Qian Liu
| Snapshot Date: 2024-11-27 13:40 -0500 (Wed, 27 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 2024-11-28 12:15 -0500 (Thu, 28 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" | 4398 |
| 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 | | ||||||||
|
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: 2024-11-28 04:59:40 -0500 (Thu, 28 Nov 2024) |
| EndedAt: 2024-11-28 05:06:00 -0500 (Thu, 28 Nov 2024) |
| EllapsedTime: 379.2 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 ...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 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 5.615 0.347 5.962
* 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...
2502c560cc6613_GRCh38.primary_assembly.genome.fa.1.bt2 added
2502c52a61405e_GRCh38.primary_assembly.genome.fa.2.bt2 added
2502c567f11bd3_GRCh38.primary_assembly.genome.fa.3.bt2 added
2502c5688ce45_GRCh38.primary_assembly.genome.fa.4.bt2 added
2502c53e4e7762_GRCh38.primary_assembly.genome.fa.rev.1.bt2 added
2502c558efafc8_GRCh38.primary_assembly.genome.fa.rev.2.bt2 added
2502c53ecc3e2_outfile.txt added
2502c51ad9c65e_GRCh37_to_GRCh38.chain added
2502c5315b66a8_GRCh37_to_NCBI34.chain added
2502c52b54c52_GRCh37_to_NCBI35.chain added
2502c562c75289_GRCh37_to_NCBI36.chain added
2502c51170286c_GRCh38_to_GRCh37.chain added
2502c56032c04f_GRCh38_to_NCBI34.chain added
2502c54e13b80e_GRCh38_to_NCBI35.chain added
2502c5678d473c_GRCh38_to_NCBI36.chain added
2502c53dc73336_NCBI34_to_GRCh37.chain added
2502c555e7ad17_NCBI34_to_GRCh38.chain added
2502c5343a37e2_NCBI35_to_GRCh37.chain added
2502c5776b1657_NCBI35_to_GRCh38.chain added
2502c546e6b9b9_NCBI36_to_GRCh37.chain added
2502c5297e9648_NCBI36_to_GRCh38.chain added
2502c5397b64b9_GRCm38_to_NCBIM36.chain added
2502c5666fb92d_GRCm38_to_NCBIM37.chain added
2502c55c3fb3ee_NCBIM36_to_GRCm38.chain added
2502c545839013_NCBIM37_to_GRCm38.chain added
2502c576ecb1e7_1000G_omni2.5.b37.vcf.gz added
2502c5128a4b04_1000G_omni2.5.b37.vcf.gz.tbi added
2502c5543b8ca1_Mills_and_1000G_gold_standard.indels.b37.vcf.gz added
2502c546c696bf_Mills_and_1000G_gold_standard.indels.b37.vcf.gz.tbi added
2502c53b2be40e_1000G_omni2.5.hg38.vcf.gz added
2502c55c061800_1000G_omni2.5.hg38.vcf.gz.tbi added
2502c52792fcd2_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz added
2502c5658d246c_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz.tbi added
2502c543f733d4_af-only-gnomad.raw.sites.vcf added
2502c52e1bcb17_af-only-gnomad.raw.sites.vcf.idx added
2502c523db9bce_Mutect2-exome-panel.vcf.idx added
2502c51ce6e39c_Mutect2-WGS-panel-b37.vcf added
2502c532088ef9_Mutect2-WGS-panel-b37.vcf.idx added
2502c53eb5622c_small_exac_common_3.vcf added
2502c54e424a45_small_exac_common_3.vcf.idx added
2502c534bddb4b_1000g_pon.hg38.vcf.gz added
2502c5217cb4b6_1000g_pon.hg38.vcf.gz.tbi added
2502c55fb272b1_af-only-gnomad.hg38.vcf.gz added
2502c514f09b9a_af-only-gnomad.hg38.vcf.gz.tbi added
2502c56f906cc4_small_exac_common_3.hg38.vcf.gz added
2502c5473fb9ed_small_exac_common_3.hg38.vcf.gz.tbi added
2502c552b7ced1_gencode.v41.annotation.gtf added
2502c5457819db_gencode.v42.annotation.gtf added
2502c57b79f1cf_gencode.vM30.annotation.gtf added
2502c54a22e528_gencode.vM31.annotation.gtf added
2502c5c5ed394_gencode.v41.transcripts.fa added
2502c524f88817_gencode.v41.transcripts.fa.fai added
2502c539e49e1_gencode.v42.transcripts.fa added
2502c572ce8cc2_gencode.v42.transcripts.fa.fai added
2502c51383c05_gencode.vM30.pc_transcripts.fa added
2502c54921d9f4_gencode.vM30.pc_transcripts.fa.fai added
2502c569bb3ea9_gencode.vM31.pc_transcripts.fa added
2502c513c28709_gencode.vM31.pc_transcripts.fa.fai added
2502c51d5d6696_GRCh38.primary_assembly.genome.fa.1.ht2 added
2502c53081d568_GRCh38.primary_assembly.genome.fa.2.ht2 added
2502c54eee6b17_GRCh38.primary_assembly.genome.fa.3.ht2 added
2502c579637e96_GRCh38.primary_assembly.genome.fa.4.ht2 added
2502c55814d23a_GRCh38.primary_assembly.genome.fa.5.ht2 added
2502c5347b8f83_GRCh38.primary_assembly.genome.fa.6.ht2 added
2502c53d5ab26a_GRCh38.primary_assembly.genome.fa.7.ht2 added
2502c56309d51_GRCh38.primary_assembly.genome.fa.8.ht2 added
2502c558572b51_GRCh38_full_analysis_set_plus_decoy_hla.fa.fai added
2502c55a419607_GRCh38_full_analysis_set_plus_decoy_hla.fa.amb added
2502c538392c4a_GRCh38_full_analysis_set_plus_decoy_hla.fa.ann added
2502c5170c8d7e_GRCh38_full_analysis_set_plus_decoy_hla.fa.bwt added
2502c52883e04c_GRCh38_full_analysis_set_plus_decoy_hla.fa.pac added
2502c56cf70795_GRCh38_full_analysis_set_plus_decoy_hla.fa.sa added
2502c538894234_GRCh38_full_analysis_set_plus_decoy_hla.fa added
2502c583652fd_GRCh38.primary_assembly.genome.fa.fai added
2502c51e7a330_GRCh38.primary_assembly.genome.fa.amb added
2502c52819aef8_GRCh38.primary_assembly.genome.fa.ann added
2502c54f760cea_GRCh38.primary_assembly.genome.fa.bwt added
2502c5549f7201_GRCh38.primary_assembly.genome.fa.pac added
2502c56d91c8d3_GRCh38.primary_assembly.genome.fa.sa added
2502c54aeffeb9_GRCh38.primary_assembly.genome.fa added
2502c51ec25729_hs37d5.fa.fai added
2502c579f09c68_hs37d5.fa.amb added
2502c56fe886d0_hs37d5.fa.ann added
2502c52260a10b_hs37d5.fa.bwt added
2502c56cbf292a_hs37d5.fa.pac added
2502c57120c2d5_hs37d5.fa.sa added
2502c56b827aff_hs37d5.fa added
2502c5567a67d3_complete_ref_lens.bin added
2502c54e349de_ctable.bin added
2502c58dfe195_ctg_offsets.bin added
2502c56fc3d3b_duplicate_clusters.tsv added
2502c553d1b4f5_info.json added
2502c5243602c_mphf.bin added
2502c55f110f75_pos.bin added
2502c584d4478_pre_indexing.log added
2502c53f9e1296_rank.bin added
2502c56541acc6_ref_indexing.log added
2502c560a46fc9_refAccumLengths.bin added
2502c519dfa89d_reflengths.bin added
2502c51d7ad910_refseq.bin added
2502c577b0fd47_seq.bin added
2502c5426388e9_versionInfo.json added
2502c5a71e0a5_salmon_index added
2502c5303a3f7b_chrLength.txt added
2502c54a99dbe6_chrName.txt added
2502c5c5983d5_chrNameLength.txt added
2502c55853ee73_chrStart.txt added
2502c51a0fe8d0_exonGeTrInfo.tab added
2502c560f8f5d6_exonInfo.tab added
2502c545e5b747_geneInfo.tab added
2502c564ffe789_Genome added
2502c57fbb4d00_genomeParameters.txt added
2502c53fd653af_Log.out added
2502c554e86e59_SA added
2502c5221bee0b_SAindex added
2502c52c957cd9_sjdbInfo.txt added
2502c54609312e_sjdbList.fromGTF.out.tab added
2502c5d9e690a_sjdbList.out.tab added
2502c530fe4ac_transcriptInfo.tab added
2502c54aec7b0c_GRCh38.GENCODE.v42_100 added
2502c5167e4aa0_knownGene_hg38.sql added
2502c5a0c21e7_knownGene_hg38.txt added
2502c51ebe3001_refGene_hg38.sql added
2502c518c1aacc_refGene_hg38.txt added
2502c5691d315c_knownGene_mm39.sql added
2502c5270b7479_knownGene_mm39.txt added
2502c5585fbd62_refGene_mm39.sql added
2502c54e5ede22_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/RtmpDe61e8/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
17.614 1.325 19.371
ReUseData.Rcheck/ReUseData-Ex.timings
| name | user | system | elapsed | |
| dataHub-class | 5.615 | 0.347 | 5.962 | |
| dataSearch | 1.095 | 0.013 | 1.109 | |
| dataUpdate | 0.001 | 0.000 | 0.001 | |
| getCloudData | 2.688 | 0.176 | 3.371 | |
| getData | 0.000 | 0.000 | 0.001 | |
| meta_data | 0.001 | 0.000 | 0.001 | |
| recipeHub-class | 0.125 | 0.007 | 0.132 | |
| recipeLoad | 1.193 | 0.140 | 1.335 | |
| recipeMake | 0.000 | 0.001 | 0.000 | |
| recipeSearch | 0.502 | 0.029 | 0.532 | |
| recipeUpdate | 0 | 0 | 0 | |