Qian Liu
| Snapshot Date: 2024-06-09 14:00 -0400 (Sun, 09 Jun 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 Multiple platform build/check report for BioC 3.19: simplified long |
|
This page was generated on 2024-06-11 14:42 -0400 (Tue, 11 Jun 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4757 |
| palomino3 | Windows Server 2022 Datacenter | x64 | 4.4.0 (2024-04-24 ucrt) -- "Puppy Cup" | 4491 |
| lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4522 |
| kjohnson3 | macOS 13.6.5 Ventura | arm64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4468 |
| 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
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino3 | 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 | | ||||||||
|
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: 1.4.0 |
| 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: 2024-06-09 22:33:26 -0400 (Sun, 09 Jun 2024) |
| EndedAt: 2024-06-09 22:35:57 -0400 (Sun, 09 Jun 2024) |
| EllapsedTime: 151.6 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_1.4.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.19-bioc/meat/ReUseData.Rcheck’
* using R version 4.4.0 (2024-04-24)
* 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 ‘1.4.0’
* 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
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
dataHub-class 7.742 0.849 8.66
* 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/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 4.4.0 (2024-04-24) -- "Puppy Cup"
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...
ac8b42fc9942_GRCh38.primary_assembly.genome.fa.1.bt2 added
ac8b55b1de69_GRCh38.primary_assembly.genome.fa.2.bt2 added
ac8b1080eb73_GRCh38.primary_assembly.genome.fa.3.bt2 added
ac8b7fe1d37b_GRCh38.primary_assembly.genome.fa.4.bt2 added
ac8b430371d4_GRCh38.primary_assembly.genome.fa.rev.1.bt2 added
ac8b172637ab_GRCh38.primary_assembly.genome.fa.rev.2.bt2 added
ac8b4e10c76c_outfile.txt added
ac8b2f94ab7e_GRCh37_to_GRCh38.chain added
ac8b4986f599_GRCh37_to_NCBI34.chain added
ac8b3b663585_GRCh37_to_NCBI35.chain added
ac8b3343cd3a_GRCh37_to_NCBI36.chain added
ac8b2856b521_GRCh38_to_GRCh37.chain added
ac8b548d9e37_GRCh38_to_NCBI34.chain added
ac8b1d8e583f_GRCh38_to_NCBI35.chain added
ac8b6c439f41_GRCh38_to_NCBI36.chain added
ac8b4b8c9bee_NCBI34_to_GRCh37.chain added
ac8b7c514d01_NCBI34_to_GRCh38.chain added
ac8b3d96bc6a_NCBI35_to_GRCh37.chain added
ac8b732bf2bc_NCBI35_to_GRCh38.chain added
ac8b4a4d4fb6_NCBI36_to_GRCh37.chain added
ac8b19ac5bd6_NCBI36_to_GRCh38.chain added
ac8b2c14bc5_GRCm38_to_NCBIM36.chain added
ac8b605573ec_GRCm38_to_NCBIM37.chain added
ac8ba2dbc5d_NCBIM36_to_GRCm38.chain added
ac8b40a982e3_NCBIM37_to_GRCm38.chain added
ac8b38d0263f_1000G_omni2.5.b37.vcf.gz added
ac8b697f0f3c_1000G_omni2.5.b37.vcf.gz.tbi added
ac8b14c16240_Mills_and_1000G_gold_standard.indels.b37.vcf.gz added
ac8b24196265_Mills_and_1000G_gold_standard.indels.b37.vcf.gz.tbi added
ac8b7e8ae766_1000G_omni2.5.hg38.vcf.gz added
ac8b515e1a71_1000G_omni2.5.hg38.vcf.gz.tbi added
ac8b791a1a72_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz added
ac8b20be707b_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz.tbi added
ac8b36caac08_af-only-gnomad.raw.sites.vcf added
ac8b33e45d52_af-only-gnomad.raw.sites.vcf.idx added
ac8b55aacd1b_Mutect2-exome-panel.vcf.idx added
ac8b407fd38d_Mutect2-WGS-panel-b37.vcf added
ac8b819ef10_Mutect2-WGS-panel-b37.vcf.idx added
ac8b5e9e0797_small_exac_common_3.vcf added
ac8b59047b08_small_exac_common_3.vcf.idx added
ac8b352977e0_1000g_pon.hg38.vcf.gz added
ac8b357d2e64_1000g_pon.hg38.vcf.gz.tbi added
ac8b2d70c2ab_af-only-gnomad.hg38.vcf.gz added
ac8b45fc7fdb_af-only-gnomad.hg38.vcf.gz.tbi added
ac8b442e26c2_small_exac_common_3.hg38.vcf.gz added
ac8b31f2ad86_small_exac_common_3.hg38.vcf.gz.tbi added
ac8b335e5208_gencode.v41.annotation.gtf added
ac8b755ba590_gencode.v42.annotation.gtf added
ac8b53d2cd21_gencode.vM30.annotation.gtf added
ac8b34995c85_gencode.vM31.annotation.gtf added
ac8b40893abd_gencode.v41.transcripts.fa added
ac8b716f6f64_gencode.v41.transcripts.fa.fai added
ac8b4afa486a_gencode.v42.transcripts.fa added
ac8b75a84d9a_gencode.v42.transcripts.fa.fai added
ac8b7c7ef5ce_gencode.vM30.pc_transcripts.fa added
ac8b733be73c_gencode.vM30.pc_transcripts.fa.fai added
ac8b61ca4f3e_gencode.vM31.pc_transcripts.fa added
ac8b2918a19a_gencode.vM31.pc_transcripts.fa.fai added
ac8b10199a8a_GRCh38.primary_assembly.genome.fa.1.ht2 added
ac8bf0e248_GRCh38.primary_assembly.genome.fa.2.ht2 added
ac8b4697e573_GRCh38.primary_assembly.genome.fa.3.ht2 added
ac8b1e59053a_GRCh38.primary_assembly.genome.fa.4.ht2 added
ac8b66663266_GRCh38.primary_assembly.genome.fa.5.ht2 added
ac8b3f76fb0f_GRCh38.primary_assembly.genome.fa.6.ht2 added
ac8b1c5cb656_GRCh38.primary_assembly.genome.fa.7.ht2 added
ac8bac6d6a6_GRCh38.primary_assembly.genome.fa.8.ht2 added
ac8b43631d1_GRCh38_full_analysis_set_plus_decoy_hla.fa.fai added
ac8b2009280_GRCh38_full_analysis_set_plus_decoy_hla.fa.amb added
ac8b73921286_GRCh38_full_analysis_set_plus_decoy_hla.fa.ann added
ac8b7afe56b0_GRCh38_full_analysis_set_plus_decoy_hla.fa.bwt added
ac8b4fed7be5_GRCh38_full_analysis_set_plus_decoy_hla.fa.pac added
ac8b70612061_GRCh38_full_analysis_set_plus_decoy_hla.fa.sa added
ac8b7894f9ea_GRCh38_full_analysis_set_plus_decoy_hla.fa added
ac8b7ca3af7e_GRCh38.primary_assembly.genome.fa.fai added
ac8b5e56b91f_GRCh38.primary_assembly.genome.fa.amb added
ac8bf93d29c_GRCh38.primary_assembly.genome.fa.ann added
ac8b31e807c1_GRCh38.primary_assembly.genome.fa.bwt added
ac8b7855297f_GRCh38.primary_assembly.genome.fa.pac added
ac8b1f178e91_GRCh38.primary_assembly.genome.fa.sa added
ac8b4390e189_GRCh38.primary_assembly.genome.fa added
ac8b5cc70c06_hs37d5.fa.fai added
ac8bfe68d80_hs37d5.fa.amb added
ac8b6953d6a7_hs37d5.fa.ann added
ac8b7f31a3f6_hs37d5.fa.bwt added
ac8b1403acb7_hs37d5.fa.pac added
ac8b7d402ca4_hs37d5.fa.sa added
ac8b33033a_hs37d5.fa added
ac8b1518d4f0_complete_ref_lens.bin added
ac8b1143e362_ctable.bin added
ac8b53fc9_ctg_offsets.bin added
ac8b589ea521_duplicate_clusters.tsv added
ac8b176b46fb_info.json added
ac8b40114c0_mphf.bin added
ac8b62f94b4d_pos.bin added
ac8b5cbedefe_pre_indexing.log added
ac8b77222543_rank.bin added
ac8b62bc8ecf_ref_indexing.log added
ac8b4943eaad_refAccumLengths.bin added
ac8b9e4296f_reflengths.bin added
ac8b625c3b7b_refseq.bin added
ac8b15453ab0_seq.bin added
ac8b741003b8_versionInfo.json added
ac8b4764608f_salmon_index added
ac8beff70e7_chrLength.txt added
ac8b244d5562_chrName.txt added
ac8b5120a78c_chrNameLength.txt added
ac8b36d801f0_chrStart.txt added
ac8b1f674fb1_exonGeTrInfo.tab added
ac8b37a0fd92_exonInfo.tab added
ac8b2a6798c6_geneInfo.tab added
ac8b775f04e9_Genome added
ac8b7f3b9a38_genomeParameters.txt added
ac8b220a13ca_Log.out added
ac8b4399443b_SA added
ac8b34ea029_SAindex added
ac8b1ef4e571_sjdbInfo.txt added
ac8b60036d97_sjdbList.fromGTF.out.tab added
ac8b11005c0_sjdbList.out.tab added
ac8b42e980cb_transcriptInfo.tab added
ac8b7006b1be_GRCh38.GENCODE.v42_100 added
ac8b477f6a67_knownGene_hg38.sql added
ac8b7e22b4dc_knownGene_hg38.txt added
ac8b18901836_refGene_hg38.sql added
ac8b1c258dd3_refGene_hg38.txt added
ac8b65822614_knownGene_mm39.sql added
ac8b43921f1c_knownGene_mm39.txt added
ac8b2e3889ec_refGene_mm39.sql added
ac8b1e6fca9_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/Rtmp1zaikI/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
24.938 3.175 29.225
ReUseData.Rcheck/ReUseData-Ex.timings
| name | user | system | elapsed | |
| dataHub-class | 7.742 | 0.849 | 8.660 | |
| dataSearch | 1.390 | 0.053 | 1.447 | |
| dataUpdate | 0 | 0 | 0 | |
| getCloudData | 2.987 | 0.159 | 4.028 | |
| getData | 0.000 | 0.000 | 0.001 | |
| meta_data | 0.001 | 0.000 | 0.001 | |
| recipeHub-class | 0.168 | 0.015 | 0.185 | |
| recipeLoad | 1.589 | 0.089 | 1.684 | |
| recipeMake | 0.000 | 0.001 | 0.001 | |
| recipeSearch | 0.665 | 0.038 | 0.705 | |
| recipeUpdate | 0 | 0 | 0 | |