Qian Liu
| Snapshot Date: 2024-10-16 14:00 -0400 (Wed, 16 Oct 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 2024-10-18 20:42 -0400 (Fri, 18 Oct 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" | 4763 |
| palomino7 | Windows Server 2022 Datacenter | x64 | 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" | 4500 |
| merida1 | macOS 12.7.5 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4530 |
| kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4480 |
| 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 | 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: 1.4.0 |
| 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: 2024-10-18 09:22:30 -0400 (Fri, 18 Oct 2024) |
| EndedAt: 2024-10-18 09:25:11 -0400 (Fri, 18 Oct 2024) |
| EllapsedTime: 160.1 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: aarch64-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 Ventura 13.6.6
* 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 7.735 0.862 8.703
getCloudData 3.007 0.155 5.098
* 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-arm64/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: aarch64-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...
b3185a9f6121_GRCh38.primary_assembly.genome.fa.1.bt2 added
b31815a1ec02_GRCh38.primary_assembly.genome.fa.2.bt2 added
b318398d8266_GRCh38.primary_assembly.genome.fa.3.bt2 added
b318796c140e_GRCh38.primary_assembly.genome.fa.4.bt2 added
b3182698e169_GRCh38.primary_assembly.genome.fa.rev.1.bt2 added
b3187ef6c84a_GRCh38.primary_assembly.genome.fa.rev.2.bt2 added
b3187bd7b364_outfile.txt added
b318e42a9c1_GRCh37_to_GRCh38.chain added
b3183a96c537_GRCh37_to_NCBI34.chain added
b3186dbbee_GRCh37_to_NCBI35.chain added
b318244d067a_GRCh37_to_NCBI36.chain added
b3183ce44634_GRCh38_to_GRCh37.chain added
b3182ebd1f27_GRCh38_to_NCBI34.chain added
b318248516a_GRCh38_to_NCBI35.chain added
b31859d90751_GRCh38_to_NCBI36.chain added
b318376f84ec_NCBI34_to_GRCh37.chain added
b3187a7fbe62_NCBI34_to_GRCh38.chain added
b31858ac52c2_NCBI35_to_GRCh37.chain added
b318196d6c09_NCBI35_to_GRCh38.chain added
b3185ecfcfe9_NCBI36_to_GRCh37.chain added
b3181d5afaa0_NCBI36_to_GRCh38.chain added
b3183ffc2d6e_GRCm38_to_NCBIM36.chain added
b318450ab193_GRCm38_to_NCBIM37.chain added
b31841104d4e_NCBIM36_to_GRCm38.chain added
b31815435d41_NCBIM37_to_GRCm38.chain added
b318799f614e_1000G_omni2.5.b37.vcf.gz added
b3184ead8643_1000G_omni2.5.b37.vcf.gz.tbi added
b3186249c10f_Mills_and_1000G_gold_standard.indels.b37.vcf.gz added
b3185821f232_Mills_and_1000G_gold_standard.indels.b37.vcf.gz.tbi added
b3181ca3ddd2_1000G_omni2.5.hg38.vcf.gz added
b3184a3814ae_1000G_omni2.5.hg38.vcf.gz.tbi added
b31827d5d193_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz added
b31846b21e53_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz.tbi added
b31857e4ff67_af-only-gnomad.raw.sites.vcf added
b3187b3bf045_af-only-gnomad.raw.sites.vcf.idx added
b3181c1b8138_Mutect2-exome-panel.vcf.idx added
b31851c091f2_Mutect2-WGS-panel-b37.vcf added
b31839add0cc_Mutect2-WGS-panel-b37.vcf.idx added
b31842671ea9_small_exac_common_3.vcf added
b318e0b4e_small_exac_common_3.vcf.idx added
b3181a082de9_1000g_pon.hg38.vcf.gz added
b318efe2959_1000g_pon.hg38.vcf.gz.tbi added
b318504c99bf_af-only-gnomad.hg38.vcf.gz added
b3185501f3c8_af-only-gnomad.hg38.vcf.gz.tbi added
b318732bfb11_small_exac_common_3.hg38.vcf.gz added
b3184c705429_small_exac_common_3.hg38.vcf.gz.tbi added
b31862a576f3_gencode.v41.annotation.gtf added
b3185d247e1d_gencode.v42.annotation.gtf added
b3186d3d1b1_gencode.vM30.annotation.gtf added
b3183c6bbef7_gencode.vM31.annotation.gtf added
b31845c6691e_gencode.v41.transcripts.fa added
b318651f545b_gencode.v41.transcripts.fa.fai added
b3186bdb563a_gencode.v42.transcripts.fa added
b318cfa3128_gencode.v42.transcripts.fa.fai added
b3187db13fbf_gencode.vM30.pc_transcripts.fa added
b3187fd05510_gencode.vM30.pc_transcripts.fa.fai added
b3184680cefe_gencode.vM31.pc_transcripts.fa added
b3183295a9db_gencode.vM31.pc_transcripts.fa.fai added
b3187fc282ce_GRCh38.primary_assembly.genome.fa.1.ht2 added
b3183b19e3e9_GRCh38.primary_assembly.genome.fa.2.ht2 added
b31820c1f44f_GRCh38.primary_assembly.genome.fa.3.ht2 added
b3181d8e7f56_GRCh38.primary_assembly.genome.fa.4.ht2 added
b3187649f642_GRCh38.primary_assembly.genome.fa.5.ht2 added
b31871c6a3b9_GRCh38.primary_assembly.genome.fa.6.ht2 added
b3182827010a_GRCh38.primary_assembly.genome.fa.7.ht2 added
b31818b54c1e_GRCh38.primary_assembly.genome.fa.8.ht2 added
b3182698523e_GRCh38_full_analysis_set_plus_decoy_hla.fa.fai added
b3185a3f783d_GRCh38_full_analysis_set_plus_decoy_hla.fa.amb added
b3187cef1b14_GRCh38_full_analysis_set_plus_decoy_hla.fa.ann added
b31835dafe20_GRCh38_full_analysis_set_plus_decoy_hla.fa.bwt added
b3183c62027f_GRCh38_full_analysis_set_plus_decoy_hla.fa.pac added
b3184691fed1_GRCh38_full_analysis_set_plus_decoy_hla.fa.sa added
b3181af06f89_GRCh38_full_analysis_set_plus_decoy_hla.fa added
b3181f2a9930_GRCh38.primary_assembly.genome.fa.fai added
b31825af2e4c_GRCh38.primary_assembly.genome.fa.amb added
b318100892e8_GRCh38.primary_assembly.genome.fa.ann added
b31822e4c591_GRCh38.primary_assembly.genome.fa.bwt added
b3185966c47c_GRCh38.primary_assembly.genome.fa.pac added
b31869edd6be_GRCh38.primary_assembly.genome.fa.sa added
b3187dad8a46_GRCh38.primary_assembly.genome.fa added
b318c513a20_hs37d5.fa.fai added
b31828bf1131_hs37d5.fa.amb added
b3181801bcdd_hs37d5.fa.ann added
b3181a165d7b_hs37d5.fa.bwt added
b3183253439e_hs37d5.fa.pac added
b318787c53e1_hs37d5.fa.sa added
b3182a671693_hs37d5.fa added
b31855fb22a4_complete_ref_lens.bin added
b3185a9f6915_ctable.bin added
b31817ac102e_ctg_offsets.bin added
b318215a4826_duplicate_clusters.tsv added
b3182e36c7e5_info.json added
b318e7da317_mphf.bin added
b3185a5e426f_pos.bin added
b318625bb3c2_pre_indexing.log added
b3187276b800_rank.bin added
b318502a42b5_ref_indexing.log added
b318681a231_refAccumLengths.bin added
b31828bf424d_reflengths.bin added
b3182499e221_refseq.bin added
b31872ccf74c_seq.bin added
b3186e7fd975_versionInfo.json added
b318b9dc900_salmon_index added
b31823f724f5_chrLength.txt added
b318369b6345_chrName.txt added
b31813926305_chrNameLength.txt added
b3186fa2e74c_chrStart.txt added
b3182fff67d6_exonGeTrInfo.tab added
b31828fa2b38_exonInfo.tab added
b318402b7e8c_geneInfo.tab added
b31867813a3d_Genome added
b3185516afe1_genomeParameters.txt added
b3184475086b_Log.out added
b3185f7bcbe9_SA added
b31838885ef8_SAindex added
b31811308c7_sjdbInfo.txt added
b3188a5415e_sjdbList.fromGTF.out.tab added
b318196686c1_sjdbList.out.tab added
b3181a18f5ee_transcriptInfo.tab added
b3185cb9e9a4_GRCh38.GENCODE.v42_100 added
b318319a3d8b_knownGene_hg38.sql added
b31853e8a1e_knownGene_hg38.txt added
b3184cddba42_refGene_hg38.sql added
b31870ef6a7a_refGene_hg38.txt added
b3187637a982_knownGene_mm39.sql added
b3184059d270_knownGene_mm39.txt added
b3184906d811_refGene_mm39.sql added
b3186053698b_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/Rtmp4KrHrL/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
26.334 3.611 31.931
ReUseData.Rcheck/ReUseData-Ex.timings
| name | user | system | elapsed | |
| dataHub-class | 7.735 | 0.862 | 8.703 | |
| dataSearch | 1.288 | 0.059 | 1.367 | |
| dataUpdate | 0.000 | 0.001 | 0.001 | |
| getCloudData | 3.007 | 0.155 | 5.098 | |
| getData | 0 | 0 | 0 | |
| meta_data | 0.001 | 0.000 | 0.002 | |
| recipeHub-class | 0.154 | 0.012 | 0.168 | |
| recipeLoad | 1.361 | 0.090 | 1.610 | |
| recipeMake | 0 | 0 | 0 | |
| recipeSearch | 0.572 | 0.037 | 0.626 | |
| recipeUpdate | 0 | 0 | 0 | |