Qian Liu
| Snapshot Date: 2024-12-30 13:00 -0500 (Mon, 30 Dec 2024) |
| 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 -0500 (Tue, 29 Oct 2024) |
| Back to Multiple platform build/check report for BioC 3.20: simplified long |
|
This page was generated on 2025-01-02 12:06 -0500 (Thu, 02 Jan 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4744 |
| palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" | 4487 |
| merida1 | macOS 12.7.5 Monterey | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4515 |
| kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4467 |
| 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 | | ||||||||
|
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: /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_1.6.0.tar.gz |
| StartedAt: 2024-12-31 09:35:53 -0500 (Tue, 31 Dec 2024) |
| EndedAt: 2024-12-31 09:43:48 -0500 (Tue, 31 Dec 2024) |
| EllapsedTime: 474.4 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_1.6.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/ReUseData.Rcheck’
* using R version 4.4.2 (2024-10-31)
* using platform: x86_64-apple-darwin20
* R was compiled by
Apple clang version 14.0.0 (clang-1400.0.29.202)
GNU Fortran (GCC) 12.2.0
* 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 ‘1.6.0’
* 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 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 12.266 1.240 20.567
getCloudData 4.602 0.205 5.759
* 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-3.20-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/4.4-x86_64/Resources/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 4.4.2 (2024-10-31) -- "Pile of Leaves"
Copyright (C) 2024 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...
104733038f4b5_GRCh38.primary_assembly.genome.fa.1.bt2 added
104736b49afce_GRCh38.primary_assembly.genome.fa.2.bt2 added
1047332b53469_GRCh38.primary_assembly.genome.fa.3.bt2 added
104731683f381_GRCh38.primary_assembly.genome.fa.4.bt2 added
1047330e7a5b3_GRCh38.primary_assembly.genome.fa.rev.1.bt2 added
10473382fa3da_GRCh38.primary_assembly.genome.fa.rev.2.bt2 added
104733fae5a07_outfile.txt added
104734f98a23a_GRCh37_to_GRCh38.chain added
104732dc2b6a9_GRCh37_to_NCBI34.chain added
104734a6628b7_GRCh37_to_NCBI35.chain added
1047378fb2c89_GRCh37_to_NCBI36.chain added
104733229146c_GRCh38_to_GRCh37.chain added
1047326fbd82e_GRCh38_to_NCBI34.chain added
10473602dc800_GRCh38_to_NCBI35.chain added
104735da5a954_GRCh38_to_NCBI36.chain added
10473270ff9d4_NCBI34_to_GRCh37.chain added
104739dae155_NCBI34_to_GRCh38.chain added
10473ff9881_NCBI35_to_GRCh37.chain added
10473c753daa_NCBI35_to_GRCh38.chain added
1047365236a49_NCBI36_to_GRCh37.chain added
104737817127e_NCBI36_to_GRCh38.chain added
1047332bf4bca_GRCm38_to_NCBIM36.chain added
104732d08d4cd_GRCm38_to_NCBIM37.chain added
104731ecaf5d4_NCBIM36_to_GRCm38.chain added
104731ed14117_NCBIM37_to_GRCm38.chain added
104733c085ccf_1000G_omni2.5.b37.vcf.gz added
10473490538d3_1000G_omni2.5.b37.vcf.gz.tbi added
1047375d5ca18_Mills_and_1000G_gold_standard.indels.b37.vcf.gz added
1047326c72a18_Mills_and_1000G_gold_standard.indels.b37.vcf.gz.tbi added
104735d9ca18b_1000G_omni2.5.hg38.vcf.gz added
104735631dcb0_1000G_omni2.5.hg38.vcf.gz.tbi added
10473638fd305_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz added
1047377672053_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz.tbi added
10473137b6663_af-only-gnomad.raw.sites.vcf added
10473a7ef793_af-only-gnomad.raw.sites.vcf.idx added
1047315afd947_Mutect2-exome-panel.vcf.idx added
104734be1cf70_Mutect2-WGS-panel-b37.vcf added
1047355f9e8fb_Mutect2-WGS-panel-b37.vcf.idx added
10473a2ee2d6_small_exac_common_3.vcf added
10473c2e54d3_small_exac_common_3.vcf.idx added
1047335c2eee4_1000g_pon.hg38.vcf.gz added
1047310d1d64f_1000g_pon.hg38.vcf.gz.tbi added
10473404ce529_af-only-gnomad.hg38.vcf.gz added
10473785907b9_af-only-gnomad.hg38.vcf.gz.tbi added
104731d0a4069_small_exac_common_3.hg38.vcf.gz added
10473c0abc64_small_exac_common_3.hg38.vcf.gz.tbi added
1047314d64f69_gencode.v41.annotation.gtf added
104731f7812f_gencode.v42.annotation.gtf added
10473204235ab_gencode.vM30.annotation.gtf added
104735ad17e18_gencode.vM31.annotation.gtf added
104736fad883c_gencode.v41.transcripts.fa added
1047369cb546b_gencode.v41.transcripts.fa.fai added
1047324137310_gencode.v42.transcripts.fa added
1047378e731f0_gencode.v42.transcripts.fa.fai added
10473127fc193_gencode.vM30.pc_transcripts.fa added
1047317da362_gencode.vM30.pc_transcripts.fa.fai added
104735f7177b1_gencode.vM31.pc_transcripts.fa added
104731269366b_gencode.vM31.pc_transcripts.fa.fai added
104733973b43e_GRCh38.primary_assembly.genome.fa.1.ht2 added
104735b3e6fe9_GRCh38.primary_assembly.genome.fa.2.ht2 added
10473602558cb_GRCh38.primary_assembly.genome.fa.3.ht2 added
1047333e8a8bd_GRCh38.primary_assembly.genome.fa.4.ht2 added
104736f9e2aea_GRCh38.primary_assembly.genome.fa.5.ht2 added
104737913a1e5_GRCh38.primary_assembly.genome.fa.6.ht2 added
1047377e9ff7c_GRCh38.primary_assembly.genome.fa.7.ht2 added
1047323846365_GRCh38.primary_assembly.genome.fa.8.ht2 added
1047348998e1a_GRCh38_full_analysis_set_plus_decoy_hla.fa.fai added
1047359407232_GRCh38_full_analysis_set_plus_decoy_hla.fa.amb added
1047316095e65_GRCh38_full_analysis_set_plus_decoy_hla.fa.ann added
1047341144430_GRCh38_full_analysis_set_plus_decoy_hla.fa.bwt added
104731988ccb1_GRCh38_full_analysis_set_plus_decoy_hla.fa.pac added
104736436858f_GRCh38_full_analysis_set_plus_decoy_hla.fa.sa added
10473377aa2af_GRCh38_full_analysis_set_plus_decoy_hla.fa added
10473544eab9d_GRCh38.primary_assembly.genome.fa.fai added
1047378e4fba8_GRCh38.primary_assembly.genome.fa.amb added
10473146109a_GRCh38.primary_assembly.genome.fa.ann added
104731eebef1d_GRCh38.primary_assembly.genome.fa.bwt added
10473139f68c7_GRCh38.primary_assembly.genome.fa.pac added
104734697eae1_GRCh38.primary_assembly.genome.fa.sa added
104731fbd7dfc_GRCh38.primary_assembly.genome.fa added
10473519a3bab_hs37d5.fa.fai added
1047364c38167_hs37d5.fa.amb added
104735f64c4df_hs37d5.fa.ann added
1047350b93d66_hs37d5.fa.bwt added
10473316e1cf1_hs37d5.fa.pac added
10473342e2b91_hs37d5.fa.sa added
10473432e575a_hs37d5.fa added
104731768f82b_complete_ref_lens.bin added
104736c7cdb0e_ctable.bin added
104737911abc6_ctg_offsets.bin added
1047377249242_duplicate_clusters.tsv added
104731fe682a_info.json added
1047365689e6b_mphf.bin added
104733778b6d0_pos.bin added
10473562a2e23_pre_indexing.log added
104736b3b2806_rank.bin added
1047378c0d8e9_ref_indexing.log added
104733ce0e6ee_refAccumLengths.bin added
104735159327b_reflengths.bin added
10473370152f6_refseq.bin added
1047337edb0b0_seq.bin added
1047355eb0f7f_versionInfo.json added
104733b4686ea_salmon_index added
1047313438b0d_chrLength.txt added
10473375e0c5c_chrName.txt added
104737f7d8869_chrNameLength.txt added
10473a86e6e3_chrStart.txt added
104731ea0467b_exonGeTrInfo.tab added
104732c7344f2_exonInfo.tab added
1047343b382aa_geneInfo.tab added
104733e47899f_Genome added
104734a9c45aa_genomeParameters.txt added
1047359a1c22a_Log.out added
10473ad2815f_SA added
1047322b8986_SAindex added
104737851bd86_sjdbInfo.txt added
104733e71e620_sjdbList.fromGTF.out.tab added
1047327bb5ee7_sjdbList.out.tab added
104737e53a411_transcriptInfo.tab added
10473253898e2_GRCh38.GENCODE.v42_100 added
1047326bd3085_knownGene_hg38.sql added
104734ebc7fa1_knownGene_hg38.txt added
10473395f4b69_refGene_hg38.sql added
104731f4ff7ec_refGene_hg38.txt added
104733b1db703_knownGene_mm39.sql added
104731bda4447_knownGene_mm39.txt added
1047316b89f9a_refGene_mm39.sql added
1047332f6431d_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/Rtmps949BZ/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
39.824 4.463 59.293
ReUseData.Rcheck/ReUseData-Ex.timings
| name | user | system | elapsed | |
| dataHub-class | 12.266 | 1.240 | 20.567 | |
| dataSearch | 2.409 | 0.075 | 2.496 | |
| dataUpdate | 0.000 | 0.001 | 0.001 | |
| getCloudData | 4.602 | 0.205 | 5.759 | |
| getData | 0.001 | 0.001 | 0.001 | |
| meta_data | 0.001 | 0.001 | 0.002 | |
| recipeHub-class | 0.273 | 0.018 | 0.333 | |
| recipeLoad | 2.845 | 0.135 | 3.056 | |
| recipeMake | 0.001 | 0.001 | 0.002 | |
| recipeSearch | 1.142 | 0.052 | 1.205 | |
| recipeUpdate | 0.000 | 0.000 | 0.001 | |