| Back to Multiple platform build/check report for BioC 3.18: simplified long |
|
This page was generated on 2023-11-29 11:38:05 -0500 (Wed, 29 Nov 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 22.04.2 LTS) | x86_64 | 4.3.2 Patched (2023-11-13 r85521) -- "Eye Holes" | 4685 |
| palomino4 | Windows Server 2022 Datacenter | x64 | 4.3.2 (2023-10-31 ucrt) -- "Eye Holes" | 4420 |
| lconway | macOS 12.7.1 Monterey | x86_64 | 4.3.2 Patched (2023-11-01 r85457) -- "Eye Holes" | 4439 |
| 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 1725/2266 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| ReUseData 1.2.1 (landing page) Qian Liu
| nebbiolo2 | Linux (Ubuntu 22.04.2 LTS) / x86_64 | OK | OK | ERROR | |||||||||
| palomino4 | Windows Server 2022 Datacenter / x64 | ... NOT SUPPORTED ... | ||||||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | ERROR | OK | |||||||||
| kjohnson1 | macOS 13.6.1 Ventura / arm64 | see weekly results here | ||||||||||||
|
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: 1.2.1 |
| 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_1.2.1.tar.gz |
| StartedAt: 2023-11-28 22:37:56 -0500 (Tue, 28 Nov 2023) |
| EndedAt: 2023-11-28 22:40:40 -0500 (Tue, 28 Nov 2023) |
| EllapsedTime: 163.4 seconds |
| RetCode: 1 |
| Status: ERROR |
| CheckDir: ReUseData.Rcheck |
| Warnings: NA |
##############################################################################
##############################################################################
###
### 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_1.2.1.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.18-bioc/meat/ReUseData.Rcheck’
* using R version 4.3.2 Patched (2023-11-01 r85457)
* using platform: x86_64-apple-darwin20 (64-bit)
* R was compiled by
Apple clang version 14.0.3 (clang-1403.0.22.14.1)
GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘ReUseData/DESCRIPTION’ ... OK
* this is package ‘ReUseData’ version ‘1.2.1’
* 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 R 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 ... ERROR
Running examples in ‘ReUseData-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: getCloudData
> ### Title: getCloudData Download the pregenerated curated data sets from
> ### ReUseData cloud bucket
> ### Aliases: getCloudData
>
> ### ** Examples
>
> outdir <- file.path(tempdir(), "gcpData")
> dataUpdate(outdir, cloud=TRUE)
Updating data record...
c7055ef38bb2_GRCh38.primary_assembly.genome.fa.1.bt2 added
c705475883d1_GRCh38.primary_assembly.genome.fa.2.bt2 added
c70543632ef_GRCh38.primary_assembly.genome.fa.3.bt2 added
c705249eb12_GRCh38.primary_assembly.genome.fa.4.bt2 added
c70542e7ebea_GRCh38.primary_assembly.genome.fa.rev.1.bt2 added
c70583171f7_GRCh38.primary_assembly.genome.fa.rev.2.bt2 added
c70566311354_outfile.txt added
c7051fec2436_GRCh37_to_GRCh38.chain added
c705483d6599_GRCh37_to_NCBI34.chain added
c70536d944dc_GRCh37_to_NCBI35.chain added
c7057237e3a5_GRCh37_to_NCBI36.chain added
c7053342a038_GRCh38_to_GRCh37.chain added
c7055b24d6d2_GRCh38_to_NCBI34.chain added
c7054f93a3bd_GRCh38_to_NCBI35.chain added
c70565e2f61b_GRCh38_to_NCBI36.chain added
c705178b9adf_NCBI34_to_GRCh37.chain added
c7054e64b28c_NCBI34_to_GRCh38.chain added
c70535062d89_NCBI35_to_GRCh37.chain added
c70528979891_NCBI35_to_GRCh38.chain added
c70578a16c68_NCBI36_to_GRCh37.chain added
c7052dd45db7_NCBI36_to_GRCh38.chain added
c7055154b0e2_GRCm38_to_NCBIM36.chain added
c705f28ef25_GRCm38_to_NCBIM37.chain added
c705486c6de9_NCBIM36_to_GRCm38.chain added
c70546a40124_NCBIM37_to_GRCm38.chain added
c705394706b7_1000G_omni2.5.b37.vcf.gz added
c7056609f5c1_1000G_omni2.5.b37.vcf.gz.tbi added
c70517e5863d_Mills_and_1000G_gold_standard.indels.b37.vcf.gz added
c7055dd01b0c_Mills_and_1000G_gold_standard.indels.b37.vcf.gz.tbi added
c70599fe0f2_1000G_omni2.5.hg38.vcf.gz added
c7055f6934cd_1000G_omni2.5.hg38.vcf.gz.tbi added
c7057409afaa_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz added
c70527ebfd6a_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz.tbi added
c705764a4e9f_af-only-gnomad.raw.sites.vcf added
c70586fe565_af-only-gnomad.raw.sites.vcf.idx added
c7056a3d4e36_Mutect2-exome-panel.vcf.idx added
c7055ed9f1b7_Mutect2-WGS-panel-b37.vcf added
c705368c5607_Mutect2-WGS-panel-b37.vcf.idx added
c7053764018b_small_exac_common_3.vcf added
c7056a16916_small_exac_common_3.vcf.idx added
c7054efa26c0_1000g_pon.hg38.vcf.gz added
c7059062fc2_1000g_pon.hg38.vcf.gz.tbi added
c70575296e2e_af-only-gnomad.hg38.vcf.gz added
c7057300ca19_af-only-gnomad.hg38.vcf.gz.tbi added
c70538d46a4b_small_exac_common_3.hg38.vcf.gz added
c70518e7f13_small_exac_common_3.hg38.vcf.gz.tbi added
c7053238b931_gencode.v41.annotation.gtf added
c7052a0659b9_gencode.v42.annotation.gtf added
c7056ec963d_gencode.vM30.annotation.gtf added
c705167b8258_gencode.vM31.annotation.gtf added
c7056aa6af0_gencode.v41.transcripts.fa added
c7051e52b5fb_gencode.v41.transcripts.fa.fai added
c7054829814a_gencode.v42.transcripts.fa added
c7051ce74649_gencode.v42.transcripts.fa.fai added
c70513b77172_gencode.vM30.pc_transcripts.fa added
c7057078fd7a_gencode.vM30.pc_transcripts.fa.fai added
c70517498e46_gencode.vM31.pc_transcripts.fa added
c7055e1ba19b_gencode.vM31.pc_transcripts.fa.fai added
c705680ef761_GRCh38.primary_assembly.genome.fa.1.ht2 added
c7052e9336a6_GRCh38.primary_assembly.genome.fa.2.ht2 added
c70542e8e42d_GRCh38.primary_assembly.genome.fa.3.ht2 added
c70547dc68ac_GRCh38.primary_assembly.genome.fa.4.ht2 added
c705575c190f_GRCh38.primary_assembly.genome.fa.5.ht2 added
c7055f715497_GRCh38.primary_assembly.genome.fa.6.ht2 added
c705968b675_GRCh38.primary_assembly.genome.fa.7.ht2 added
c70539a2c026_GRCh38.primary_assembly.genome.fa.8.ht2 added
c7056bf51c59_GRCh38_full_analysis_set_plus_decoy_hla.fa.fai added
c70529184e6e_GRCh38_full_analysis_set_plus_decoy_hla.fa.amb added
c7057ac52cd5_GRCh38_full_analysis_set_plus_decoy_hla.fa.ann added
c705270292eb_GRCh38_full_analysis_set_plus_decoy_hla.fa.bwt added
c70519fb964f_GRCh38_full_analysis_set_plus_decoy_hla.fa.pac added
c705544929dc_GRCh38_full_analysis_set_plus_decoy_hla.fa.sa added
c705f5b55bf_GRCh38_full_analysis_set_plus_decoy_hla.fa added
c705355a7679_GRCh38.primary_assembly.genome.fa.fai added
c70546181d4c_GRCh38.primary_assembly.genome.fa.amb added
c705592b8c87_GRCh38.primary_assembly.genome.fa.ann added
c7053a1720cd_GRCh38.primary_assembly.genome.fa.bwt added
c705446a9086_GRCh38.primary_assembly.genome.fa.pac added
c70530367081_GRCh38.primary_assembly.genome.fa.sa added
c70546143de1_GRCh38.primary_assembly.genome.fa added
c7055aeaa2b8_hs37d5.fa.fai added
c70562610ca9_hs37d5.fa.amb added
c70551865db4_hs37d5.fa.ann added
c7054c71fe3c_hs37d5.fa.bwt added
c7054fea3c59_hs37d5.fa.pac added
c7051b20200c_hs37d5.fa.sa added
c7055a1801bd_hs37d5.fa added
c7055e1a4d80_complete_ref_lens.bin added
c70510d63ec4_ctable.bin added
c70561b2be7e_ctg_offsets.bin added
c7051df8744e_duplicate_clusters.tsv added
c705229bbc41_info.json added
c7051e646127_mphf.bin added
c70550265707_pos.bin added
c70551bb5ad_pre_indexing.log added
c7055e347379_rank.bin added
c70545893d40_ref_indexing.log added
c7053514586a_refAccumLengths.bin added
c7054ab8b25f_reflengths.bin added
c70523c6a14c_refseq.bin added
c705458796ed_seq.bin added
c70548c5c544_versionInfo.json added
c705301a18af_salmon_index added
c70514aa1d5_chrLength.txt added
c7054ac6a79c_chrName.txt added
c7053826191e_chrNameLength.txt added
c7054d3b1d5e_chrStart.txt added
c70564052dee_exonGeTrInfo.tab added
c705100a978f_exonInfo.tab added
c70527643583_geneInfo.tab added
c70523f53fa9_Genome added
c7053a2682b0_genomeParameters.txt added
c705364e0ea3_Log.out added
c7053ea30b2f_SA added
c70542335ac9_SAindex added
c705398d6413_sjdbInfo.txt added
c70571a538e9_sjdbList.fromGTF.out.tab added
c705163b8349_sjdbList.out.tab added
c7051d283906_transcriptInfo.tab added
c7053bb7c7de_GRCh38.GENCODE.v42_100 added
c7051ea2de73_knownGene_hg38.sql added
c70556ba5fbb_knownGene_hg38.txt added
c70565e31a78_refGene_hg38.sql added
c70520def08a_refGene_hg38.txt added
c705c8204e2_knownGene_mm39.sql added
c7052c0e97d8_knownGene_mm39.txt added
c7057212fc80_refGene_mm39.sql added
c7053c7f7202_refGene_mm39.txt added
dataHub with 152 records
cache path: /Users/biocbuild/Library/Caches/org.R-project.R/R/ReUseData
# dataUpdate() to update the local data cache
# dataSearch() to query a specific dataset
# Additional information can be retrieved using:
# dataNames(), dataParams(), dataNotes(), dataPaths(), dataTag() or mcols()
name
BFC115764 | outfile.txt
BFC116021 | GRCh37_to_GRCh38.chain
BFC116022 | outfile.txt
BFC116280 | outfile.txt
BFC116537 | outfile.txt
... ...
BFC121682 | refGene_hg38.txt
BFC121683 | knownGene_mm39.sql
BFC121684 | knownGene_mm39.txt
BFC121685 | refGene_mm39.sql
BFC121686 | refGene_mm39.txt
Path
BFC115764 /tmp/RtmpcS9XlD/SharedData/outfile.txt
BFC116021 /tmp/RtmpcS9XlD/gcpData/GRCh37_to_GRCh38.chain
BFC116022 /tmp/Rtmpac1QuT/test_SharedData/outfile.txt
BFC116280 /tmp/RtmpGSLB4k/SharedData/outfile.txt
BFC116537 /tmp/RtmpgiyQTL/test_SharedData/outfile.txt
... ...
BFC121682 https://storage.googleapis.com/reusedata/ucsc_database/refGene_h...
BFC121683 https://storage.googleapis.com/reusedata/ucsc_database/knownGene...
BFC121684 https://storage.googleapis.com/reusedata/ucsc_database/knownGene...
BFC121685 https://storage.googleapis.com/reusedata/ucsc_database/refGene_m...
BFC121686 https://storage.googleapis.com/reusedata/ucsc_database/refGene_m...
> dh <- dataSearch(c("ensembl", "GRCh38"))
>
> ## download data from google bucket
> getCloudData(dh[1], outdir = outdir)
Error in getCloudData(dh[1], outdir = outdir) :
The 'data' is not a cloud object. Please double check the data name(s).
Execution halted
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’
OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: 1 ERROR, 1 NOTE
See
‘/Users/biocbuild/bbs-3.18-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/4.3-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 4.3.2 Patched (2023-11-01 r85457) -- "Eye Holes"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20 (64-bit)
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...
d5ad7ada7ef4_GRCh38.primary_assembly.genome.fa.1.bt2 added
d5ad1ec5042f_GRCh38.primary_assembly.genome.fa.2.bt2 added
d5ad1895b971_GRCh38.primary_assembly.genome.fa.3.bt2 added
d5addc1b653_GRCh38.primary_assembly.genome.fa.4.bt2 added
d5ad28a90a33_GRCh38.primary_assembly.genome.fa.rev.1.bt2 added
d5ad71dcaf1f_GRCh38.primary_assembly.genome.fa.rev.2.bt2 added
d5ad4f6d569f_outfile.txt added
d5ad13520976_GRCh37_to_GRCh38.chain added
d5ad6eeb2be2_GRCh37_to_NCBI34.chain added
d5ad118e3b52_GRCh37_to_NCBI35.chain added
d5ad10d88d7f_GRCh37_to_NCBI36.chain added
d5ad7931957c_GRCh38_to_GRCh37.chain added
d5ad264d3e0d_GRCh38_to_NCBI34.chain added
d5ad1924db20_GRCh38_to_NCBI35.chain added
d5ad42ae1ec5_GRCh38_to_NCBI36.chain added
d5ad356639b6_NCBI34_to_GRCh37.chain added
d5ad4a56f71d_NCBI34_to_GRCh38.chain added
d5ad1379b70c_NCBI35_to_GRCh37.chain added
d5ad1be07ed1_NCBI35_to_GRCh38.chain added
d5ad2fa5d9a3_NCBI36_to_GRCh37.chain added
d5ad317374c5_NCBI36_to_GRCh38.chain added
d5ad12f74ae0_GRCm38_to_NCBIM36.chain added
d5ad2954c1da_GRCm38_to_NCBIM37.chain added
d5ad7b82e468_NCBIM36_to_GRCm38.chain added
d5ad4e61a731_NCBIM37_to_GRCm38.chain added
d5ad6d27aa2a_1000G_omni2.5.b37.vcf.gz added
d5ad4714e362_1000G_omni2.5.b37.vcf.gz.tbi added
d5ad2c5c5b63_Mills_and_1000G_gold_standard.indels.b37.vcf.gz added
d5ad6373d755_Mills_and_1000G_gold_standard.indels.b37.vcf.gz.tbi added
d5ad4a3e4075_1000G_omni2.5.hg38.vcf.gz added
d5ad3cf9e767_1000G_omni2.5.hg38.vcf.gz.tbi added
d5ad3ac73a77_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz added
d5ad6dcf78c6_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz.tbi added
d5ad5002477c_af-only-gnomad.raw.sites.vcf added
d5ad45a346ed_af-only-gnomad.raw.sites.vcf.idx added
d5ad62859552_Mutect2-exome-panel.vcf.idx added
d5ad300e6d06_Mutect2-WGS-panel-b37.vcf added
d5ad317bd90_Mutect2-WGS-panel-b37.vcf.idx added
d5adb9e3a86_small_exac_common_3.vcf added
d5ad4114395f_small_exac_common_3.vcf.idx added
d5ad16c2ad5a_1000g_pon.hg38.vcf.gz added
d5ad4702fb62_1000g_pon.hg38.vcf.gz.tbi added
d5ad14c6035a_af-only-gnomad.hg38.vcf.gz added
d5ad5406145d_af-only-gnomad.hg38.vcf.gz.tbi added
d5ad5b2310c3_small_exac_common_3.hg38.vcf.gz added
d5ad5b21a0f3_small_exac_common_3.hg38.vcf.gz.tbi added
d5ad7ccde042_gencode.v41.annotation.gtf added
d5ad303e4d11_gencode.v42.annotation.gtf added
d5ad4a35afd5_gencode.vM30.annotation.gtf added
d5adaaaef03_gencode.vM31.annotation.gtf added
d5ad5c31b36d_gencode.v41.transcripts.fa added
d5ad42fae864_gencode.v41.transcripts.fa.fai added
d5ad66af1f96_gencode.v42.transcripts.fa added
d5ad7342e584_gencode.v42.transcripts.fa.fai added
d5ad2cea783a_gencode.vM30.pc_transcripts.fa added
d5ad557b3edf_gencode.vM30.pc_transcripts.fa.fai added
d5ade5cce51_gencode.vM31.pc_transcripts.fa added
d5ad6eed2f34_gencode.vM31.pc_transcripts.fa.fai added
d5ad15b637d1_GRCh38.primary_assembly.genome.fa.1.ht2 added
d5ad6e0a8579_GRCh38.primary_assembly.genome.fa.2.ht2 added
d5ad74c1035f_GRCh38.primary_assembly.genome.fa.3.ht2 added
d5ad2bc48ddb_GRCh38.primary_assembly.genome.fa.4.ht2 added
d5ad753d3b4f_GRCh38.primary_assembly.genome.fa.5.ht2 added
d5ad700fbab_GRCh38.primary_assembly.genome.fa.6.ht2 added
d5ad518a9b24_GRCh38.primary_assembly.genome.fa.7.ht2 added
d5ad62cf824e_GRCh38.primary_assembly.genome.fa.8.ht2 added
d5ad25740190_GRCh38_full_analysis_set_plus_decoy_hla.fa.fai added
d5ad6312a825_GRCh38_full_analysis_set_plus_decoy_hla.fa.amb added
d5ad5ddd47f3_GRCh38_full_analysis_set_plus_decoy_hla.fa.ann added
d5ad6a9ed2a9_GRCh38_full_analysis_set_plus_decoy_hla.fa.bwt added
d5ad61188bee_GRCh38_full_analysis_set_plus_decoy_hla.fa.pac added
d5ad128ae80f_GRCh38_full_analysis_set_plus_decoy_hla.fa.sa added
d5ad5d893a4b_GRCh38_full_analysis_set_plus_decoy_hla.fa added
d5ad5c5241e6_GRCh38.primary_assembly.genome.fa.fai added
d5ad1c649264_GRCh38.primary_assembly.genome.fa.amb added
d5adec6f1cc_GRCh38.primary_assembly.genome.fa.ann added
d5ad272c8fa8_GRCh38.primary_assembly.genome.fa.bwt added
d5ad5e8b72af_GRCh38.primary_assembly.genome.fa.pac added
d5ad15166fa7_GRCh38.primary_assembly.genome.fa.sa added
d5ad73fc47c1_GRCh38.primary_assembly.genome.fa added
d5ad37cb0b64_hs37d5.fa.fai added
d5ad7358eed9_hs37d5.fa.amb added
d5ad53a923b8_hs37d5.fa.ann added
d5ad5682ff1_hs37d5.fa.bwt added
d5ad7b2379fc_hs37d5.fa.pac added
d5ad561dce8c_hs37d5.fa.sa added
d5ad3ee3757f_hs37d5.fa added
d5ad4737051a_complete_ref_lens.bin added
d5ad6d30127c_ctable.bin added
d5ad6f0dc2e4_ctg_offsets.bin added
d5ad70763fb1_duplicate_clusters.tsv added
d5ad634fb725_info.json added
d5ad6811113_mphf.bin added
d5ad387f9bb_pos.bin added
d5ad541c65cc_pre_indexing.log added
d5ad145f5f38_rank.bin added
d5ad1645ffb_ref_indexing.log added
d5ad64d95873_refAccumLengths.bin added
d5ad793e19be_reflengths.bin added
d5ad5c0c4721_refseq.bin added
d5ad2a11f6bd_seq.bin added
d5ad15e07df_versionInfo.json added
d5ad4456c22c_salmon_index added
d5ad1be5f9c1_chrLength.txt added
d5ad176ffc36_chrName.txt added
d5ad3917493f_chrNameLength.txt added
d5ad27c9e461_chrStart.txt added
d5ad37b0b0af_exonGeTrInfo.tab added
d5ad311fcdb9_exonInfo.tab added
d5ad1efb45e1_geneInfo.tab added
d5ad2a8c6ab_Genome added
d5ad168b05ea_genomeParameters.txt added
d5ad1315136_Log.out added
d5ad4ccab0d6_SA added
d5adf1fd8fd_SAindex added
d5ad73ded1cc_sjdbInfo.txt added
d5ad299fe382_sjdbList.fromGTF.out.tab added
d5ad40118127_sjdbList.out.tab added
d5ad3d36484d_transcriptInfo.tab added
d5ad36c4d6a0_GRCh38.GENCODE.v42_100 added
d5ad34e6be77_knownGene_hg38.sql added
d5ad18e291c3_knownGene_hg38.txt added
d5ad42cfa5f8_refGene_hg38.sql added
d5ad4e995f0c_refGene_hg38.txt added
d5ad372f3524_knownGene_mm39.sql added
d5ad7c49eac9_knownGene_mm39.txt added
d5ad58d571de_refGene_mm39.sql added
d5ad2526d362_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/RtmpgV4nJR/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
24.268 3.091 28.779
ReUseData.Rcheck/ReUseData-Ex.timings
| name | user | system | elapsed | |
| dataHub-class | 7.382 | 0.844 | 8.323 | |
| dataSearch | 1.382 | 0.055 | 1.445 | |
| dataUpdate | 13.297 | 2.079 | 15.925 | |