Qian Liu
| Snapshot Date: 2024-05-06 14:00:02 -0400 (Mon, 06 May 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 Mac ARM64 build report for BioC 3.19 |
|
This page was generated on 2024-05-07 11:32:43 -0400 (Tue, 07 May 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| kjohnson3 | macOS 13.6.5 Ventura | arm64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4461 |
| 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
| kjohnson3 | macOS 13.6.5 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: 1.4.0 |
| 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: 2024-05-07 00:18:39 -0400 (Tue, 07 May 2024) |
| EndedAt: 2024-05-07 00:19:26 -0400 (Tue, 07 May 2024) |
| EllapsedTime: 47.5 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: ReUseData.Rcheck |
| Warnings: 0 |
##############################################################################
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###
### 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-mac-arm64/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
* 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-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 (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...
146db3e166686_GRCh38.primary_assembly.genome.fa.1.bt2 added
146db30a50742_GRCh38.primary_assembly.genome.fa.2.bt2 added
146db227f9701_GRCh38.primary_assembly.genome.fa.3.bt2 added
146db6692d458_GRCh38.primary_assembly.genome.fa.4.bt2 added
146db31b31204_GRCh38.primary_assembly.genome.fa.rev.1.bt2 added
146db6363de19_GRCh38.primary_assembly.genome.fa.rev.2.bt2 added
146db318a6e49_outfile.txt added
146db774e9407_GRCh37_to_GRCh38.chain added
146db47d894c2_GRCh37_to_NCBI34.chain added
146db5c0e7167_GRCh37_to_NCBI35.chain added
146db38375068_GRCh37_to_NCBI36.chain added
146db377ff8ad_GRCh38_to_GRCh37.chain added
146db329f4252_GRCh38_to_NCBI34.chain added
146db75bb2f74_GRCh38_to_NCBI35.chain added
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146db386c654c_NCBI34_to_GRCh37.chain added
146db546e7d84_NCBI34_to_GRCh38.chain added
146db21f2906a_NCBI35_to_GRCh37.chain added
146db3be7308f_NCBI35_to_GRCh38.chain added
146db47251b02_NCBI36_to_GRCh37.chain added
146db551044cb_NCBI36_to_GRCh38.chain added
146db1f14970e_GRCm38_to_NCBIM36.chain added
146dbc92813_GRCm38_to_NCBIM37.chain added
146db1665f7cc_NCBIM36_to_GRCm38.chain added
146db6f7d91_NCBIM37_to_GRCm38.chain added
146db179cbad0_1000G_omni2.5.b37.vcf.gz added
146db32acb9cc_1000G_omni2.5.b37.vcf.gz.tbi added
146db69da1a11_Mills_and_1000G_gold_standard.indels.b37.vcf.gz added
146db6de58861_Mills_and_1000G_gold_standard.indels.b37.vcf.gz.tbi added
146db785cd0a4_1000G_omni2.5.hg38.vcf.gz added
146db1585fcb8_1000G_omni2.5.hg38.vcf.gz.tbi added
146dbf929f12_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz added
146db63095eba_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz.tbi added
146db7c2a3821_af-only-gnomad.raw.sites.vcf added
146db37cb3e36_af-only-gnomad.raw.sites.vcf.idx added
146db6167d8_Mutect2-exome-panel.vcf.idx added
146db7ae89619_Mutect2-WGS-panel-b37.vcf added
146db3bd68259_Mutect2-WGS-panel-b37.vcf.idx added
146db7bfc0_small_exac_common_3.vcf added
146db7cbdd643_small_exac_common_3.vcf.idx added
146db133e08b0_1000g_pon.hg38.vcf.gz added
146db4dac64ae_1000g_pon.hg38.vcf.gz.tbi added
146db71060358_af-only-gnomad.hg38.vcf.gz added
146db41c5c060_af-only-gnomad.hg38.vcf.gz.tbi added
146db1dd9005c_small_exac_common_3.hg38.vcf.gz added
146db11a6a753_small_exac_common_3.hg38.vcf.gz.tbi added
146db54334332_gencode.v41.annotation.gtf added
146db7180b2cd_gencode.v42.annotation.gtf added
146db385aeaf2_gencode.vM30.annotation.gtf added
146db58f6d2c5_gencode.vM31.annotation.gtf added
146db3487b124_gencode.v41.transcripts.fa added
146db387ecd6d_gencode.v41.transcripts.fa.fai added
146dbce0cc15_gencode.v42.transcripts.fa added
146db7a767d4d_gencode.v42.transcripts.fa.fai added
146db791c890a_gencode.vM30.pc_transcripts.fa added
146db40692da4_gencode.vM30.pc_transcripts.fa.fai added
146db39338b05_gencode.vM31.pc_transcripts.fa added
146db66ec1299_gencode.vM31.pc_transcripts.fa.fai added
146db14b92f99_GRCh38.primary_assembly.genome.fa.1.ht2 added
146db9e3f070_GRCh38.primary_assembly.genome.fa.2.ht2 added
146db53be4e22_GRCh38.primary_assembly.genome.fa.3.ht2 added
146db72fbc521_GRCh38.primary_assembly.genome.fa.4.ht2 added
146db6f4b3480_GRCh38.primary_assembly.genome.fa.5.ht2 added
146db3263f895_GRCh38.primary_assembly.genome.fa.6.ht2 added
146db4155180b_GRCh38.primary_assembly.genome.fa.7.ht2 added
146db399d9baf_GRCh38.primary_assembly.genome.fa.8.ht2 added
146db1a581bb6_GRCh38_full_analysis_set_plus_decoy_hla.fa.fai added
146dbe83573d_GRCh38_full_analysis_set_plus_decoy_hla.fa.amb added
146db50d46d3c_GRCh38_full_analysis_set_plus_decoy_hla.fa.ann added
146db2a4fa799_GRCh38_full_analysis_set_plus_decoy_hla.fa.bwt added
146db53844382_GRCh38_full_analysis_set_plus_decoy_hla.fa.pac added
146db106c36a4_GRCh38_full_analysis_set_plus_decoy_hla.fa.sa added
146db30775168_GRCh38_full_analysis_set_plus_decoy_hla.fa added
146db69819bb3_GRCh38.primary_assembly.genome.fa.fai added
146db3c153ae2_GRCh38.primary_assembly.genome.fa.amb added
146db15ccea3f_GRCh38.primary_assembly.genome.fa.ann added
146db4026d947_GRCh38.primary_assembly.genome.fa.bwt added
146db3682e538_GRCh38.primary_assembly.genome.fa.pac added
146db4b96db7d_GRCh38.primary_assembly.genome.fa.sa added
146db1d241250_GRCh38.primary_assembly.genome.fa added
146db2b2e5122_hs37d5.fa.fai added
146db6dd0a553_hs37d5.fa.amb added
146db1d162478_hs37d5.fa.ann added
146db18b45133_hs37d5.fa.bwt added
146db663ef7f0_hs37d5.fa.pac added
146db3007e201_hs37d5.fa.sa added
146db5586c849_hs37d5.fa added
146db3c75c7d_complete_ref_lens.bin added
146db1589147b_ctable.bin added
146db5a9fa248_ctg_offsets.bin added
146db26575373_duplicate_clusters.tsv added
146db2f27b6af_info.json added
146db584ab358_mphf.bin added
146db104483b1_pos.bin added
146db221e1cf_pre_indexing.log added
146db7e6fde20_rank.bin added
146db626047b9_ref_indexing.log added
146db1f04f524_refAccumLengths.bin added
146db7e7a1e64_reflengths.bin added
146db361781b_refseq.bin added
146db74143658_seq.bin added
146db5afc06f1_versionInfo.json added
146db582be6e1_salmon_index added
146db2a42eb00_chrLength.txt added
146dbf5262ad_chrName.txt added
146db69cc53b6_chrNameLength.txt added
146db658c07fd_chrStart.txt added
146db4c60a720_exonGeTrInfo.tab added
146db5d7c4d0c_exonInfo.tab added
146dbba67ec7_geneInfo.tab added
146db5fcd40ca_Genome added
146db1c58bee9_genomeParameters.txt added
146db65dc189_Log.out added
146db754d0ca2_SA added
146db15789bd8_SAindex added
146db213f8ceb_sjdbInfo.txt added
146db533ca95a_sjdbList.fromGTF.out.tab added
146db33927e67_sjdbList.out.tab added
146db56a8b6a4_transcriptInfo.tab added
146db5e6ef56e_GRCh38.GENCODE.v42_100 added
146db46b33931_knownGene_hg38.sql added
146db206fe43a_knownGene_hg38.txt added
146db11f0ac79_refGene_hg38.sql added
146db4fcb4522_refGene_hg38.txt added
146db2a27e41b_knownGene_mm39.sql added
146db20f0be3c_knownGene_mm39.txt added
146db1d596609_refGene_mm39.sql added
146db5839e7ec_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:
/var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpoPW75v/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
6.716 0.860 7.782
ReUseData.Rcheck/ReUseData-Ex.timings
| name | user | system | elapsed | |
| dataHub-class | 1.852 | 0.191 | 2.046 | |
| dataSearch | 0.297 | 0.011 | 0.309 | |
| dataUpdate | 0 | 0 | 0 | |
| getCloudData | 0.726 | 0.046 | 1.312 | |
| getData | 0 | 0 | 0 | |
| meta_data | 0.000 | 0.000 | 0.001 | |
| recipeHub-class | 0.034 | 0.003 | 0.037 | |
| recipeLoad | 0.337 | 0.019 | 0.360 | |
| recipeMake | 0 | 0 | 0 | |
| recipeSearch | 0.157 | 0.011 | 0.169 | |
| recipeUpdate | 0.000 | 0.000 | 0.001 | |