Qian Liu
| Snapshot Date: 2024-06-25 14:00 -0400 (Tue, 25 Jun 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 2024-06-26 11:38 -0400 (Wed, 26 Jun 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.0 RC (2024-04-16 r86468) -- "Puppy Cup" | 4691 |
| lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.1 RC (2024-06-06 r86719) -- "Race for Your Life" | 4405 |
| kjohnson3 | macOS 13.6.5 Ventura | arm64 | 4.4.1 RC (2024-06-06 r86719) -- "Race for Your Life" | 4355 |
| 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 | | ||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson3 | macOS 13.6.5 Ventura / arm64 | OK | OK | OK | OK | | ||||||||
|
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: 2024-06-25 22:31:25 -0400 (Tue, 25 Jun 2024) |
| EndedAt: 2024-06-25 22:34:03 -0400 (Tue, 25 Jun 2024) |
| EllapsedTime: 158.2 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 RC (2024-06-06 r86719)
* using platform: x86_64-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 Monterey 12.7.1
* 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 7.707 0.878 8.692
getCloudData 2.930 0.163 7.206
* 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-x86_64/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 RC (2024-06-06 r86719) -- "Race for Your Life"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-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...
b08c6a47efe7_GRCh38.primary_assembly.genome.fa.1.bt2 added
b08c18d75d34_GRCh38.primary_assembly.genome.fa.2.bt2 added
b08c63280da9_GRCh38.primary_assembly.genome.fa.3.bt2 added
b08c5a99051a_GRCh38.primary_assembly.genome.fa.4.bt2 added
b08c741e1c6d_GRCh38.primary_assembly.genome.fa.rev.1.bt2 added
b08c64dc73a9_GRCh38.primary_assembly.genome.fa.rev.2.bt2 added
b08c452d8ffa_outfile.txt added
b08c32478991_GRCh37_to_GRCh38.chain added
b08c7698a860_GRCh37_to_NCBI34.chain added
b08c20567374_GRCh37_to_NCBI35.chain added
b08cbb5d542_GRCh37_to_NCBI36.chain added
b08c4ec3e60f_GRCh38_to_GRCh37.chain added
b08c1f350b2f_GRCh38_to_NCBI34.chain added
b08c53714aaa_GRCh38_to_NCBI35.chain added
b08c32dd09b2_GRCh38_to_NCBI36.chain added
b08c4da79f34_NCBI34_to_GRCh37.chain added
b08c37c536c0_NCBI34_to_GRCh38.chain added
b08c748d93da_NCBI35_to_GRCh37.chain added
b08c7ae608fd_NCBI35_to_GRCh38.chain added
b08c14585914_NCBI36_to_GRCh37.chain added
b08c34403a7b_NCBI36_to_GRCh38.chain added
b08c64bf7c09_GRCm38_to_NCBIM36.chain added
b08c5768668b_GRCm38_to_NCBIM37.chain added
b08c7245c82_NCBIM36_to_GRCm38.chain added
b08c64355e77_NCBIM37_to_GRCm38.chain added
b08c6bcd0a06_1000G_omni2.5.b37.vcf.gz added
b08c624d4734_1000G_omni2.5.b37.vcf.gz.tbi added
b08c3f7dd957_Mills_and_1000G_gold_standard.indels.b37.vcf.gz added
b08c5f47ff51_Mills_and_1000G_gold_standard.indels.b37.vcf.gz.tbi added
b08c6fcb4fb5_1000G_omni2.5.hg38.vcf.gz added
b08ccde2d6a_1000G_omni2.5.hg38.vcf.gz.tbi added
b08c4e7790bf_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz added
b08cbc013d8_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz.tbi added
b08c6f56cfee_af-only-gnomad.raw.sites.vcf added
b08c2c6d4b5d_af-only-gnomad.raw.sites.vcf.idx added
b08c3b6edd74_Mutect2-exome-panel.vcf.idx added
b08c6b8d0927_Mutect2-WGS-panel-b37.vcf added
b08c7854169a_Mutect2-WGS-panel-b37.vcf.idx added
b08c5898162d_small_exac_common_3.vcf added
b08c68d811cb_small_exac_common_3.vcf.idx added
b08c41785c33_1000g_pon.hg38.vcf.gz added
b08c44ed39d9_1000g_pon.hg38.vcf.gz.tbi added
b08c3270f8e9_af-only-gnomad.hg38.vcf.gz added
b08c16e5a2de_af-only-gnomad.hg38.vcf.gz.tbi added
b08c3e27a890_small_exac_common_3.hg38.vcf.gz added
b08c1daba5d1_small_exac_common_3.hg38.vcf.gz.tbi added
b08c70134b8e_gencode.v41.annotation.gtf added
b08c2c5911e_gencode.v42.annotation.gtf added
b08c78ba49fd_gencode.vM30.annotation.gtf added
b08ce4fbef7_gencode.vM31.annotation.gtf added
b08c15825178_gencode.v41.transcripts.fa added
b08c1eb2a850_gencode.v41.transcripts.fa.fai added
b08c63482bee_gencode.v42.transcripts.fa added
b08c173c492e_gencode.v42.transcripts.fa.fai added
b08c76e876ec_gencode.vM30.pc_transcripts.fa added
b08c17d7bcf1_gencode.vM30.pc_transcripts.fa.fai added
b08c54b57e71_gencode.vM31.pc_transcripts.fa added
b08c57805829_gencode.vM31.pc_transcripts.fa.fai added
b08c2b1c18a0_GRCh38.primary_assembly.genome.fa.1.ht2 added
b08c4194c67c_GRCh38.primary_assembly.genome.fa.2.ht2 added
b08ce731887_GRCh38.primary_assembly.genome.fa.3.ht2 added
b08c264f4e7a_GRCh38.primary_assembly.genome.fa.4.ht2 added
b08c20a93f3c_GRCh38.primary_assembly.genome.fa.5.ht2 added
b08c47768ce4_GRCh38.primary_assembly.genome.fa.6.ht2 added
b08c381bf163_GRCh38.primary_assembly.genome.fa.7.ht2 added
b08c3284b75c_GRCh38.primary_assembly.genome.fa.8.ht2 added
b08c272212ed_GRCh38_full_analysis_set_plus_decoy_hla.fa.fai added
b08c2e0899ad_GRCh38_full_analysis_set_plus_decoy_hla.fa.amb added
b08c36a14477_GRCh38_full_analysis_set_plus_decoy_hla.fa.ann added
b08c1595fca6_GRCh38_full_analysis_set_plus_decoy_hla.fa.bwt added
b08c29fe015c_GRCh38_full_analysis_set_plus_decoy_hla.fa.pac added
b08c630b548d_GRCh38_full_analysis_set_plus_decoy_hla.fa.sa added
b08c7cdc27c7_GRCh38_full_analysis_set_plus_decoy_hla.fa added
b08c59b7b9db_GRCh38.primary_assembly.genome.fa.fai added
b08c2d0b06e1_GRCh38.primary_assembly.genome.fa.amb added
b08c2ef0b4e1_GRCh38.primary_assembly.genome.fa.ann added
b08c3cf337da_GRCh38.primary_assembly.genome.fa.bwt added
b08c3d7e879_GRCh38.primary_assembly.genome.fa.pac added
b08c53df61e7_GRCh38.primary_assembly.genome.fa.sa added
b08c6e94afb5_GRCh38.primary_assembly.genome.fa added
b08c639bccca_hs37d5.fa.fai added
b08c9a214dd_hs37d5.fa.amb added
b08c7007be1b_hs37d5.fa.ann added
b08cc521813_hs37d5.fa.bwt added
b08c61aa8db6_hs37d5.fa.pac added
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b08c37ae7748_complete_ref_lens.bin added
b08c1f193487_ctable.bin added
b08c2fc79b04_ctg_offsets.bin added
b08c59923c1d_duplicate_clusters.tsv added
b08cfa8c1dc_info.json added
b08c104f5a8c_mphf.bin added
b08c49c1a5b1_pos.bin added
b08c48652d4b_pre_indexing.log added
b08c6a80bc0e_rank.bin added
b08c29ba71c2_ref_indexing.log added
b08cf828cf5_refAccumLengths.bin added
b08c43f430c7_reflengths.bin added
b08c54ae7bab_refseq.bin added
b08cb3942fc_seq.bin added
b08c5c5cb425_versionInfo.json added
b08c4a371882_salmon_index added
b08c672a24de_chrLength.txt added
b08c7fda9fbb_chrName.txt added
b08c6a2cef90_chrNameLength.txt added
b08c2c240d65_chrStart.txt added
b08c72eb7886_exonGeTrInfo.tab added
b08c4135e05b_exonInfo.tab added
b08c381c97cf_geneInfo.tab added
b08c5d32b3d0_Genome added
b08c2bbb4c7d_genomeParameters.txt added
b08c159ab8f9_Log.out added
b08c60e5ee83_SA added
b08c178e0c28_SAindex added
b08c6ec0222c_sjdbInfo.txt added
b08c803af82_sjdbList.fromGTF.out.tab added
b08c29f783ea_sjdbList.out.tab added
b08c38f58d2c_transcriptInfo.tab added
b08c10760eb_GRCh38.GENCODE.v42_100 added
b08cb6be4d4_knownGene_hg38.sql added
b08c587c2027_knownGene_hg38.txt added
b08c3d230dd3_refGene_hg38.sql added
b08c4860b700_refGene_hg38.txt added
b08c458e861f_knownGene_mm39.sql added
b08c100780e6_knownGene_mm39.txt added
b08c5c9f8442_refGene_mm39.sql added
b08c6ca4388f_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/RtmpiNBfra/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
24.834 3.250 29.237
ReUseData.Rcheck/ReUseData-Ex.timings
| name | user | system | elapsed | |
| dataHub-class | 7.707 | 0.878 | 8.692 | |
| dataSearch | 1.443 | 0.061 | 1.514 | |
| dataUpdate | 0 | 0 | 0 | |
| getCloudData | 2.930 | 0.163 | 7.206 | |
| getData | 0.001 | 0.001 | 0.001 | |
| meta_data | 0.001 | 0.000 | 0.001 | |
| recipeHub-class | 0.166 | 0.013 | 0.181 | |
| recipeLoad | 1.689 | 0.103 | 1.805 | |
| recipeMake | 0.000 | 0.001 | 0.001 | |
| recipeSearch | 0.796 | 0.054 | 0.859 | |
| recipeUpdate | 0.000 | 0.001 | 0.001 | |