Qian Liu
| Snapshot Date: 2024-12-23 13:40 -0500 (Mon, 23 Dec 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 2024-12-24 11:40 -0500 (Tue, 24 Dec 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" | 4754 |
| palomino7 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2024-10-26 r87273 ucrt) -- "Unsuffered Consequences" | 4472 |
| lconway | macOS 12.7.1 Monterey | x86_64 | R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" | 4426 |
| kjohnson3 | macOS 13.7.1 Ventura | arm64 | R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" | 4381 |
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | R Under development (unstable) (2024-11-24 r87369) -- "Unsuffered Consequences" | 4373 |
| 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 1714/2274 | 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 | | ||||||||
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | 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: /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:ReUseData.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings ReUseData_1.7.0.tar.gz |
| StartedAt: 2024-12-24 01:27:12 -0500 (Tue, 24 Dec 2024) |
| EndedAt: 2024-12-24 01:30:00 -0500 (Tue, 24 Dec 2024) |
| EllapsedTime: 168.4 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: ReUseData.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:ReUseData.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings ReUseData_1.7.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/ReUseData.Rcheck’
* using R Under development (unstable) (2024-10-21 r87258)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0
GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0
* running under: Ubuntu 24.04.1 LTS
* using session charset: UTF-8
* 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 ... 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 loading without being on the library search path ... 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 6.036 0.362 6.402
* 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 re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE
Status: 1 NOTE
See
‘/home/biocbuild/bbs-3.21-bioc/meat/ReUseData.Rcheck/00check.log’
for details.
ReUseData.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD INSTALL ReUseData ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.21-bioc/R/site-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) (2024-10-21 r87258) -- "Unsuffered Consequences"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu
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...
23588e795c2f0_GRCh38.primary_assembly.genome.fa.1.bt2 added
23588e3ca07dae_GRCh38.primary_assembly.genome.fa.2.bt2 added
23588e37f69873_GRCh38.primary_assembly.genome.fa.3.bt2 added
23588e72864769_GRCh38.primary_assembly.genome.fa.4.bt2 added
23588e4bf410b6_GRCh38.primary_assembly.genome.fa.rev.1.bt2 added
23588e7cb18ea7_GRCh38.primary_assembly.genome.fa.rev.2.bt2 added
23588e3a85c03_outfile.txt added
23588e68e9e7a6_GRCh37_to_GRCh38.chain added
23588e79a73452_GRCh37_to_NCBI34.chain added
23588e1c0ea01c_GRCh37_to_NCBI35.chain added
23588e44bfabb8_GRCh37_to_NCBI36.chain added
23588e56296645_GRCh38_to_GRCh37.chain added
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23588e217c9948_GRCh38_to_NCBI36.chain added
23588e79d70b1c_NCBI34_to_GRCh37.chain added
23588e3fa19303_NCBI34_to_GRCh38.chain added
23588e7ac7706d_NCBI35_to_GRCh37.chain added
23588e7d3edd72_NCBI35_to_GRCh38.chain added
23588e7c1c8c66_NCBI36_to_GRCh37.chain added
23588e765ac63e_NCBI36_to_GRCh38.chain added
23588e49cbac11_GRCm38_to_NCBIM36.chain added
23588e7c5a824a_GRCm38_to_NCBIM37.chain added
23588e62efef2e_NCBIM36_to_GRCm38.chain added
23588e4469e5ef_NCBIM37_to_GRCm38.chain added
23588e794ea591_1000G_omni2.5.b37.vcf.gz added
23588e6cb58212_1000G_omni2.5.b37.vcf.gz.tbi added
23588e4b1f5271_Mills_and_1000G_gold_standard.indels.b37.vcf.gz added
23588e268c95db_Mills_and_1000G_gold_standard.indels.b37.vcf.gz.tbi added
23588e52f39be1_1000G_omni2.5.hg38.vcf.gz added
23588e9c961a_1000G_omni2.5.hg38.vcf.gz.tbi added
23588e2e2258cb_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz added
23588ef941990_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz.tbi added
23588e38932e8d_af-only-gnomad.raw.sites.vcf added
23588e20a8a035_af-only-gnomad.raw.sites.vcf.idx added
23588e5b882a46_Mutect2-exome-panel.vcf.idx added
23588e3544bd34_Mutect2-WGS-panel-b37.vcf added
23588e2450fc38_Mutect2-WGS-panel-b37.vcf.idx added
23588e447211ec_small_exac_common_3.vcf added
23588e2eebf186_small_exac_common_3.vcf.idx added
23588e405f9c55_1000g_pon.hg38.vcf.gz added
23588e931bda4_1000g_pon.hg38.vcf.gz.tbi added
23588e51557cc_af-only-gnomad.hg38.vcf.gz added
23588eddbd2a4_af-only-gnomad.hg38.vcf.gz.tbi added
23588e27165c51_small_exac_common_3.hg38.vcf.gz added
23588e2691f114_small_exac_common_3.hg38.vcf.gz.tbi added
23588e7b2ddc0_gencode.v41.annotation.gtf added
23588e66b7ef54_gencode.v42.annotation.gtf added
23588e21596181_gencode.vM30.annotation.gtf added
23588e4f1bb32_gencode.vM31.annotation.gtf added
23588e62d47bba_gencode.v41.transcripts.fa added
23588e17b427bf_gencode.v41.transcripts.fa.fai added
23588e4ebd6744_gencode.v42.transcripts.fa added
23588e5f2efe05_gencode.v42.transcripts.fa.fai added
23588e7aa416ed_gencode.vM30.pc_transcripts.fa added
23588e13274d33_gencode.vM30.pc_transcripts.fa.fai added
23588e587da396_gencode.vM31.pc_transcripts.fa added
23588e67599900_gencode.vM31.pc_transcripts.fa.fai added
23588e5e469fa5_GRCh38.primary_assembly.genome.fa.1.ht2 added
23588e7f0a3971_GRCh38.primary_assembly.genome.fa.2.ht2 added
23588e3a4d34e1_GRCh38.primary_assembly.genome.fa.3.ht2 added
23588e5ee335bf_GRCh38.primary_assembly.genome.fa.4.ht2 added
23588e2d2c923c_GRCh38.primary_assembly.genome.fa.5.ht2 added
23588e49e14e71_GRCh38.primary_assembly.genome.fa.6.ht2 added
23588e1776644d_GRCh38.primary_assembly.genome.fa.7.ht2 added
23588e4dd53271_GRCh38.primary_assembly.genome.fa.8.ht2 added
23588e256978b7_GRCh38_full_analysis_set_plus_decoy_hla.fa.fai added
23588e4cbb2181_GRCh38_full_analysis_set_plus_decoy_hla.fa.amb added
23588e72262eaa_GRCh38_full_analysis_set_plus_decoy_hla.fa.ann added
23588e69db8aa3_GRCh38_full_analysis_set_plus_decoy_hla.fa.bwt added
23588e7ba71308_GRCh38_full_analysis_set_plus_decoy_hla.fa.pac added
23588e3285caff_GRCh38_full_analysis_set_plus_decoy_hla.fa.sa added
23588e730d4847_GRCh38_full_analysis_set_plus_decoy_hla.fa added
23588ebc6ad4_GRCh38.primary_assembly.genome.fa.fai added
23588e40619da3_GRCh38.primary_assembly.genome.fa.amb added
23588e1a23a499_GRCh38.primary_assembly.genome.fa.ann added
23588e274e5be8_GRCh38.primary_assembly.genome.fa.bwt added
23588e48147b63_GRCh38.primary_assembly.genome.fa.pac added
23588edb93ed_GRCh38.primary_assembly.genome.fa.sa added
23588e48a7bd69_GRCh38.primary_assembly.genome.fa added
23588e4d063696_hs37d5.fa.fai added
23588e63b00fa8_hs37d5.fa.amb added
23588e605be528_hs37d5.fa.ann added
23588e1bc39dda_hs37d5.fa.bwt added
23588e42df0dad_hs37d5.fa.pac added
23588e5afffc16_hs37d5.fa.sa added
23588e2eeaeb0d_hs37d5.fa added
23588e1b5cb143_complete_ref_lens.bin added
23588e42599516_ctable.bin added
23588ed318ab2_ctg_offsets.bin added
23588e1a66eab4_duplicate_clusters.tsv added
23588e7ca6c9f7_info.json added
23588e6c14c072_mphf.bin added
23588e47937cf0_pos.bin added
23588e46881869_pre_indexing.log added
23588e38b24bf_rank.bin added
23588e1568af62_ref_indexing.log added
23588e6bf19120_refAccumLengths.bin added
23588e50464640_reflengths.bin added
23588e78ede0c_refseq.bin added
23588e55cd1bc4_seq.bin added
23588e4bed5948_versionInfo.json added
23588e3a14a90b_salmon_index added
23588e48da640b_chrLength.txt added
23588e4ca9c41c_chrName.txt added
23588e7a7646ae_chrNameLength.txt added
23588e62fe08a4_chrStart.txt added
23588e73f82004_exonGeTrInfo.tab added
23588e428ac211_exonInfo.tab added
23588e63d99c92_geneInfo.tab added
23588e3c9fdd6d_Genome added
23588ef90f8a7_genomeParameters.txt added
23588e4789ac3a_Log.out added
23588e1cfbc296_SA added
23588e2b549681_SAindex added
23588ea68b9e7_sjdbInfo.txt added
23588e77fbbeac_sjdbList.fromGTF.out.tab added
23588e5a3f818f_sjdbList.out.tab added
23588e25c56b2a_transcriptInfo.tab added
23588e3a5553c2_GRCh38.GENCODE.v42_100 added
23588e67710c41_knownGene_hg38.sql added
23588e402c55de_knownGene_hg38.txt added
23588e36fc1db9_refGene_hg38.sql added
23588e5385ccb3_refGene_hg38.txt added
23588e7bfd2ce_knownGene_mm39.sql added
23588e7d843622_knownGene_mm39.txt added
23588e5710f172_refGene_mm39.sql added
23588e1d288230_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/RtmpaTkI6S/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
19.370 1.538 21.156
ReUseData.Rcheck/ReUseData-Ex.timings
| name | user | system | elapsed | |
| dataHub-class | 6.036 | 0.362 | 6.402 | |
| dataSearch | 1.159 | 0.044 | 1.202 | |
| dataUpdate | 0.000 | 0.000 | 0.001 | |
| getCloudData | 2.662 | 0.139 | 3.326 | |
| getData | 0 | 0 | 0 | |
| meta_data | 0 | 0 | 0 | |
| recipeHub-class | 0.119 | 0.005 | 0.125 | |
| recipeLoad | 1.265 | 0.093 | 1.359 | |
| recipeMake | 0.000 | 0.001 | 0.001 | |
| recipeSearch | 0.563 | 0.030 | 0.593 | |
| recipeUpdate | 0 | 0 | 0 | |