Qian Liu
| Snapshot Date: 2024-08-04 14:00 -0400 (Sun, 04 Aug 2024) |
| git_url: https://git.bioconductor.org/packages/ReUseData |
| git_branch: RELEASE_3_19 |
| git_last_commit: 801f620 |
| git_last_commit_date: 2024-04-30 11:46:52 -0400 (Tue, 30 Apr 2024) |
| Back to Multiple platform build/check report for BioC 3.19: simplified long |
|
This page was generated on 2024-08-06 17:41 -0400 (Tue, 06 Aug 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4756 |
| palomino7 | Windows Server 2022 Datacenter | x64 | 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" | 4490 |
| merida1 | macOS 12.7.5 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4519 |
| kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4468 |
| 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 1745/2300 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| ReUseData 1.4.0 (landing page) Qian Liu
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino7 | 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 | NA | |||||||||
|
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: 1.4.0 |
| 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_1.4.0.tar.gz |
| StartedAt: 2024-08-05 10:40:56 -0400 (Mon, 05 Aug 2024) |
| EndedAt: 2024-08-05 10:45:50 -0400 (Mon, 05 Aug 2024) |
| EllapsedTime: 293.6 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_1.4.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.19-bioc/meat/ReUseData.Rcheck’
* using R version 4.4.1 (2024-06-14)
* 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 12.7.5
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘ReUseData/DESCRIPTION’ ... OK
* this is package ‘ReUseData’ version ‘1.4.0’
* 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 12.710 1.271 16.087
getCloudData 4.693 0.204 6.273
* 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-3.19-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 4.4.1 (2024-06-14) -- "Race for Your Life"
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...
171ff3d031628_GRCh38.primary_assembly.genome.fa.1.bt2 added
171ff15a3bb63_GRCh38.primary_assembly.genome.fa.2.bt2 added
171ff30636bae_GRCh38.primary_assembly.genome.fa.3.bt2 added
171ff4f328553_GRCh38.primary_assembly.genome.fa.4.bt2 added
171ff7dcf34c3_GRCh38.primary_assembly.genome.fa.rev.1.bt2 added
171ff2e912ebc_GRCh38.primary_assembly.genome.fa.rev.2.bt2 added
171ff3d935086_outfile.txt added
171ff128bacff_GRCh37_to_GRCh38.chain added
171ff100aa2dc_GRCh37_to_NCBI34.chain added
171ff2a4a21be_GRCh37_to_NCBI35.chain added
171ff68ed56a2_GRCh37_to_NCBI36.chain added
171ff35d2db7f_GRCh38_to_GRCh37.chain added
171ff26488a74_GRCh38_to_NCBI34.chain added
171ff6479d94e_GRCh38_to_NCBI35.chain added
171ff7ba9c36a_GRCh38_to_NCBI36.chain added
171ff465ca393_NCBI34_to_GRCh37.chain added
171ff6bf72bfb_NCBI34_to_GRCh38.chain added
171ff3068a31d_NCBI35_to_GRCh37.chain added
171ff25acddbf_NCBI35_to_GRCh38.chain added
171ff781239eb_NCBI36_to_GRCh37.chain added
171ff7498b0e2_NCBI36_to_GRCh38.chain added
171ff5485013b_GRCm38_to_NCBIM36.chain added
171ff6813f3d6_GRCm38_to_NCBIM37.chain added
171ff75ed9bfb_NCBIM36_to_GRCm38.chain added
171ff429bb839_NCBIM37_to_GRCm38.chain added
171ff7d5bc858_1000G_omni2.5.b37.vcf.gz added
171ff14be49b4_1000G_omni2.5.b37.vcf.gz.tbi added
171ff58d8d30f_Mills_and_1000G_gold_standard.indels.b37.vcf.gz added
171ff308ab5b_Mills_and_1000G_gold_standard.indels.b37.vcf.gz.tbi added
171ff2e29e4eb_1000G_omni2.5.hg38.vcf.gz added
171ff407417fa_1000G_omni2.5.hg38.vcf.gz.tbi added
171ff5d23f25_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz added
171ff2e2f991f_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz.tbi added
171ff36edd9e9_af-only-gnomad.raw.sites.vcf added
171ff397d6c2b_af-only-gnomad.raw.sites.vcf.idx added
171ff59489889_Mutect2-exome-panel.vcf.idx added
171ff2d16782a_Mutect2-WGS-panel-b37.vcf added
171ff1e2b2486_Mutect2-WGS-panel-b37.vcf.idx added
171ff226ae8e3_small_exac_common_3.vcf added
171ff18dfa0bc_small_exac_common_3.vcf.idx added
171ff1b1a366_1000g_pon.hg38.vcf.gz added
171ff355e7e68_1000g_pon.hg38.vcf.gz.tbi added
171ff4ebcf937_af-only-gnomad.hg38.vcf.gz added
171ff588db243_af-only-gnomad.hg38.vcf.gz.tbi added
171ff3eb27a20_small_exac_common_3.hg38.vcf.gz added
171ff376feb08_small_exac_common_3.hg38.vcf.gz.tbi added
171ff14af76a7_gencode.v41.annotation.gtf added
171ffb96d88d_gencode.v42.annotation.gtf added
171ff5c6316ec_gencode.vM30.annotation.gtf added
171ff6d760f56_gencode.vM31.annotation.gtf added
171ff61e90f3e_gencode.v41.transcripts.fa added
171ffbe7e1aa_gencode.v41.transcripts.fa.fai added
171ff24906601_gencode.v42.transcripts.fa added
171ff418de68_gencode.v42.transcripts.fa.fai added
171ff7cb17ff1_gencode.vM30.pc_transcripts.fa added
171ff6946e72b_gencode.vM30.pc_transcripts.fa.fai added
171ff2df2ee0c_gencode.vM31.pc_transcripts.fa added
171ff27ea6d65_gencode.vM31.pc_transcripts.fa.fai added
171fffb4165c_GRCh38.primary_assembly.genome.fa.1.ht2 added
171ff7827fa11_GRCh38.primary_assembly.genome.fa.2.ht2 added
171ff892afb8_GRCh38.primary_assembly.genome.fa.3.ht2 added
171ff564e5d6d_GRCh38.primary_assembly.genome.fa.4.ht2 added
171ff32d7cb5f_GRCh38.primary_assembly.genome.fa.5.ht2 added
171ff7568e40c_GRCh38.primary_assembly.genome.fa.6.ht2 added
171ff39540c0c_GRCh38.primary_assembly.genome.fa.7.ht2 added
171ff3ce3053b_GRCh38.primary_assembly.genome.fa.8.ht2 added
171ff5c6c83b7_GRCh38_full_analysis_set_plus_decoy_hla.fa.fai added
171ff583b92c8_GRCh38_full_analysis_set_plus_decoy_hla.fa.amb added
171ff2f21b5b9_GRCh38_full_analysis_set_plus_decoy_hla.fa.ann added
171ff4e219cdb_GRCh38_full_analysis_set_plus_decoy_hla.fa.bwt added
171ffc115f0_GRCh38_full_analysis_set_plus_decoy_hla.fa.pac added
171ff4873ff3_GRCh38_full_analysis_set_plus_decoy_hla.fa.sa added
171ff4b776cd7_GRCh38_full_analysis_set_plus_decoy_hla.fa added
171ffd8abdf6_GRCh38.primary_assembly.genome.fa.fai added
171fffbd686c_GRCh38.primary_assembly.genome.fa.amb added
171ff5c129286_GRCh38.primary_assembly.genome.fa.ann added
171ff4751caa3_GRCh38.primary_assembly.genome.fa.bwt added
171ff4aceb7e9_GRCh38.primary_assembly.genome.fa.pac added
171ff498c485d_GRCh38.primary_assembly.genome.fa.sa added
171ff18e2f764_GRCh38.primary_assembly.genome.fa added
171ff5cdfd2ff_hs37d5.fa.fai added
171ff6a9592fb_hs37d5.fa.amb added
171ff1e4d368_hs37d5.fa.ann added
171ff55f351d0_hs37d5.fa.bwt added
171ff59805ac5_hs37d5.fa.pac added
171ff79c7696a_hs37d5.fa.sa added
171ff12d9ec9c_hs37d5.fa added
171ff213cff6f_complete_ref_lens.bin added
171ff2ba5e175_ctable.bin added
171ff1774deb6_ctg_offsets.bin added
171ff79c98ac1_duplicate_clusters.tsv added
171ff1eb4c35e_info.json added
171ff6d866011_mphf.bin added
171ff110d3444_pos.bin added
171ff79e2651a_pre_indexing.log added
171ff7e5bcc79_rank.bin added
171ff3ccd5cbe_ref_indexing.log added
171ff4e83dd21_refAccumLengths.bin added
171ff332ac9cc_reflengths.bin added
171ff3e268a52_refseq.bin added
171ff54432d5e_seq.bin added
171ff657a18a_versionInfo.json added
171ff632e6e46_salmon_index added
171ff7d49e888_chrLength.txt added
171ff7f4178fa_chrName.txt added
171ff236da65b_chrNameLength.txt added
171ff73c4b288_chrStart.txt added
171ff76a53a18_exonGeTrInfo.tab added
171ff59893a82_exonInfo.tab added
171ff40605aba_geneInfo.tab added
171ff75e48a5a_Genome added
171ff6f37572d_genomeParameters.txt added
171ff1a3c8466_Log.out added
171ff7b1851fe_SA added
171ff79af39d4_SAindex added
171ff5efdcbb5_sjdbInfo.txt added
171ff684908cb_sjdbList.fromGTF.out.tab added
171ff12e07cea_sjdbList.out.tab added
171ff5028f054_transcriptInfo.tab added
171ff2fba43e9_GRCh38.GENCODE.v42_100 added
171ff6dc08e79_knownGene_hg38.sql added
171ff7cc9e239_knownGene_hg38.txt added
171ff2a234c30_refGene_hg38.sql added
171ff735ef8ec_refGene_hg38.txt added
171ff60288920_knownGene_mm39.sql added
171ff542c532_knownGene_mm39.txt added
171ff62a05850_refGene_mm39.sql added
171ffd061ec6_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/RtmpxlkIpo/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
43.877 5.222 56.793
ReUseData.Rcheck/ReUseData-Ex.timings
| name | user | system | elapsed | |
| dataHub-class | 12.710 | 1.271 | 16.087 | |
| dataSearch | 2.577 | 0.081 | 2.997 | |
| dataUpdate | 0.001 | 0.001 | 0.002 | |
| getCloudData | 4.693 | 0.204 | 6.273 | |
| getData | 0.000 | 0.001 | 0.002 | |
| meta_data | 0.002 | 0.001 | 0.002 | |
| recipeHub-class | 0.274 | 0.020 | 0.369 | |
| recipeLoad | 2.896 | 0.144 | 3.665 | |
| recipeMake | 0.000 | 0.001 | 0.002 | |
| recipeSearch | 1.191 | 0.057 | 1.494 | |
| recipeUpdate | 0.001 | 0.000 | 0.001 | |