Qian Liu
| Snapshot Date: 2024-07-05 14:00 -0400 (Fri, 05 Jul 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 Multiple platform build/check report for BioC 3.20: simplified long |
|
This page was generated on 2024-07-06 11:43 -0400 (Sat, 06 Jul 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4643 |
| palomino6 | Windows Server 2022 Datacenter | x64 | 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" | 4414 |
| lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4442 |
| kjohnson3 | macOS 13.6.5 Ventura | arm64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4391 |
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 3833 |
| 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 1695/2243 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| ReUseData 1.5.0 (landing page) Qian Liu
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino6 | Windows Server 2022 Datacenter / x64 | ... NOT SUPPORTED ... | ||||||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson3 | macOS 13.6.5 Ventura / arm64 | OK | OK | OK | OK | | ||||||||
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | NA | ERROR | skipped | ||||||||||
|
To the developers/maintainers of the ReUseData package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/ReUseData.git to reflect on this report. See Troubleshooting Build Report for more information. - 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: 2024-07-06 04:27:50 -0400 (Sat, 06 Jul 2024) |
| EndedAt: 2024-07-06 04:29:04 -0400 (Sat, 06 Jul 2024) |
| EllapsedTime: 73.7 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/meat/ReUseData.Rcheck’
* using R version 4.4.1 (2024-06-14)
* 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 ‘1.5.0’
* 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
* 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/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 4.4.1 (2024-06-14) -- "Race for Your Life"
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...
33ad6b8e1728_GRCh38.primary_assembly.genome.fa.1.bt2 added
33ad3d927a42_GRCh38.primary_assembly.genome.fa.2.bt2 added
33ad5b98a2a2_GRCh38.primary_assembly.genome.fa.3.bt2 added
33ad1dd68a9_GRCh38.primary_assembly.genome.fa.4.bt2 added
33ad6f023033_GRCh38.primary_assembly.genome.fa.rev.1.bt2 added
33ad78aa9d34_GRCh38.primary_assembly.genome.fa.rev.2.bt2 added
33ad936fed0_outfile.txt added
33ad79930e69_GRCh37_to_GRCh38.chain added
33ad25974dda_GRCh37_to_NCBI34.chain added
33ad7078367d_GRCh37_to_NCBI35.chain added
33ad6441823a_GRCh37_to_NCBI36.chain added
33ad8cce142_GRCh38_to_GRCh37.chain added
33ad42d8b891_GRCh38_to_NCBI34.chain added
33ad223d59e0_GRCh38_to_NCBI35.chain added
33ad69d792af_GRCh38_to_NCBI36.chain added
33ad47df5572_NCBI34_to_GRCh37.chain added
33ad1762d43b_NCBI34_to_GRCh38.chain added
33ad595b797b_NCBI35_to_GRCh37.chain added
33ad484a812_NCBI35_to_GRCh38.chain added
33ad2136380f_NCBI36_to_GRCh37.chain added
33ad6e9a71d1_NCBI36_to_GRCh38.chain added
33ad5da68911_GRCm38_to_NCBIM36.chain added
33ad6070eb1f_GRCm38_to_NCBIM37.chain added
33ad155c71b0_NCBIM36_to_GRCm38.chain added
33ad682be4c4_NCBIM37_to_GRCm38.chain added
33ad19b8354a_1000G_omni2.5.b37.vcf.gz added
33adcb29a77_1000G_omni2.5.b37.vcf.gz.tbi added
33ad21bb0124_Mills_and_1000G_gold_standard.indels.b37.vcf.gz added
33ad7c47f3c8_Mills_and_1000G_gold_standard.indels.b37.vcf.gz.tbi added
33ad57d60f36_1000G_omni2.5.hg38.vcf.gz added
33ad2680cf47_1000G_omni2.5.hg38.vcf.gz.tbi added
33ad52a85210_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz added
33ad28a3c2d5_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz.tbi added
33ad174c42cb_af-only-gnomad.raw.sites.vcf added
33adfb52960_af-only-gnomad.raw.sites.vcf.idx added
33ad3eaf65ae_Mutect2-exome-panel.vcf.idx added
33ad6d3ca2a8_Mutect2-WGS-panel-b37.vcf added
33ad27dafb9f_Mutect2-WGS-panel-b37.vcf.idx added
33ad19bd982a_small_exac_common_3.vcf added
33ad6e50fa99_small_exac_common_3.vcf.idx added
33ad6748b64_1000g_pon.hg38.vcf.gz added
33ad4d6b558b_1000g_pon.hg38.vcf.gz.tbi added
33ad41bd4062_af-only-gnomad.hg38.vcf.gz added
33ad6fce03a5_af-only-gnomad.hg38.vcf.gz.tbi added
33ad3e517efb_small_exac_common_3.hg38.vcf.gz added
33ad5867b0b3_small_exac_common_3.hg38.vcf.gz.tbi added
33ad7f81e51c_gencode.v41.annotation.gtf added
33ad28e8d2aa_gencode.v42.annotation.gtf added
33ad4d5eabe1_gencode.vM30.annotation.gtf added
33ad2666876_gencode.vM31.annotation.gtf added
33ad11541c35_gencode.v41.transcripts.fa added
33ad2907e476_gencode.v41.transcripts.fa.fai added
33ad45281405_gencode.v42.transcripts.fa added
33ad4a3a77bb_gencode.v42.transcripts.fa.fai added
33ad448abc0f_gencode.vM30.pc_transcripts.fa added
33ad70409ff0_gencode.vM30.pc_transcripts.fa.fai added
33ad22c47f23_gencode.vM31.pc_transcripts.fa added
33ad1276e4aa_gencode.vM31.pc_transcripts.fa.fai added
33ad3b9e5e5e_GRCh38.primary_assembly.genome.fa.1.ht2 added
33ad1a458be6_GRCh38.primary_assembly.genome.fa.2.ht2 added
33ad4be3b683_GRCh38.primary_assembly.genome.fa.3.ht2 added
33ad52e37961_GRCh38.primary_assembly.genome.fa.4.ht2 added
33ad5435f9ca_GRCh38.primary_assembly.genome.fa.5.ht2 added
33ad23a267f7_GRCh38.primary_assembly.genome.fa.6.ht2 added
33ad7b579b67_GRCh38.primary_assembly.genome.fa.7.ht2 added
33ad349bc674_GRCh38.primary_assembly.genome.fa.8.ht2 added
33ad5f0204a7_GRCh38_full_analysis_set_plus_decoy_hla.fa.fai added
33ad7d7fa0ab_GRCh38_full_analysis_set_plus_decoy_hla.fa.amb added
33ad460d7aeb_GRCh38_full_analysis_set_plus_decoy_hla.fa.ann added
33ad1f00fe3b_GRCh38_full_analysis_set_plus_decoy_hla.fa.bwt added
33ad7a32e363_GRCh38_full_analysis_set_plus_decoy_hla.fa.pac added
33ad22eeb742_GRCh38_full_analysis_set_plus_decoy_hla.fa.sa added
33ad66415ff8_GRCh38_full_analysis_set_plus_decoy_hla.fa added
33ad4e03c73a_GRCh38.primary_assembly.genome.fa.fai added
33ad5a0cd8d9_GRCh38.primary_assembly.genome.fa.amb added
33ad170bcbf_GRCh38.primary_assembly.genome.fa.ann added
33ad1077a056_GRCh38.primary_assembly.genome.fa.bwt added
33ad1dbf768c_GRCh38.primary_assembly.genome.fa.pac added
33ad4fff096_GRCh38.primary_assembly.genome.fa.sa added
33ad3f0c0a6a_GRCh38.primary_assembly.genome.fa added
33ad2f7fd57c_hs37d5.fa.fai added
33ad7198d840_hs37d5.fa.amb added
33ad699d8c03_hs37d5.fa.ann added
33ad66534f20_hs37d5.fa.bwt added
33ad676ff25b_hs37d5.fa.pac added
33ad6690696a_hs37d5.fa.sa added
33ad12f8e2c1_hs37d5.fa added
33ad11eef6a2_complete_ref_lens.bin added
33ad5f820ee0_ctable.bin added
33ad539ec51c_ctg_offsets.bin added
33ad5c9edc27_duplicate_clusters.tsv added
33ad4187b3f2_info.json added
33ad3436f67a_mphf.bin added
33ad46fde5e_pos.bin added
33ad4c6fef98_pre_indexing.log added
33ad48db0b5c_rank.bin added
33ad24c6ea62_ref_indexing.log added
33ad7f45daca_refAccumLengths.bin added
33ad431f450d_reflengths.bin added
33ad39ee7ae8_refseq.bin added
33ad57c7330e_seq.bin added
33ad56e90927_versionInfo.json added
33ad5d580c04_salmon_index added
33ad3f7d0a7c_chrLength.txt added
33ad2a3b7374_chrName.txt added
33ad2518da55_chrNameLength.txt added
33ad2a6157a_chrStart.txt added
33ad65cbfdf1_exonGeTrInfo.tab added
33ad338d0d6d_exonInfo.tab added
33ad716c898b_geneInfo.tab added
33adcba3eda_Genome added
33ad177460bd_genomeParameters.txt added
33ad597b2452_Log.out added
33ad238db163_SA added
33ad2b78ecd1_SAindex added
33ad1003a3a3_sjdbInfo.txt added
33ad5eec2a8b_sjdbList.fromGTF.out.tab added
33ad62dd3c5c_sjdbList.out.tab added
33ad2aa5eeb9_transcriptInfo.tab added
33ad73dbc98e_GRCh38.GENCODE.v42_100 added
33ad628dc50e_knownGene_hg38.sql added
33ad49844cae_knownGene_hg38.txt added
33adcc65937_refGene_hg38.sql added
33ad320b306e_refGene_hg38.txt added
33ad7c989f6c_knownGene_mm39.sql added
33ad80aab5c_knownGene_mm39.txt added
33ad74782923_refGene_mm39.sql added
33ad7cd4f491_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//RtmpeBgykg/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
9.272 1.327 12.713
ReUseData.Rcheck/ReUseData-Ex.timings
| name | user | system | elapsed | |
| dataHub-class | 2.432 | 0.265 | 3.465 | |
| dataSearch | 0.455 | 0.020 | 0.677 | |
| dataUpdate | 0 | 0 | 0 | |
| getCloudData | 1.072 | 0.062 | 2.145 | |
| getData | 0 | 0 | 0 | |
| meta_data | 0.001 | 0.000 | 0.000 | |
| recipeHub-class | 0.050 | 0.007 | 0.093 | |
| recipeLoad | 0.535 | 0.037 | 0.798 | |
| recipeMake | 0.000 | 0.000 | 0.001 | |
| recipeSearch | 0.243 | 0.016 | 0.362 | |
| recipeUpdate | 0.000 | 0.001 | 0.000 | |