Qian Liu
| Snapshot Date: 2024-06-09 14:00 -0400 (Sun, 09 Jun 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 2024-06-11 14:44 -0400 (Tue, 11 Jun 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4757 |
| palomino3 | Windows Server 2022 Datacenter | x64 | 4.4.0 (2024-04-24 ucrt) -- "Puppy Cup" | 4491 |
| lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4522 |
| kjohnson3 | macOS 13.6.5 Ventura | arm64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 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 | | ||||||||
| palomino3 | Windows Server 2022 Datacenter / x64 | ... NOT SUPPORTED ... | ||||||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson3 | macOS 13.6.5 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: 2024-06-11 02:56:28 -0400 (Tue, 11 Jun 2024) |
| EndedAt: 2024-06-11 03:00:44 -0400 (Tue, 11 Jun 2024) |
| EllapsedTime: 256.2 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 4.4.0 (2024-04-24)
* 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 13.6.5
* 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 8.854 1.257 15.523
getCloudData 3.406 0.226 5.820
* 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 4.4.0 (2024-04-24) -- "Puppy Cup"
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...
b876437642f0_GRCh38.primary_assembly.genome.fa.1.bt2 added
b876924bd2a_GRCh38.primary_assembly.genome.fa.2.bt2 added
b8764aff1516_GRCh38.primary_assembly.genome.fa.3.bt2 added
b87630c17dd1_GRCh38.primary_assembly.genome.fa.4.bt2 added
b8766f2b3d58_GRCh38.primary_assembly.genome.fa.rev.1.bt2 added
b8767fc8956c_GRCh38.primary_assembly.genome.fa.rev.2.bt2 added
b87649ca26fe_outfile.txt added
b87676c6138a_GRCh37_to_GRCh38.chain added
b876462d05f1_GRCh37_to_NCBI34.chain added
b87635e13535_GRCh37_to_NCBI35.chain added
b876546c4635_GRCh37_to_NCBI36.chain added
b87610756ce0_GRCh38_to_GRCh37.chain added
b876d3eee91_GRCh38_to_NCBI34.chain added
b8761ea07862_GRCh38_to_NCBI35.chain added
b876393f79a3_GRCh38_to_NCBI36.chain added
b876764ad9b1_NCBI34_to_GRCh37.chain added
b8762c1a3023_NCBI34_to_GRCh38.chain added
b8766b4e6073_NCBI35_to_GRCh37.chain added
b876669e550e_NCBI35_to_GRCh38.chain added
b87624e23ec4_NCBI36_to_GRCh37.chain added
b876186c8c7_NCBI36_to_GRCh38.chain added
b87637e78199_GRCm38_to_NCBIM36.chain added
b8763fed807b_GRCm38_to_NCBIM37.chain added
b87618e2c07_NCBIM36_to_GRCm38.chain added
b8761cec805d_NCBIM37_to_GRCm38.chain added
b8766adf6880_1000G_omni2.5.b37.vcf.gz added
b8767145e250_1000G_omni2.5.b37.vcf.gz.tbi added
b876230d2c49_Mills_and_1000G_gold_standard.indels.b37.vcf.gz added
b87635d67e99_Mills_and_1000G_gold_standard.indels.b37.vcf.gz.tbi added
b87615118a6c_1000G_omni2.5.hg38.vcf.gz added
b8763296c342_1000G_omni2.5.hg38.vcf.gz.tbi added
b87647ed3c00_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz added
b87627fe48e4_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz.tbi added
b8762763853f_af-only-gnomad.raw.sites.vcf added
b87676c0ff4c_af-only-gnomad.raw.sites.vcf.idx added
b87678b9137c_Mutect2-exome-panel.vcf.idx added
b8763eae6fcf_Mutect2-WGS-panel-b37.vcf added
b8762e2e9f2f_Mutect2-WGS-panel-b37.vcf.idx added
b87676d4de58_small_exac_common_3.vcf added
b8761151a05b_small_exac_common_3.vcf.idx added
b8765f6bf3f_1000g_pon.hg38.vcf.gz added
b876a85c428_1000g_pon.hg38.vcf.gz.tbi added
b8765411237d_af-only-gnomad.hg38.vcf.gz added
b87631310ea9_af-only-gnomad.hg38.vcf.gz.tbi added
b876bb9927a_small_exac_common_3.hg38.vcf.gz added
b876443f8d99_small_exac_common_3.hg38.vcf.gz.tbi added
b87628695ad0_gencode.v41.annotation.gtf added
b8761cc9226a_gencode.v42.annotation.gtf added
b87658f26be9_gencode.vM30.annotation.gtf added
b876138abb9e_gencode.vM31.annotation.gtf added
b87679238c17_gencode.v41.transcripts.fa added
b876cc27823_gencode.v41.transcripts.fa.fai added
b876335d4860_gencode.v42.transcripts.fa added
b876313ab0f8_gencode.v42.transcripts.fa.fai added
b8764388308_gencode.vM30.pc_transcripts.fa added
b8761a228462_gencode.vM30.pc_transcripts.fa.fai added
b87650214b55_gencode.vM31.pc_transcripts.fa added
b87639d8e28c_gencode.vM31.pc_transcripts.fa.fai added
b8764e0172ff_GRCh38.primary_assembly.genome.fa.1.ht2 added
b8764124eb5b_GRCh38.primary_assembly.genome.fa.2.ht2 added
b8765ed7c4c6_GRCh38.primary_assembly.genome.fa.3.ht2 added
b87627b7d3cf_GRCh38.primary_assembly.genome.fa.4.ht2 added
b87615b2cf68_GRCh38.primary_assembly.genome.fa.5.ht2 added
b876e4ebff9_GRCh38.primary_assembly.genome.fa.6.ht2 added
b876541d7bc5_GRCh38.primary_assembly.genome.fa.7.ht2 added
b8765ba8eda7_GRCh38.primary_assembly.genome.fa.8.ht2 added
b8762f8a9df4_GRCh38_full_analysis_set_plus_decoy_hla.fa.fai added
b8763588168e_GRCh38_full_analysis_set_plus_decoy_hla.fa.amb added
b8767980e016_GRCh38_full_analysis_set_plus_decoy_hla.fa.ann added
b8767bf802ab_GRCh38_full_analysis_set_plus_decoy_hla.fa.bwt added
b87657776822_GRCh38_full_analysis_set_plus_decoy_hla.fa.pac added
b8766055bd0a_GRCh38_full_analysis_set_plus_decoy_hla.fa.sa added
b8761cee0cef_GRCh38_full_analysis_set_plus_decoy_hla.fa added
b87650932dbf_GRCh38.primary_assembly.genome.fa.fai added
b8766ea07fec_GRCh38.primary_assembly.genome.fa.amb added
b8766b2e97b1_GRCh38.primary_assembly.genome.fa.ann added
b8763fe91c70_GRCh38.primary_assembly.genome.fa.bwt added
b876614a1dd7_GRCh38.primary_assembly.genome.fa.pac added
b87648ed4027_GRCh38.primary_assembly.genome.fa.sa added
b876500ee5d8_GRCh38.primary_assembly.genome.fa added
b876213f0f8_hs37d5.fa.fai added
b8766b312ad8_hs37d5.fa.amb added
b87668f401e2_hs37d5.fa.ann added
b8766ba7d242_hs37d5.fa.bwt added
b87656dd2245_hs37d5.fa.pac added
b8764ff50c90_hs37d5.fa.sa added
b876610beaf2_hs37d5.fa added
b876556de7a4_complete_ref_lens.bin added
b8762282ebcd_ctable.bin added
b8764146f16e_ctg_offsets.bin added
b87618948e3d_duplicate_clusters.tsv added
b87641065366_info.json added
b87664d6ee4_mphf.bin added
b87645ab3df7_pos.bin added
b8766d7146dc_pre_indexing.log added
b87627e34da6_rank.bin added
b8763bfee1bf_ref_indexing.log added
b8765a96e15e_refAccumLengths.bin added
b87667a610c8_reflengths.bin added
b8764797efa1_refseq.bin added
b87647f557bf_seq.bin added
b8763c53e181_versionInfo.json added
b87626f9fb18_salmon_index added
b87665d3f8a5_chrLength.txt added
b8763f694cdd_chrName.txt added
b8761a3561b1_chrNameLength.txt added
b87626a0b8e8_chrStart.txt added
b8761cb9b28_exonGeTrInfo.tab added
b8765e376003_exonInfo.tab added
b8765809548_geneInfo.tab added
b8763cc8acca_Genome added
b8761ac820f3_genomeParameters.txt added
b87648eb3f41_Log.out added
b8764c85e9cd_SA added
b8766bb8b8fa_SAindex added
b8762c785c56_sjdbInfo.txt added
b87611f628e9_sjdbList.fromGTF.out.tab added
b87637f7e235_sjdbList.out.tab added
b87673242247_transcriptInfo.tab added
b87649469e5f_GRCh38.GENCODE.v42_100 added
b8763b47948e_knownGene_hg38.sql added
b876586a1509_knownGene_hg38.txt added
b8761c8b2f38_refGene_hg38.sql added
b87675c9142b_refGene_hg38.txt added
b876644b4f76_knownGene_mm39.sql added
b876c4dff6b_knownGene_mm39.txt added
b87654bbd01c_refGene_mm39.sql added
b876765c09b9_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/RtmpRx4C4K/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
29.429 4.316 57.769
ReUseData.Rcheck/ReUseData-Ex.timings
| name | user | system | elapsed | |
| dataHub-class | 8.854 | 1.257 | 15.523 | |
| dataSearch | 1.456 | 0.081 | 2.666 | |
| dataUpdate | 0.000 | 0.001 | 0.000 | |
| getCloudData | 3.406 | 0.226 | 5.820 | |
| getData | 0 | 0 | 0 | |
| meta_data | 0.000 | 0.001 | 0.001 | |
| recipeHub-class | 0.174 | 0.022 | 0.355 | |
| recipeLoad | 1.780 | 0.138 | 3.177 | |
| recipeMake | 0 | 0 | 0 | |
| recipeSearch | 0.690 | 0.063 | 0.892 | |
| recipeUpdate | 0 | 0 | 0 | |