Qian Liu
| Snapshot Date: 2024-05-18 09:00:01 -0400 (Sat, 18 May 2024) |
| git_url: https://git.bioconductor.org/packages/ReUseData |
| git_branch: devel |
| git_last_commit: cbe4e73 |
| git_last_commit_date: 2024-04-30 11:46:52 -0400 (Tue, 30 Apr 2024) |
| Back to Mac ARM64 build report for BioC 3.20 |
|
This page was generated on 2024-05-20 11:32:18 -0400 (Mon, 20 May 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup" | 4381 |
| 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 1688/2233 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| ReUseData 1.5.0 (landing page) Qian Liu
| kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | OK | OK | OK | | |||||||
|
To the developers/maintainers of the ReUseData package: - 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: 1.5.0 |
| 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_1.5.0.tar.gz |
| StartedAt: 2024-05-20 00:06:57 -0400 (Mon, 20 May 2024) |
| EndedAt: 2024-05-20 00:09:24 -0400 (Mon, 20 May 2024) |
| EllapsedTime: 147.1 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_1.5.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.20-bioc-mac-arm64/meat/ReUseData.Rcheck’
* using R version 4.4.0 Patched (2024-04-24 r86482)
* 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 ‘1.5.0’
* 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 6.701 0.723 7.451
getCloudData 2.788 0.156 5.304
* 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-3.20-bioc-mac-arm64/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 Patched (2024-04-24 r86482) -- "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...
5382731c9b6_GRCh38.primary_assembly.genome.fa.1.bt2 added
53835b1dfd4_GRCh38.primary_assembly.genome.fa.2.bt2 added
53830ddf2d6_GRCh38.primary_assembly.genome.fa.3.bt2 added
5383b71d8aa_GRCh38.primary_assembly.genome.fa.4.bt2 added
5382f479f63_GRCh38.primary_assembly.genome.fa.rev.1.bt2 added
53873134d5_GRCh38.primary_assembly.genome.fa.rev.2.bt2 added
5382f838fa3_outfile.txt added
538664b2eb3_GRCh37_to_GRCh38.chain added
53851e71e3c_GRCh37_to_NCBI34.chain added
5381c721f26_GRCh37_to_NCBI35.chain added
53885b0661_GRCh37_to_NCBI36.chain added
538fffce90_GRCh38_to_GRCh37.chain added
53863525824_GRCh38_to_NCBI34.chain added
5383318d66d_GRCh38_to_NCBI35.chain added
53823a5a850_GRCh38_to_NCBI36.chain added
53850cd2e78_NCBI34_to_GRCh37.chain added
5384ea5f1b9_NCBI34_to_GRCh38.chain added
53870a0d105_NCBI35_to_GRCh37.chain added
5384dfad907_NCBI35_to_GRCh38.chain added
538fbe8290_NCBI36_to_GRCh37.chain added
538246dc403_NCBI36_to_GRCh38.chain added
538225fb3a4_GRCm38_to_NCBIM36.chain added
538390ae59d_GRCm38_to_NCBIM37.chain added
5387a68c3ac_NCBIM36_to_GRCm38.chain added
53874068ffc_NCBIM37_to_GRCm38.chain added
5385ad724e6_1000G_omni2.5.b37.vcf.gz added
53862b7a6a1_1000G_omni2.5.b37.vcf.gz.tbi added
53871cc6a9_Mills_and_1000G_gold_standard.indels.b37.vcf.gz added
538723684e4_Mills_and_1000G_gold_standard.indels.b37.vcf.gz.tbi added
538594ecf50_1000G_omni2.5.hg38.vcf.gz added
538450cbafe_1000G_omni2.5.hg38.vcf.gz.tbi added
53846c89d1c_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz added
5381cc2bd92_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz.tbi added
538352bcafe_af-only-gnomad.raw.sites.vcf added
5384e1c04f7_af-only-gnomad.raw.sites.vcf.idx added
538118a1c31_Mutect2-exome-panel.vcf.idx added
538240ddf6_Mutect2-WGS-panel-b37.vcf added
53870ac42a1_Mutect2-WGS-panel-b37.vcf.idx added
5383d4a91d1_small_exac_common_3.vcf added
5386aab4fc6_small_exac_common_3.vcf.idx added
538150286e0_1000g_pon.hg38.vcf.gz added
53858e4e6e6_1000g_pon.hg38.vcf.gz.tbi added
5381bf333a2_af-only-gnomad.hg38.vcf.gz added
5387bc2df03_af-only-gnomad.hg38.vcf.gz.tbi added
53836bf7d6f_small_exac_common_3.hg38.vcf.gz added
53855c41e7d_small_exac_common_3.hg38.vcf.gz.tbi added
5383eadcc88_gencode.v41.annotation.gtf added
53844f14de_gencode.v42.annotation.gtf added
53863e2fd07_gencode.vM30.annotation.gtf added
5384b5209cc_gencode.vM31.annotation.gtf added
538770156b5_gencode.v41.transcripts.fa added
53878e3c21c_gencode.v41.transcripts.fa.fai added
53830dcfa45_gencode.v42.transcripts.fa added
5387bb2e112_gencode.v42.transcripts.fa.fai added
5381cd6a430_gencode.vM30.pc_transcripts.fa added
5384fb55a1a_gencode.vM30.pc_transcripts.fa.fai added
538b2e89d8_gencode.vM31.pc_transcripts.fa added
5381c5bc9a4_gencode.vM31.pc_transcripts.fa.fai added
5384e133c87_GRCh38.primary_assembly.genome.fa.1.ht2 added
53850eaeb1c_GRCh38.primary_assembly.genome.fa.2.ht2 added
5386ef1a4c4_GRCh38.primary_assembly.genome.fa.3.ht2 added
5383a7878c3_GRCh38.primary_assembly.genome.fa.4.ht2 added
5383b406832_GRCh38.primary_assembly.genome.fa.5.ht2 added
538178c902_GRCh38.primary_assembly.genome.fa.6.ht2 added
53820d4a30f_GRCh38.primary_assembly.genome.fa.7.ht2 added
538681d3e9f_GRCh38.primary_assembly.genome.fa.8.ht2 added
53857fa6e1f_GRCh38_full_analysis_set_plus_decoy_hla.fa.fai added
5387a53e258_GRCh38_full_analysis_set_plus_decoy_hla.fa.amb added
53819313e26_GRCh38_full_analysis_set_plus_decoy_hla.fa.ann added
5386fe73db5_GRCh38_full_analysis_set_plus_decoy_hla.fa.bwt added
53836846f78_GRCh38_full_analysis_set_plus_decoy_hla.fa.pac added
53830b24b3e_GRCh38_full_analysis_set_plus_decoy_hla.fa.sa added
538969ec6c_GRCh38_full_analysis_set_plus_decoy_hla.fa added
538920ab48_GRCh38.primary_assembly.genome.fa.fai added
5383fcd08a6_GRCh38.primary_assembly.genome.fa.amb added
5382df2eb03_GRCh38.primary_assembly.genome.fa.ann added
53827232986_GRCh38.primary_assembly.genome.fa.bwt added
538757b307c_GRCh38.primary_assembly.genome.fa.pac added
5386aac5925_GRCh38.primary_assembly.genome.fa.sa added
5385910c2d9_GRCh38.primary_assembly.genome.fa added
5385b68623d_hs37d5.fa.fai added
5382209c1ad_hs37d5.fa.amb added
5382e8a5650_hs37d5.fa.ann added
5387c28b60e_hs37d5.fa.bwt added
53854c890d0_hs37d5.fa.pac added
5383b9b732c_hs37d5.fa.sa added
5385aa66c46_hs37d5.fa added
538640e9628_complete_ref_lens.bin added
53879a44f69_ctable.bin added
5381259b4e3_ctg_offsets.bin added
5383f72ac7e_duplicate_clusters.tsv added
53819aa4bd_info.json added
5384fb5751d_mphf.bin added
538121bebcd_pos.bin added
5386715e904_pre_indexing.log added
5384f753a7b_rank.bin added
538195289fe_ref_indexing.log added
53879e18fae_refAccumLengths.bin added
53847a02705_reflengths.bin added
5386361ddff_refseq.bin added
5382e35c352_seq.bin added
5384baa5431_versionInfo.json added
5381b7d83c6_salmon_index added
5384d564a43_chrLength.txt added
5385c259c5f_chrName.txt added
538293d503c_chrNameLength.txt added
538785ea84a_chrStart.txt added
538e7ad003_exonGeTrInfo.tab added
53820ee7c62_exonInfo.tab added
53892816d2_geneInfo.tab added
53826f239b0_Genome added
53868a965c9_genomeParameters.txt added
5384959a4cd_Log.out added
5381c52b45a_SA added
53879be8f3c_SAindex added
5384dadea95_sjdbInfo.txt added
5385504040a_sjdbList.fromGTF.out.tab added
5387aa55820_sjdbList.out.tab added
5387d3cdbc7_transcriptInfo.tab added
5382681260d_GRCh38.GENCODE.v42_100 added
53868e9333a_knownGene_hg38.sql added
53826225aa5_knownGene_hg38.txt added
538196d1a32_refGene_hg38.sql added
53849d2d5a8_refGene_hg38.txt added
53830c92e75_knownGene_mm39.sql added
53868091c58_knownGene_mm39.txt added
5382e240ac4_refGene_mm39.sql added
538403ee186_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/RtmpBvnSbb/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
24.558 2.973 29.827
ReUseData.Rcheck/ReUseData-Ex.timings
| name | user | system | elapsed | |
| dataHub-class | 6.701 | 0.723 | 7.451 | |
| dataSearch | 1.154 | 0.048 | 1.202 | |
| dataUpdate | 0.000 | 0.001 | 0.000 | |
| getCloudData | 2.788 | 0.156 | 5.304 | |
| getData | 0.000 | 0.001 | 0.001 | |
| meta_data | 0.001 | 0.000 | 0.001 | |
| recipeHub-class | 0.140 | 0.013 | 0.154 | |
| recipeLoad | 1.348 | 0.080 | 1.434 | |
| recipeMake | 0.001 | 0.000 | 0.001 | |
| recipeSearch | 0.606 | 0.036 | 0.642 | |
| recipeUpdate | 0.000 | 0.000 | 0.001 | |