Qian Liu
| Snapshot Date: 2023-06-29 14:00:14 -0400 (Thu, 29 Jun 2023) |
| git_url: https://git.bioconductor.org/packages/ReUseData |
| git_branch: RELEASE_3_17 |
| git_last_commit: 3bb82e3 |
| git_last_commit_date: 2023-04-25 11:42:19 -0400 (Tue, 25 Apr 2023) |
| Back to Multiple platform build/check report for BioC 3.17: simplified long |
|
This page was generated on 2023-06-30 11:37:01 -0400 (Fri, 30 Jun 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 22.04.2 LTS) | x86_64 | 4.3.1 (2023-06-16) -- "Beagle Scouts" | 4607 |
| palomino3 | Windows Server 2022 Datacenter | x64 | 4.3.1 (2023-06-16 ucrt) -- "Beagle Scouts" | 4362 |
| merida1 | macOS 12.6.4 Monterey | x86_64 | 4.3.1 (2023-06-16) -- "Beagle Scouts" | 4370 |
| 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 1692/2229 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| ReUseData 1.0.0 (landing page) Qian Liu
| nebbiolo1 | Linux (Ubuntu 22.04.2 LTS) / x86_64 | OK | OK | ERROR | |||||||||
| palomino3 | Windows Server 2022 Datacenter / x64 | ... NOT SUPPORTED ... | ||||||||||||
| merida1 | macOS 12.6.4 Monterey / x86_64 | 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: 1.0.0 |
| 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_1.0.0.tar.gz |
| StartedAt: 2023-06-30 05:31:38 -0400 (Fri, 30 Jun 2023) |
| EndedAt: 2023-06-30 05:38:09 -0400 (Fri, 30 Jun 2023) |
| EllapsedTime: 391.0 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_1.0.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.17-bioc/meat/ReUseData.Rcheck’
* using R version 4.3.1 (2023-06-16)
* 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 12.6.4
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘ReUseData/DESCRIPTION’ ... OK
* this is package ‘ReUseData’ version ‘1.0.0’
* 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 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 ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
dataUpdate 21.978 2.778 30.483
getCloudData 12.788 1.178 19.819
dataHub-class 11.914 1.238 17.604
getData 7.818 0.844 10.844
recipeMake 7.521 0.838 10.752
* 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 NOTE
See
‘/Users/biocbuild/bbs-3.17-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 4.3.1 (2023-06-16) -- "Beagle Scouts"
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...
81f8993d8a7_GRCh38.primary_assembly.genome.fa.1.bt2 added
81f84974c0da_GRCh38.primary_assembly.genome.fa.2.bt2 added
81f810214de3_GRCh38.primary_assembly.genome.fa.3.bt2 added
81f87a807a5a_GRCh38.primary_assembly.genome.fa.4.bt2 added
81f88e0e98b_GRCh38.primary_assembly.genome.fa.rev.1.bt2 added
81f86604a93a_GRCh38.primary_assembly.genome.fa.rev.2.bt2 added
81f83c025329_outfile.txt added
81f83ca1c786_GRCh37_to_GRCh38.chain added
81f821324d83_GRCh37_to_NCBI34.chain added
81f86d7ee47b_GRCh37_to_NCBI35.chain added
81f825ca7f66_GRCh37_to_NCBI36.chain added
81f8117214ec_GRCh38_to_GRCh37.chain added
81f858bb9ae6_GRCh38_to_NCBI34.chain added
81f84b69f8d_GRCh38_to_NCBI35.chain added
81f871a4e465_GRCh38_to_NCBI36.chain added
81f88edd2d_NCBI34_to_GRCh37.chain added
81f8235ab5a4_NCBI34_to_GRCh38.chain added
81f8184b341e_NCBI35_to_GRCh37.chain added
81f8714aaa07_NCBI35_to_GRCh38.chain added
81f85ce0ebac_NCBI36_to_GRCh37.chain added
81f8329098d7_NCBI36_to_GRCh38.chain added
81f833226530_GRCm38_to_NCBIM36.chain added
81f817214c8a_GRCm38_to_NCBIM37.chain added
81f8b2803e3_NCBIM36_to_GRCm38.chain added
81f8701731cd_NCBIM37_to_GRCm38.chain added
81f82c6c339_1000G_omni2.5.b37.vcf.gz added
81f8473ad49b_1000G_omni2.5.b37.vcf.gz.tbi added
81f8675c30a5_Mills_and_1000G_gold_standard.indels.b37.vcf.gz added
81f8557dd5a6_Mills_and_1000G_gold_standard.indels.b37.vcf.gz.tbi added
81f83855b123_1000G_omni2.5.hg38.vcf.gz added
81f81e08dba_1000G_omni2.5.hg38.vcf.gz.tbi added
81f83d78af4c_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz added
81f83e3cc61b_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz.tbi added
81f87f23689_af-only-gnomad.raw.sites.vcf added
81f82eda6072_af-only-gnomad.raw.sites.vcf.idx added
81f82f1f466_Mutect2-exome-panel.vcf.idx added
81f85ae4560c_Mutect2-WGS-panel-b37.vcf added
81f844cd5c72_Mutect2-WGS-panel-b37.vcf.idx added
81f867063a8_small_exac_common_3.vcf added
81f83c9eade5_small_exac_common_3.vcf.idx added
81f855aab47a_1000g_pon.hg38.vcf.gz added
81f83a2ee186_1000g_pon.hg38.vcf.gz.tbi added
81f85bd84241_af-only-gnomad.hg38.vcf.gz added
81f852e5e882_af-only-gnomad.hg38.vcf.gz.tbi added
81f87403d952_small_exac_common_3.hg38.vcf.gz added
81f828b0d1ff_small_exac_common_3.hg38.vcf.gz.tbi added
81f870aad137_gencode.v41.annotation.gtf added
81f85e8dabaa_gencode.v42.annotation.gtf added
81f827015665_gencode.vM30.annotation.gtf added
81f848cf14e4_gencode.vM31.annotation.gtf added
81f81364aa14_gencode.v41.transcripts.fa added
81f835da10fe_gencode.v41.transcripts.fa.fai added
81f87f91af50_gencode.v42.transcripts.fa added
81f8358cee9e_gencode.v42.transcripts.fa.fai added
81f83785e289_gencode.vM30.pc_transcripts.fa added
81f836dbacd9_gencode.vM30.pc_transcripts.fa.fai added
81f81030f6b2_gencode.vM31.pc_transcripts.fa added
81f87e94286b_gencode.vM31.pc_transcripts.fa.fai added
81f830e9c9b9_GRCh38.primary_assembly.genome.fa.1.ht2 added
81f844baa9c5_GRCh38.primary_assembly.genome.fa.2.ht2 added
81f83adfe7c3_GRCh38.primary_assembly.genome.fa.3.ht2 added
81f841e8d167_GRCh38.primary_assembly.genome.fa.4.ht2 added
81f81c0be2ff_GRCh38.primary_assembly.genome.fa.5.ht2 added
81f85063e1bb_GRCh38.primary_assembly.genome.fa.6.ht2 added
81f84d78e538_GRCh38.primary_assembly.genome.fa.7.ht2 added
81f83c10e744_GRCh38.primary_assembly.genome.fa.8.ht2 added
81f879bf402a_GRCh38_full_analysis_set_plus_decoy_hla.fa.fai added
81f87b0dc3d7_GRCh38_full_analysis_set_plus_decoy_hla.fa.amb added
81f844b4975e_GRCh38_full_analysis_set_plus_decoy_hla.fa.ann added
81f82c3dbf8f_GRCh38_full_analysis_set_plus_decoy_hla.fa.bwt added
81f89eb5bfa_GRCh38_full_analysis_set_plus_decoy_hla.fa.pac added
81f83ae37f2c_GRCh38_full_analysis_set_plus_decoy_hla.fa.sa added
81f82db23fe8_GRCh38_full_analysis_set_plus_decoy_hla.fa added
81f81181afc8_GRCh38.primary_assembly.genome.fa.fai added
81f8593b7c72_GRCh38.primary_assembly.genome.fa.amb added
81f850674e22_GRCh38.primary_assembly.genome.fa.ann added
81f82e3ac36b_GRCh38.primary_assembly.genome.fa.bwt added
81f813f3bd83_GRCh38.primary_assembly.genome.fa.pac added
81f8671eedb0_GRCh38.primary_assembly.genome.fa.sa added
81f81f86f2b4_GRCh38.primary_assembly.genome.fa added
81f854a81797_hs37d5.fa.fai added
81f867a4e5ec_hs37d5.fa.amb added
81f87af31e1c_hs37d5.fa.ann added
81f86f3dff53_hs37d5.fa.bwt added
81f84f45db33_hs37d5.fa.pac added
81f8733a19ed_hs37d5.fa.sa added
81f86b7c51b4_hs37d5.fa added
81f82ed8378d_complete_ref_lens.bin added
81f875272201_ctable.bin added
81f85c29abbd_ctg_offsets.bin added
81f833ca3490_duplicate_clusters.tsv added
81f82040f480_info.json added
81f8874100b_mphf.bin added
81f87bc94682_pos.bin added
81f85b34404b_pre_indexing.log added
81f843692ab4_rank.bin added
81f82d72b1ff_ref_indexing.log added
81f84503f3a8_refAccumLengths.bin added
81f8671bdfe_reflengths.bin added
81f815707200_refseq.bin added
81f894c68ff_seq.bin added
81f87781421d_versionInfo.json added
81f8471bbb36_salmon_index added
81f86d9ffab2_chrLength.txt added
81f82203f458_chrName.txt added
81f8319eceda_chrNameLength.txt added
81f8311e63a9_chrStart.txt added
81f842210570_exonGeTrInfo.tab added
81f85ec1dfb_exonInfo.tab added
81f850a44cc6_geneInfo.tab added
81f852ac8486_Genome added
81f83c30a3d1_genomeParameters.txt added
81f81d530d36_Log.out added
81f837886344_SA added
81f85b2d21d7_SAindex added
81f87008d904_sjdbInfo.txt added
81f854dfcf12_sjdbList.fromGTF.out.tab added
81f83193d246_sjdbList.out.tab added
81f85fd20b17_transcriptInfo.tab added
81f856d64426_GRCh38.GENCODE.v42_100 added
81f8d144754_knownGene_hg38.sql added
81f82e56e281_knownGene_hg38.txt added
81f84a309aeb_refGene_hg38.sql added
81f83d0ae05a_refGene_hg38.txt added
81f8150f5405_knownGene_mm39.sql added
81f821551f10_knownGene_mm39.txt added
81f85b6a6488_refGene_mm39.sql added
81f825ee4b9b_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/RtmphSd1Wd/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 ]
>
> proc.time()
user system elapsed
44.159 4.958 67.256
ReUseData.Rcheck/ReUseData-Ex.timings
| name | user | system | elapsed | |
| dataHub-class | 11.914 | 1.238 | 17.604 | |
| dataSearch | 2.058 | 0.074 | 2.670 | |
| dataUpdate | 21.978 | 2.778 | 30.483 | |
| getCloudData | 12.788 | 1.178 | 19.819 | |
| getData | 7.818 | 0.844 | 10.844 | |
| meta_data | 0.023 | 0.002 | 0.025 | |
| recipeHub-class | 0.355 | 0.018 | 0.428 | |
| recipeLoad | 2.225 | 0.102 | 2.868 | |
| recipeMake | 7.521 | 0.838 | 10.752 | |
| recipeSearch | 1.025 | 0.055 | 1.386 | |
| recipeUpdate | 0.005 | 0.000 | 0.008 | |