Qian Liu
| Snapshot Date: 2024-04-16 09:00:03 -0400 (Tue, 16 Apr 2024) |
| git_url: https://git.bioconductor.org/packages/ReUseData |
| git_branch: RELEASE_3_18 |
| git_last_commit: 836e03f |
| git_last_commit_date: 2023-12-08 16:02:19 -0400 (Fri, 08 Dec 2023) |
| Back to Mac ARM64 build report for BioC 3.18 |
|
This page was generated on 2024-04-18 11:32:17 -0400 (Thu, 18 Apr 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| kjohnson1 | macOS 13.6.1 Ventura | arm64 | 4.3.3 (2024-02-29) -- "Angel Food Cake" | 4388 |
| 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 1725/2266 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| ReUseData 1.2.2 (landing page) Qian Liu
| kjohnson1 | macOS 13.6.1 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: 1.2.2 |
| 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_1.2.2.tar.gz |
| StartedAt: 2024-04-18 01:02:42 -0400 (Thu, 18 Apr 2024) |
| EndedAt: 2024-04-18 01:05:12 -0400 (Thu, 18 Apr 2024) |
| EllapsedTime: 150.6 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_1.2.2.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.18-bioc-mac-arm64/meat/ReUseData.Rcheck’
* using R version 4.3.3 (2024-02-29)
* using platform: aarch64-apple-darwin20 (64-bit)
* 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 13.6.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘ReUseData/DESCRIPTION’ ... OK
* this is package ‘ReUseData’ version ‘1.2.2’
* 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
dataHub-class 6.814 0.736 7.593
* 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-3.18-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/4.3-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 4.3.3 (2024-02-29) -- "Angel Food Cake"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: aarch64-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...
1536efe8ab40_GRCh38.primary_assembly.genome.fa.1.bt2 added
1536e7442fee8_GRCh38.primary_assembly.genome.fa.2.bt2 added
1536e5a6d6cf9_GRCh38.primary_assembly.genome.fa.3.bt2 added
1536e460d7dd0_GRCh38.primary_assembly.genome.fa.4.bt2 added
1536e1fbf069e_GRCh38.primary_assembly.genome.fa.rev.1.bt2 added
1536e364b7f5a_GRCh38.primary_assembly.genome.fa.rev.2.bt2 added
1536e1696098f_outfile.txt added
1536e544d96de_GRCh37_to_GRCh38.chain added
1536e31ebf40f_GRCh37_to_NCBI34.chain added
1536e79e41e63_GRCh37_to_NCBI35.chain added
1536e6f873419_GRCh37_to_NCBI36.chain added
1536e156d8e83_GRCh38_to_GRCh37.chain added
1536e4ba74572_GRCh38_to_NCBI34.chain added
1536e52c0662b_GRCh38_to_NCBI35.chain added
1536e5573bb7e_GRCh38_to_NCBI36.chain added
1536e211a7906_NCBI34_to_GRCh37.chain added
1536e50ff89e4_NCBI34_to_GRCh38.chain added
1536e38b60147_NCBI35_to_GRCh37.chain added
1536e350df967_NCBI35_to_GRCh38.chain added
1536e2870f467_NCBI36_to_GRCh37.chain added
1536efbdaaef_NCBI36_to_GRCh38.chain added
1536e6d2138fb_GRCm38_to_NCBIM36.chain added
1536e20241eb6_GRCm38_to_NCBIM37.chain added
1536e235c4f36_NCBIM36_to_GRCm38.chain added
1536e154745d_NCBIM37_to_GRCm38.chain added
1536e4fa38659_1000G_omni2.5.b37.vcf.gz added
1536e78c965e7_1000G_omni2.5.b37.vcf.gz.tbi added
1536e6e415ea4_Mills_and_1000G_gold_standard.indels.b37.vcf.gz added
1536e5ac9989_Mills_and_1000G_gold_standard.indels.b37.vcf.gz.tbi added
1536e693f448_1000G_omni2.5.hg38.vcf.gz added
1536e5b8aa657_1000G_omni2.5.hg38.vcf.gz.tbi added
1536e6baec8b4_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz added
1536e1ffad8a7_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz.tbi added
1536eda5cc58_af-only-gnomad.raw.sites.vcf added
1536eaac68_af-only-gnomad.raw.sites.vcf.idx added
1536e3cbcdfdd_Mutect2-exome-panel.vcf.idx added
1536e140d4552_Mutect2-WGS-panel-b37.vcf added
1536e734214c6_Mutect2-WGS-panel-b37.vcf.idx added
1536e77620e47_small_exac_common_3.vcf added
1536e4697948c_small_exac_common_3.vcf.idx added
1536e9999789_1000g_pon.hg38.vcf.gz added
1536e42aba84b_1000g_pon.hg38.vcf.gz.tbi added
1536e13b5f61f_af-only-gnomad.hg38.vcf.gz added
1536ef317755_af-only-gnomad.hg38.vcf.gz.tbi added
1536e7891753d_small_exac_common_3.hg38.vcf.gz added
1536e15a835a2_small_exac_common_3.hg38.vcf.gz.tbi added
1536e565929c9_gencode.v41.annotation.gtf added
1536e77c67768_gencode.v42.annotation.gtf added
1536e6c98a47_gencode.vM30.annotation.gtf added
1536e19953ecc_gencode.vM31.annotation.gtf added
1536e154dd033_gencode.v41.transcripts.fa added
1536e279fcf32_gencode.v41.transcripts.fa.fai added
1536e6cdbeff0_gencode.v42.transcripts.fa added
1536e5b65ad65_gencode.v42.transcripts.fa.fai added
1536e705af0c3_gencode.vM30.pc_transcripts.fa added
1536e6274cbd5_gencode.vM30.pc_transcripts.fa.fai added
1536e61f23f72_gencode.vM31.pc_transcripts.fa added
1536e6723879a_gencode.vM31.pc_transcripts.fa.fai added
1536e4d9bc45c_GRCh38.primary_assembly.genome.fa.1.ht2 added
1536e2d789bd2_GRCh38.primary_assembly.genome.fa.2.ht2 added
1536e493e0f50_GRCh38.primary_assembly.genome.fa.3.ht2 added
1536e95f72c1_GRCh38.primary_assembly.genome.fa.4.ht2 added
1536e5966e1b5_GRCh38.primary_assembly.genome.fa.5.ht2 added
1536e716c5fed_GRCh38.primary_assembly.genome.fa.6.ht2 added
1536e20dfac8_GRCh38.primary_assembly.genome.fa.7.ht2 added
1536e63cb6185_GRCh38.primary_assembly.genome.fa.8.ht2 added
1536e3d6f95f2_GRCh38_full_analysis_set_plus_decoy_hla.fa.fai added
1536e68dd6260_GRCh38_full_analysis_set_plus_decoy_hla.fa.amb added
1536e1e65c269_GRCh38_full_analysis_set_plus_decoy_hla.fa.ann added
1536e2abe8b16_GRCh38_full_analysis_set_plus_decoy_hla.fa.bwt added
1536e439d6746_GRCh38_full_analysis_set_plus_decoy_hla.fa.pac added
1536e12e74758_GRCh38_full_analysis_set_plus_decoy_hla.fa.sa added
1536edfcec1a_GRCh38_full_analysis_set_plus_decoy_hla.fa added
1536e57f0a622_GRCh38.primary_assembly.genome.fa.fai added
1536e782b2f48_GRCh38.primary_assembly.genome.fa.amb added
1536e5b2d5d9a_GRCh38.primary_assembly.genome.fa.ann added
1536e7f5c5839_GRCh38.primary_assembly.genome.fa.bwt added
1536e7a44782_GRCh38.primary_assembly.genome.fa.pac added
1536e3252abb9_GRCh38.primary_assembly.genome.fa.sa added
1536e5188187e_GRCh38.primary_assembly.genome.fa added
1536e3e002203_hs37d5.fa.fai added
1536e7ab912c1_hs37d5.fa.amb added
1536ec7e7bd9_hs37d5.fa.ann added
1536e43f4e9f7_hs37d5.fa.bwt added
1536e42c79fc_hs37d5.fa.pac added
1536e3fc9188_hs37d5.fa.sa added
1536e3ab679c3_hs37d5.fa added
1536e21f40f52_complete_ref_lens.bin added
1536e1e19e1e8_ctable.bin added
1536e353e55c8_ctg_offsets.bin added
1536ef71d8c7_duplicate_clusters.tsv added
1536e7b4ef8bc_info.json added
1536e7dac3de2_mphf.bin added
1536e371300e3_pos.bin added
1536e409f5354_pre_indexing.log added
1536e1c17d0f1_rank.bin added
1536e5f968c9f_ref_indexing.log added
1536e14ea4bc0_refAccumLengths.bin added
1536e221334fa_reflengths.bin added
1536e1afb1a90_refseq.bin added
1536e5b8cf1c6_seq.bin added
1536e2552d1f_versionInfo.json added
1536e26054f6b_salmon_index added
1536e26a10d4d_chrLength.txt added
1536e17704e0b_chrName.txt added
1536e4e13c032_chrNameLength.txt added
1536e72af3aa9_chrStart.txt added
1536e4e346811_exonGeTrInfo.tab added
1536e529c5c33_exonInfo.tab added
1536e176942a4_geneInfo.tab added
1536e7f9628fd_Genome added
1536e5b5d3b7b_genomeParameters.txt added
1536e45ec3719_Log.out added
1536e17156e2c_SA added
1536e7ff4168a_SAindex added
1536e71f3ffa6_sjdbInfo.txt added
1536e4a1525bc_sjdbList.fromGTF.out.tab added
1536e32607fa3_sjdbList.out.tab added
1536e5d5bc02b_transcriptInfo.tab added
1536e32a576ef_GRCh38.GENCODE.v42_100 added
1536ed235ee3_knownGene_hg38.sql added
1536ed2a8fd2_knownGene_hg38.txt added
1536e65482abe_refGene_hg38.sql added
1536e64ee53e4_refGene_hg38.txt added
1536e5ac5d180_knownGene_mm39.sql added
1536e713d590e_knownGene_mm39.txt added
1536e72a1e036_refGene_mm39.sql added
1536e61873405_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/RtmpNvfFgH/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
24.869 2.865 29.085
ReUseData.Rcheck/ReUseData-Ex.timings
| name | user | system | elapsed | |
| dataHub-class | 6.814 | 0.736 | 7.593 | |
| dataSearch | 1.164 | 0.048 | 1.212 | |
| dataUpdate | 0.000 | 0.001 | 0.000 | |
| getCloudData | 2.677 | 0.124 | 4.604 | |
| getData | 0 | 0 | 0 | |
| meta_data | 0.000 | 0.001 | 0.001 | |
| recipeHub-class | 0.130 | 0.013 | 0.144 | |
| recipeLoad | 1.379 | 0.097 | 1.481 | |
| recipeMake | 0.000 | 0.000 | 0.001 | |
| recipeSearch | 0.604 | 0.038 | 0.644 | |
| recipeUpdate | 0 | 0 | 0 | |