Qian Liu
| Snapshot Date: 2024-05-11 09:00:03 -0400 (Sat, 11 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 2024-05-13 11:32:11 -0400 (Mon, 13 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" | 4378 |
| 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 1687/2230 | 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: 2024-05-13 00:29:33 -0400 (Mon, 13 May 2024) |
| EndedAt: 2024-05-13 00:32:01 -0400 (Mon, 13 May 2024) |
| EllapsedTime: 148.4 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 6.862 0.732 7.637
getCloudData 2.736 0.134 5.986
* 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...
168f5e52017b_GRCh38.primary_assembly.genome.fa.1.bt2 added
168f59df629d_GRCh38.primary_assembly.genome.fa.2.bt2 added
168f58c35f83_GRCh38.primary_assembly.genome.fa.3.bt2 added
168f2b3befc_GRCh38.primary_assembly.genome.fa.4.bt2 added
168f66bf93c6_GRCh38.primary_assembly.genome.fa.rev.1.bt2 added
168f2b7ee0dd_GRCh38.primary_assembly.genome.fa.rev.2.bt2 added
168f16dce37a_outfile.txt added
168f7fda6a4f_GRCh37_to_GRCh38.chain added
168f5c79aa1c_GRCh37_to_NCBI34.chain added
168f378f43b2_GRCh37_to_NCBI35.chain added
168f1ea5779d_GRCh37_to_NCBI36.chain added
168f14ff423_GRCh38_to_GRCh37.chain added
168f28252681_GRCh38_to_NCBI34.chain added
168f1f02f3be_GRCh38_to_NCBI35.chain added
168f7ad04ed9_GRCh38_to_NCBI36.chain added
168f1e8c78d_NCBI34_to_GRCh37.chain added
168f5984faf5_NCBI34_to_GRCh38.chain added
168f297818bd_NCBI35_to_GRCh37.chain added
168fba03590_NCBI35_to_GRCh38.chain added
168f431c86e6_NCBI36_to_GRCh37.chain added
168f5dc8876_NCBI36_to_GRCh38.chain added
168f5182fdfb_GRCm38_to_NCBIM36.chain added
168f6ef0938b_GRCm38_to_NCBIM37.chain added
168f7466c393_NCBIM36_to_GRCm38.chain added
168f6b22399_NCBIM37_to_GRCm38.chain added
168f193f153e_1000G_omni2.5.b37.vcf.gz added
168f7c8ba664_1000G_omni2.5.b37.vcf.gz.tbi added
168f34592f1d_Mills_and_1000G_gold_standard.indels.b37.vcf.gz added
168f4b2433c4_Mills_and_1000G_gold_standard.indels.b37.vcf.gz.tbi added
168f35c2af66_1000G_omni2.5.hg38.vcf.gz added
168f896d1d_1000G_omni2.5.hg38.vcf.gz.tbi added
168f3e5a8b31_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz added
168f2a685df2_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz.tbi added
168f29efd09e_af-only-gnomad.raw.sites.vcf added
168f3f694a94_af-only-gnomad.raw.sites.vcf.idx added
168f199f5b12_Mutect2-exome-panel.vcf.idx added
168f2d1407e2_Mutect2-WGS-panel-b37.vcf added
168f7e119d8c_Mutect2-WGS-panel-b37.vcf.idx added
168f367e92fd_small_exac_common_3.vcf added
168f2fe43bfe_small_exac_common_3.vcf.idx added
168f311eb942_1000g_pon.hg38.vcf.gz added
168f5814b53f_1000g_pon.hg38.vcf.gz.tbi added
168f37876846_af-only-gnomad.hg38.vcf.gz added
168f1acee825_af-only-gnomad.hg38.vcf.gz.tbi added
168f5eae2e3_small_exac_common_3.hg38.vcf.gz added
168f7fd5a81d_small_exac_common_3.hg38.vcf.gz.tbi added
168f2410497c_gencode.v41.annotation.gtf added
168f29487e63_gencode.v42.annotation.gtf added
168f5661aac1_gencode.vM30.annotation.gtf added
168f26119135_gencode.vM31.annotation.gtf added
168f4b544219_gencode.v41.transcripts.fa added
168f8bf9df2_gencode.v41.transcripts.fa.fai added
168f5c1a7f5a_gencode.v42.transcripts.fa added
168f4f9f1cf3_gencode.v42.transcripts.fa.fai added
168f5725be5b_gencode.vM30.pc_transcripts.fa added
168f6ef4750f_gencode.vM30.pc_transcripts.fa.fai added
168f733164b1_gencode.vM31.pc_transcripts.fa added
168f2fc9db8c_gencode.vM31.pc_transcripts.fa.fai added
168f6d6cdcd6_GRCh38.primary_assembly.genome.fa.1.ht2 added
168f6169dba_GRCh38.primary_assembly.genome.fa.2.ht2 added
168f36cd2175_GRCh38.primary_assembly.genome.fa.3.ht2 added
168f554fa46e_GRCh38.primary_assembly.genome.fa.4.ht2 added
168f5fb45d83_GRCh38.primary_assembly.genome.fa.5.ht2 added
168f3a67748b_GRCh38.primary_assembly.genome.fa.6.ht2 added
168f5e146fa1_GRCh38.primary_assembly.genome.fa.7.ht2 added
168fface348_GRCh38.primary_assembly.genome.fa.8.ht2 added
168f1f7d9402_GRCh38_full_analysis_set_plus_decoy_hla.fa.fai added
168f6d801f74_GRCh38_full_analysis_set_plus_decoy_hla.fa.amb added
168f769130d5_GRCh38_full_analysis_set_plus_decoy_hla.fa.ann added
168f361d2cc3_GRCh38_full_analysis_set_plus_decoy_hla.fa.bwt added
168f3565d1f6_GRCh38_full_analysis_set_plus_decoy_hla.fa.pac added
168f2fbb88dd_GRCh38_full_analysis_set_plus_decoy_hla.fa.sa added
168f41167da6_GRCh38_full_analysis_set_plus_decoy_hla.fa added
168f2b933eac_GRCh38.primary_assembly.genome.fa.fai added
168f4ff7a48d_GRCh38.primary_assembly.genome.fa.amb added
168fb544dff_GRCh38.primary_assembly.genome.fa.ann added
168f4bcca628_GRCh38.primary_assembly.genome.fa.bwt added
168f68b0b2f8_GRCh38.primary_assembly.genome.fa.pac added
168f28b5ed7a_GRCh38.primary_assembly.genome.fa.sa added
168f3ff9f977_GRCh38.primary_assembly.genome.fa added
168f34691471_hs37d5.fa.fai added
168f5ebd2198_hs37d5.fa.amb added
168f52e8b2bf_hs37d5.fa.ann added
168f2b2f441f_hs37d5.fa.bwt added
168f2c21655f_hs37d5.fa.pac added
168f4486569b_hs37d5.fa.sa added
168f4f9ffd42_hs37d5.fa added
168f10ac20e5_complete_ref_lens.bin added
168f14a3a2f0_ctable.bin added
168f31e4526_ctg_offsets.bin added
168f384dc363_duplicate_clusters.tsv added
168f7956b575_info.json added
168f2ba3528f_mphf.bin added
168f6f8140aa_pos.bin added
168febc9217_pre_indexing.log added
168f7e1b2b8f_rank.bin added
168f29c8f9f7_ref_indexing.log added
168f4992dc8f_refAccumLengths.bin added
168f48ce5605_reflengths.bin added
168f6271879a_refseq.bin added
168fb7dc1f4_seq.bin added
168f6d488010_versionInfo.json added
168f32cfd27d_salmon_index added
168f6a04269a_chrLength.txt added
168f36827ed6_chrName.txt added
168f31552f8f_chrNameLength.txt added
168f4fa56e96_chrStart.txt added
168f75ff62b3_exonGeTrInfo.tab added
168f51a9124a_exonInfo.tab added
168f32efe228_geneInfo.tab added
168f22e8ca38_Genome added
168f6134346f_genomeParameters.txt added
168f2a5e9544_Log.out added
168f2799b917_SA added
168f5d46a950_SAindex added
168f4a15f307_sjdbInfo.txt added
168f67067690_sjdbList.fromGTF.out.tab added
168f59521cc7_sjdbList.out.tab added
168f1ddf7aa1_transcriptInfo.tab added
168f3aebef59_GRCh38.GENCODE.v42_100 added
168f57aeda47_knownGene_hg38.sql added
168f187c984a_knownGene_hg38.txt added
168f1bf22ed5_refGene_hg38.sql added
168f38e0b048_refGene_hg38.txt added
168f27556424_knownGene_mm39.sql added
168f57218ba8_knownGene_mm39.txt added
168f5b57ef48_refGene_mm39.sql added
168f6a1e8ed1_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/RtmpH6cXZM/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
24.453 2.968 29.047
ReUseData.Rcheck/ReUseData-Ex.timings
| name | user | system | elapsed | |
| dataHub-class | 6.862 | 0.732 | 7.637 | |
| dataSearch | 1.151 | 0.054 | 1.206 | |
| dataUpdate | 0.000 | 0.001 | 0.000 | |
| getCloudData | 2.736 | 0.134 | 5.986 | |
| getData | 0.000 | 0.001 | 0.000 | |
| meta_data | 0.001 | 0.000 | 0.001 | |
| recipeHub-class | 0.149 | 0.017 | 0.167 | |
| recipeLoad | 1.399 | 0.083 | 1.488 | |
| recipeMake | 0.000 | 0.001 | 0.000 | |
| recipeSearch | 0.544 | 0.031 | 0.575 | |
| recipeUpdate | 0 | 0 | 0 | |