Qian Liu
| Snapshot Date: 2024-11-26 13:40 -0500 (Tue, 26 Nov 2024) |
| git_url: https://git.bioconductor.org/packages/ReUseData |
| git_branch: devel |
| git_last_commit: 85fc756 |
| git_last_commit_date: 2024-10-29 11:17:22 -0500 (Tue, 29 Oct 2024) |
| Back to Multiple platform build/check report for BioC 3.21: simplified long |
|
This page was generated on 2024-11-27 11:44 -0500 (Wed, 27 Nov 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | R Under development (unstable) (2024-10-21 r87258) -- "Unsuffered Consequences" | 4748 |
| palomino7 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2024-10-26 r87273 ucrt) -- "Unsuffered Consequences" | 4459 |
| lconway | macOS 12.7.1 Monterey | x86_64 | R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" | 4396 |
| kjohnson3 | macOS 13.7.1 Ventura | arm64 | R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" | 4110 |
| 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 1712/2272 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| ReUseData 1.7.0 (landing page) Qian Liu
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino7 | Windows Server 2022 Datacenter / x64 | ... NOT SUPPORTED ... | ||||||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson3 | macOS 13.7.1 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: 1.7.0 |
| 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_1.7.0.tar.gz |
| StartedAt: 2024-11-27 03:44:26 -0500 (Wed, 27 Nov 2024) |
| EndedAt: 2024-11-27 03:48:52 -0500 (Wed, 27 Nov 2024) |
| EllapsedTime: 266.7 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_1.7.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/ReUseData.Rcheck’
* using R Under development (unstable) (2024-11-20 r87352)
* 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 13.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘ReUseData/DESCRIPTION’ ... OK
* this is package ‘ReUseData’ version ‘1.7.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
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-3.21-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/4.5-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 Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences"
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...
32e9228927f6_GRCh38.primary_assembly.genome.fa.1.bt2 added
32e95a9e9930_GRCh38.primary_assembly.genome.fa.2.bt2 added
32e9625b4cca_GRCh38.primary_assembly.genome.fa.3.bt2 added
32e9580e9438_GRCh38.primary_assembly.genome.fa.4.bt2 added
32e9252515b2_GRCh38.primary_assembly.genome.fa.rev.1.bt2 added
32e925b36c2b_GRCh38.primary_assembly.genome.fa.rev.2.bt2 added
32e926828e63_outfile.txt added
32e945521955_GRCh37_to_GRCh38.chain added
32e910fd3f01_GRCh37_to_NCBI34.chain added
32e96233635d_GRCh37_to_NCBI35.chain added
32e91bc0a109_GRCh37_to_NCBI36.chain added
32e938c641b_GRCh38_to_GRCh37.chain added
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32e9107152a6_NCBI34_to_GRCh37.chain added
32e97fe918b8_NCBI34_to_GRCh38.chain added
32e9205619a3_NCBI35_to_GRCh37.chain added
32e974ad2cea_NCBI35_to_GRCh38.chain added
32e9155ff27e_NCBI36_to_GRCh37.chain added
32e94e293928_NCBI36_to_GRCh38.chain added
32e97467992e_GRCm38_to_NCBIM36.chain added
32e93d79d6b6_GRCm38_to_NCBIM37.chain added
32e99ff6642_NCBIM36_to_GRCm38.chain added
32e95e927c2e_NCBIM37_to_GRCm38.chain added
32e96316e083_1000G_omni2.5.b37.vcf.gz added
32e972edeb47_1000G_omni2.5.b37.vcf.gz.tbi added
32e961f1bd43_Mills_and_1000G_gold_standard.indels.b37.vcf.gz added
32e945c0abf1_Mills_and_1000G_gold_standard.indels.b37.vcf.gz.tbi added
32e96c587efd_1000G_omni2.5.hg38.vcf.gz added
32e925f94b9d_1000G_omni2.5.hg38.vcf.gz.tbi added
32e911d343e5_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz added
32e9450e7887_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz.tbi added
32e9390b0a7c_af-only-gnomad.raw.sites.vcf added
32e93dd7026_af-only-gnomad.raw.sites.vcf.idx added
32e93eedd0c5_Mutect2-exome-panel.vcf.idx added
32e96f2555c9_Mutect2-WGS-panel-b37.vcf added
32e97c233820_Mutect2-WGS-panel-b37.vcf.idx added
32e96c39fc8b_small_exac_common_3.vcf added
32e952f3412f_small_exac_common_3.vcf.idx added
32e9603c9f34_1000g_pon.hg38.vcf.gz added
32e92bf84048_1000g_pon.hg38.vcf.gz.tbi added
32e937444d85_af-only-gnomad.hg38.vcf.gz added
32e9653d731b_af-only-gnomad.hg38.vcf.gz.tbi added
32e92550258a_small_exac_common_3.hg38.vcf.gz added
32e930d09a29_small_exac_common_3.hg38.vcf.gz.tbi added
32e94f3912c8_gencode.v41.annotation.gtf added
32e92c00311a_gencode.v42.annotation.gtf added
32e94097b887_gencode.vM30.annotation.gtf added
32e928d3c832_gencode.vM31.annotation.gtf added
32e967fc5f8e_gencode.v41.transcripts.fa added
32e969e598f7_gencode.v41.transcripts.fa.fai added
32e9609db671_gencode.v42.transcripts.fa added
32e91234e645_gencode.v42.transcripts.fa.fai added
32e94ef9c559_gencode.vM30.pc_transcripts.fa added
32e9700b7e90_gencode.vM30.pc_transcripts.fa.fai added
32e92a25968_gencode.vM31.pc_transcripts.fa added
32e9709bbc31_gencode.vM31.pc_transcripts.fa.fai added
32e9606eb9_GRCh38.primary_assembly.genome.fa.1.ht2 added
32e93b0533e0_GRCh38.primary_assembly.genome.fa.2.ht2 added
32e95290d565_GRCh38.primary_assembly.genome.fa.3.ht2 added
32e922aa043c_GRCh38.primary_assembly.genome.fa.4.ht2 added
32e947fc10eb_GRCh38.primary_assembly.genome.fa.5.ht2 added
32e975bad938_GRCh38.primary_assembly.genome.fa.6.ht2 added
32e93e0b27ea_GRCh38.primary_assembly.genome.fa.7.ht2 added
32e94e699378_GRCh38.primary_assembly.genome.fa.8.ht2 added
32e97550d37f_GRCh38_full_analysis_set_plus_decoy_hla.fa.fai added
32e9d6d7305_GRCh38_full_analysis_set_plus_decoy_hla.fa.amb added
32e9c9a5426_GRCh38_full_analysis_set_plus_decoy_hla.fa.ann added
32e9680a9140_GRCh38_full_analysis_set_plus_decoy_hla.fa.bwt added
32e9dc6361d_GRCh38_full_analysis_set_plus_decoy_hla.fa.pac added
32e9500ab0fb_GRCh38_full_analysis_set_plus_decoy_hla.fa.sa added
32e96de957ca_GRCh38_full_analysis_set_plus_decoy_hla.fa added
32e97282c725_GRCh38.primary_assembly.genome.fa.fai added
32e967e088de_GRCh38.primary_assembly.genome.fa.amb added
32e94639dc19_GRCh38.primary_assembly.genome.fa.ann added
32e9a11154_GRCh38.primary_assembly.genome.fa.bwt added
32e94e78a21e_GRCh38.primary_assembly.genome.fa.pac added
32e951db87d1_GRCh38.primary_assembly.genome.fa.sa added
32e923b1d453_GRCh38.primary_assembly.genome.fa added
32e96feaa773_hs37d5.fa.fai added
32e91697a86c_hs37d5.fa.amb added
32e93eb2560a_hs37d5.fa.ann added
32e92e2ecaae_hs37d5.fa.bwt added
32e91fc7d32_hs37d5.fa.pac added
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32e91361eef1_complete_ref_lens.bin added
32e928e1a28_ctable.bin added
32e93f573967_ctg_offsets.bin added
32e97779b9ad_duplicate_clusters.tsv added
32e9588d4a22_info.json added
32e923fe2b99_mphf.bin added
32e93e05c45_pos.bin added
32e97ec9b7ff_pre_indexing.log added
32e96d4f0760_rank.bin added
32e95f6d67b0_ref_indexing.log added
32e97b284c2_refAccumLengths.bin added
32e95929e080_reflengths.bin added
32e94c52213b_refseq.bin added
32e92403cfa2_seq.bin added
32e97634a726_versionInfo.json added
32e97ac9ec6a_salmon_index added
32e95ec06220_chrLength.txt added
32e9286a5379_chrName.txt added
32e95c8e41a9_chrNameLength.txt added
32e97f78edb7_chrStart.txt added
32e95c3ecac2_exonGeTrInfo.tab added
32e91e71b5de_exonInfo.tab added
32e93b5b116f_geneInfo.tab added
32e957d5acda_Genome added
32e9d474943_genomeParameters.txt added
32e9431ad484_Log.out added
32e916764887_SA added
32e92f93a296_SAindex added
32e95973e41_sjdbInfo.txt added
32e9c782045_sjdbList.fromGTF.out.tab added
32e9228e9868_sjdbList.out.tab added
32e93fb7e591_transcriptInfo.tab added
32e94240b345_GRCh38.GENCODE.v42_100 added
32e925b998fe_knownGene_hg38.sql added
32e93beb5f0b_knownGene_hg38.txt added
32e959ace9e8_refGene_hg38.sql added
32e96730ac56_refGene_hg38.txt added
32e92c827707_knownGene_mm39.sql added
32e929548365_knownGene_mm39.txt added
32e96b7e7115_refGene_mm39.sql added
32e93a3250d5_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//RtmpLakf6d/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
5.849 0.640 6.864
ReUseData.Rcheck/ReUseData-Ex.timings
| name | user | system | elapsed | |
| dataHub-class | 1.582 | 0.170 | 1.755 | |
| dataSearch | 0.273 | 0.011 | 0.284 | |
| dataUpdate | 0 | 0 | 0 | |
| getCloudData | 0.692 | 0.037 | 1.727 | |
| getData | 0 | 0 | 0 | |
| meta_data | 0 | 0 | 0 | |
| recipeHub-class | 0.031 | 0.004 | 0.035 | |
| recipeLoad | 0.329 | 0.020 | 0.350 | |
| recipeMake | 0 | 0 | 0 | |
| recipeSearch | 0.131 | 0.007 | 0.139 | |
| recipeUpdate | 0 | 0 | 0 | |