Qian Liu
| Snapshot Date: 2023-10-15 14:00:07 -0400 (Sun, 15 Oct 2023) |
| git_url: https://git.bioconductor.org/packages/ReUseData |
| git_branch: RELEASE_3_17 |
| git_last_commit: d07a228 |
| git_last_commit_date: 2023-07-28 12:18:11 -0400 (Fri, 28 Jul 2023) |
| Back to Mac ARM64 build report for BioC 3.17 |
|
This page was generated on 2023-10-20 09:38:10 -0400 (Fri, 20 Oct 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| kjohnson2 | macOS 12.6.1 Monterey | arm64 | 4.3.1 (2023-06-16) -- "Beagle Scouts" | 4347 |
| 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 1693/2230 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| ReUseData 1.0.1 (landing page) Qian Liu
| kjohnson2 | macOS 12.6.1 Monterey / 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: 1.0.1 |
| 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_1.0.1.tar.gz |
| StartedAt: 2023-10-18 18:33:13 -0400 (Wed, 18 Oct 2023) |
| EndedAt: 2023-10-18 18:38:07 -0400 (Wed, 18 Oct 2023) |
| EllapsedTime: 294.6 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_1.0.1.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/ReUseData.Rcheck’
* using R version 4.3.1 (2023-06-16)
* 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 Monterey 12.6.7
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘ReUseData/DESCRIPTION’ ... OK
* this is package ‘ReUseData’ version ‘1.0.1’
* 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
dataUpdate 16.108 2.485 30.265
getCloudData 10.854 0.949 25.577
dataHub-class 9.925 0.976 15.472
getData 4.368 0.590 6.656
recipeMake 4.163 0.575 6.306
* 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-3.17-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 4.3.1 (2023-06-16) -- "Beagle Scouts"
Copyright (C) 2023 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...
5d8a24efb540_GRCh38.primary_assembly.genome.fa.1.bt2 added
5d8a75648fb1_GRCh38.primary_assembly.genome.fa.2.bt2 added
5d8a1d15e9ad_GRCh38.primary_assembly.genome.fa.3.bt2 added
5d8a9a06bc6_GRCh38.primary_assembly.genome.fa.4.bt2 added
5d8a303991a_GRCh38.primary_assembly.genome.fa.rev.1.bt2 added
5d8a61387b81_GRCh38.primary_assembly.genome.fa.rev.2.bt2 added
5d8a43348404_outfile.txt added
5d8a2cc74514_GRCh37_to_GRCh38.chain added
5d8a4e883b03_GRCh37_to_NCBI34.chain added
5d8a51da6a3c_GRCh37_to_NCBI35.chain added
5d8a5a74b31f_GRCh37_to_NCBI36.chain added
5d8a239be69e_GRCh38_to_GRCh37.chain added
5d8a5041a155_GRCh38_to_NCBI34.chain added
5d8a4c6fc9d_GRCh38_to_NCBI35.chain added
5d8a23f2a9de_GRCh38_to_NCBI36.chain added
5d8a106e4042_NCBI34_to_GRCh37.chain added
5d8a363cb57b_NCBI34_to_GRCh38.chain added
5d8a4baeba0e_NCBI35_to_GRCh37.chain added
5d8a3c3913f3_NCBI35_to_GRCh38.chain added
5d8a474cd568_NCBI36_to_GRCh37.chain added
5d8a54ec36a_NCBI36_to_GRCh38.chain added
5d8a75ff66de_GRCm38_to_NCBIM36.chain added
5d8a52bab557_GRCm38_to_NCBIM37.chain added
5d8a5fd78d2f_NCBIM36_to_GRCm38.chain added
5d8a407639d1_NCBIM37_to_GRCm38.chain added
5d8a11cde967_1000G_omni2.5.b37.vcf.gz added
5d8a65967252_1000G_omni2.5.b37.vcf.gz.tbi added
5d8a782b9998_Mills_and_1000G_gold_standard.indels.b37.vcf.gz added
5d8a767107ca_Mills_and_1000G_gold_standard.indels.b37.vcf.gz.tbi added
5d8a76b69b85_1000G_omni2.5.hg38.vcf.gz added
5d8a4e9c75a6_1000G_omni2.5.hg38.vcf.gz.tbi added
5d8a1f00d9c_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz added
5d8a370d7dc2_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz.tbi added
5d8a56bb67ca_af-only-gnomad.raw.sites.vcf added
5d8a299b2b42_af-only-gnomad.raw.sites.vcf.idx added
5d8aa350f65_Mutect2-exome-panel.vcf.idx added
5d8a2185b51f_Mutect2-WGS-panel-b37.vcf added
5d8a5136176a_Mutect2-WGS-panel-b37.vcf.idx added
5d8a363b59cd_small_exac_common_3.vcf added
5d8a7284bd8b_small_exac_common_3.vcf.idx added
5d8a68b82b69_1000g_pon.hg38.vcf.gz added
5d8a132a3035_1000g_pon.hg38.vcf.gz.tbi added
5d8a36c2f167_af-only-gnomad.hg38.vcf.gz added
5d8a3876bd47_af-only-gnomad.hg38.vcf.gz.tbi added
5d8a7b849d46_small_exac_common_3.hg38.vcf.gz added
5d8a3f719e04_small_exac_common_3.hg38.vcf.gz.tbi added
5d8a3c3d3926_gencode.v41.annotation.gtf added
5d8a57730caf_gencode.v42.annotation.gtf added
5d8a4245e203_gencode.vM30.annotation.gtf added
5d8a79f954f2_gencode.vM31.annotation.gtf added
5d8a60381a6d_gencode.v41.transcripts.fa added
5d8a34f1b75_gencode.v41.transcripts.fa.fai added
5d8a3e93a005_gencode.v42.transcripts.fa added
5d8a4deec85b_gencode.v42.transcripts.fa.fai added
5d8a77a3f655_gencode.vM30.pc_transcripts.fa added
5d8a2d8183d0_gencode.vM30.pc_transcripts.fa.fai added
5d8a11f4e407_gencode.vM31.pc_transcripts.fa added
5d8a64a690c6_gencode.vM31.pc_transcripts.fa.fai added
5d8a736aeac9_GRCh38.primary_assembly.genome.fa.1.ht2 added
5d8a705c6d51_GRCh38.primary_assembly.genome.fa.2.ht2 added
5d8a440d1a78_GRCh38.primary_assembly.genome.fa.3.ht2 added
5d8a3844df2f_GRCh38.primary_assembly.genome.fa.4.ht2 added
5d8a3198a385_GRCh38.primary_assembly.genome.fa.5.ht2 added
5d8a1c178a33_GRCh38.primary_assembly.genome.fa.6.ht2 added
5d8a4d7228ad_GRCh38.primary_assembly.genome.fa.7.ht2 added
5d8a1cc9d94_GRCh38.primary_assembly.genome.fa.8.ht2 added
5d8a207d6078_GRCh38_full_analysis_set_plus_decoy_hla.fa.fai added
5d8a74876f2_GRCh38_full_analysis_set_plus_decoy_hla.fa.amb added
5d8a26790d9a_GRCh38_full_analysis_set_plus_decoy_hla.fa.ann added
5d8a556c0d31_GRCh38_full_analysis_set_plus_decoy_hla.fa.bwt added
5d8a28d637c7_GRCh38_full_analysis_set_plus_decoy_hla.fa.pac added
5d8a7e7fec3_GRCh38_full_analysis_set_plus_decoy_hla.fa.sa added
5d8a1006b843_GRCh38_full_analysis_set_plus_decoy_hla.fa added
5d8a292b3eed_GRCh38.primary_assembly.genome.fa.fai added
5d8a56304eb8_GRCh38.primary_assembly.genome.fa.amb added
5d8a7d803e3c_GRCh38.primary_assembly.genome.fa.ann added
5d8a6e761582_GRCh38.primary_assembly.genome.fa.bwt added
5d8aa7e4276_GRCh38.primary_assembly.genome.fa.pac added
5d8a673d565b_GRCh38.primary_assembly.genome.fa.sa added
5d8a6bf0a550_GRCh38.primary_assembly.genome.fa added
5d8a3f55e8d_hs37d5.fa.fai added
5d8a62127d02_hs37d5.fa.amb added
5d8a2bcd409b_hs37d5.fa.ann added
5d8a304c9694_hs37d5.fa.bwt added
5d8a7431e751_hs37d5.fa.pac added
5d8a7849b26f_hs37d5.fa.sa added
5d8a2e61d31b_hs37d5.fa added
5d8a186aa967_complete_ref_lens.bin added
5d8a297b5b7_ctable.bin added
5d8a361b02b5_ctg_offsets.bin added
5d8a274ed4d3_duplicate_clusters.tsv added
5d8a28767cce_info.json added
5d8a7afbcd22_mphf.bin added
5d8a2958b242_pos.bin added
5d8a7e1f2042_pre_indexing.log added
5d8a2d7f0dbe_rank.bin added
5d8a705f4c47_ref_indexing.log added
5d8a8902f4_refAccumLengths.bin added
5d8a2320e172_reflengths.bin added
5d8a43b11562_refseq.bin added
5d8a1ef2f7a6_seq.bin added
5d8a6160c329_versionInfo.json added
5d8a17aceab1_salmon_index added
5d8a5964169b_chrLength.txt added
5d8a3a0847f6_chrName.txt added
5d8a75ac853d_chrNameLength.txt added
5d8a115fa426_chrStart.txt added
5d8a1e11c3b3_exonGeTrInfo.tab added
5d8a20472c31_exonInfo.tab added
5d8a20a65585_geneInfo.tab added
5d8a8389f82_Genome added
5d8a3d701405_genomeParameters.txt added
5d8a93273c6_Log.out added
5d8a4f4ed0e1_SA added
5d8a3f738c74_SAindex added
5d8a3b0a3437_sjdbInfo.txt added
5d8a1aea2529_sjdbList.fromGTF.out.tab added
5d8a22db48d_sjdbList.out.tab added
5d8a6a89619_transcriptInfo.tab added
5d8a261646b9_GRCh38.GENCODE.v42_100 added
5d8a7d2f38_knownGene_hg38.sql added
5d8a1aa705c8_knownGene_hg38.txt added
5d8a4b6c9b23_refGene_hg38.sql added
5d8a473d3d84_refGene_hg38.txt added
5d8a591c9a6_knownGene_mm39.sql added
5d8a264db425_knownGene_mm39.txt added
5d8a376dfcc8_refGene_mm39.sql added
5d8a15eecae6_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/RtmptaUDLf/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 ]
>
> proc.time()
user system elapsed
30.606 3.455 46.940
ReUseData.Rcheck/ReUseData-Ex.timings
| name | user | system | elapsed | |
| dataHub-class | 9.925 | 0.976 | 15.472 | |
| dataSearch | 1.348 | 0.063 | 2.145 | |
| dataUpdate | 16.108 | 2.485 | 30.265 | |
| getCloudData | 10.854 | 0.949 | 25.577 | |
| getData | 4.368 | 0.590 | 6.656 | |
| meta_data | 0.012 | 0.001 | 0.017 | |
| recipeHub-class | 0.253 | 0.018 | 0.350 | |
| recipeLoad | 1.580 | 0.093 | 2.237 | |
| recipeMake | 4.163 | 0.575 | 6.306 | |
| recipeSearch | 0.717 | 0.047 | 1.005 | |
| recipeUpdate | 0.003 | 0.001 | 0.003 | |