168b_salmon_index added
ef405af30c6d_chrLength.txt added
ef40ab4f6c1_chrName.txt added
ef406eb3fe64_chrNameLength.txt added
ef406b029003_chrStart.txt added
ef40753cebd7_exonGeTrInfo.tab added
ef40729fac62_exonInfo.tab added
ef4050ee90b8_geneInfo.tab added
ef405e5f498a_Genome added
ef4041d5336d_genomeParameters.txt added
ef4014235adf_Log.out added
ef401d22f0cd_SA added
ef4060ef31ac_SAindex added
ef4077a644eb_sjdbInfo.txt added
ef4044f6ddab_sjdbList.fromGTF.out.tab added
ef402b5328ec_sjdbList.out.tab added
ef4060a3b42c_transcriptInfo.tab added
ef401b89e645_GRCh38.GENCODE.v42_100 added
ef407a6cca22_knownGene_hg38.sql added
ef407c4abcf8_knownGene_hg38.txt added
ef40ebc7d88_refGene_hg38.sql added
ef4078d57346_refGene_hg38.txt added
ef4058336a4_knownGene_mm39.sql added
ef4069784bcf_knownGene_mm39.txt added
ef4058b93921_refGene_mm39.sql added
ef406855d308_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/RtmpXZ5Wp4/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
24.769 3.730 29.508
ReUseData.Rcheck/ReUseData-Ex.timings
| name | user | system | elapsed | |
| dataHub-class | 7.243 | 0.872 | 8.222 | |
| dataSearch | 1.295 | 0.055 | 1.356 | |
| dataUpdate | 0.000 | 0.000 | 0.001 | |
| getCloudData | 2.657 | 0.154 | 6.544 | |
| getData | 0.000 | 0.001 | 0.000 | |
| meta_data | 0.001 | 0.000 | 0.001 | |
| recipeHub-class | 0.159 | 0.014 | 0.176 | |
| recipeLoad | 1.582 | 0.103 | 1.697 | |
| recipeMake | 0.000 | 0.001 | 0.002 | |
| recipeSearch | 0.687 | 0.044 | 0.734 | |
| recipeUpdate | 0.000 | 0.000 | 0.001 | |