Qian Liu
| Snapshot Date: 2025-02-12 13:40 -0500 (Wed, 12 Feb 2025) |
| 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 2025-02-13 11:40 -0500 (Thu, 13 Feb 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | R Under development (unstable) (2025-01-20 r87609) -- "Unsuffered Consequences" | 4719 |
| palomino7 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2025-01-21 r87610 ucrt) -- "Unsuffered Consequences" | 4481 |
| lconway | macOS 12.7.1 Monterey | x86_64 | R Under development (unstable) (2025-01-22 r87618) -- "Unsuffered Consequences" | 4492 |
| kjohnson3 | macOS 13.7.1 Ventura | arm64 | R Under development (unstable) (2025-01-20 r87609) -- "Unsuffered Consequences" | 4445 |
| 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 1728/2295 | 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: /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: 2025-02-13 01:51:24 -0500 (Thu, 13 Feb 2025) |
| EndedAt: 2025-02-13 01:54:22 -0500 (Thu, 13 Feb 2025) |
| EllapsedTime: 177.3 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) (2025-01-20 r87609)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* 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 5.816 0.381 6.2
* 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’ ... ** this is package ‘ReUseData’ version ‘1.7.0’ ** 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) (2025-01-20 r87609) -- "Unsuffered Consequences"
Copyright (C) 2025 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...
197cb5723a520c_GRCh38.primary_assembly.genome.fa.1.bt2 added
197cb5462caea1_GRCh38.primary_assembly.genome.fa.2.bt2 added
197cb51d4d5426_GRCh38.primary_assembly.genome.fa.3.bt2 added
197cb517d15b87_GRCh38.primary_assembly.genome.fa.4.bt2 added
197cb51814bde9_GRCh38.primary_assembly.genome.fa.rev.1.bt2 added
197cb55f0e096d_GRCh38.primary_assembly.genome.fa.rev.2.bt2 added
197cb5420b5bb5_outfile.txt added
197cb513dbccca_GRCh37_to_GRCh38.chain added
197cb53b3da781_GRCh37_to_NCBI34.chain added
197cb56ea00567_GRCh37_to_NCBI35.chain added
197cb53ab40e3b_GRCh37_to_NCBI36.chain added
197cb526997c0b_GRCh38_to_GRCh37.chain added
197cb55d5c06d4_GRCh38_to_NCBI34.chain added
197cb57e30b771_GRCh38_to_NCBI35.chain added
197cb51197ef3d_GRCh38_to_NCBI36.chain added
197cb54ee33477_NCBI34_to_GRCh37.chain added
197cb56e90040b_NCBI34_to_GRCh38.chain added
197cb5781196f7_NCBI35_to_GRCh37.chain added
197cb5599fe02_NCBI35_to_GRCh38.chain added
197cb55586b997_NCBI36_to_GRCh37.chain added
197cb53797b79c_NCBI36_to_GRCh38.chain added
197cb53e5cd06d_GRCm38_to_NCBIM36.chain added
197cb531860d3e_GRCm38_to_NCBIM37.chain added
197cb517439e85_NCBIM36_to_GRCm38.chain added
197cb56f259ed0_NCBIM37_to_GRCm38.chain added
197cb52fcc2585_1000G_omni2.5.b37.vcf.gz added
197cb5285faab_1000G_omni2.5.b37.vcf.gz.tbi added
197cb5175d09ba_Mills_and_1000G_gold_standard.indels.b37.vcf.gz added
197cb524334326_Mills_and_1000G_gold_standard.indels.b37.vcf.gz.tbi added
197cb567b4415f_1000G_omni2.5.hg38.vcf.gz added
197cb5123267cc_1000G_omni2.5.hg38.vcf.gz.tbi added
197cb5166d9533_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz added
197cb52de0f000_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz.tbi added
197cb52f7fbbf2_af-only-gnomad.raw.sites.vcf added
197cb52e3ef0ba_af-only-gnomad.raw.sites.vcf.idx added
197cb545f5ade9_Mutect2-exome-panel.vcf.idx added
197cb5e8dc55f_Mutect2-WGS-panel-b37.vcf added
197cb5704a4c70_Mutect2-WGS-panel-b37.vcf.idx added
197cb559d17ab3_small_exac_common_3.vcf added
197cb549cb6ce1_small_exac_common_3.vcf.idx added
197cb55eea51d7_1000g_pon.hg38.vcf.gz added
197cb5148588ef_1000g_pon.hg38.vcf.gz.tbi added
197cb57064e8ec_af-only-gnomad.hg38.vcf.gz added
197cb53c4658ac_af-only-gnomad.hg38.vcf.gz.tbi added
197cb512b64060_small_exac_common_3.hg38.vcf.gz added
197cb51fcd829_small_exac_common_3.hg38.vcf.gz.tbi added
197cb5b298d23_gencode.v41.annotation.gtf added
197cb5146446b_gencode.v42.annotation.gtf added
197cb57a0e6f21_gencode.vM30.annotation.gtf added
197cb510c38b25_gencode.vM31.annotation.gtf added
197cb556ccfe02_gencode.v41.transcripts.fa added
197cb531a626bd_gencode.v41.transcripts.fa.fai added
197cb54f205b92_gencode.v42.transcripts.fa added
197cb58530b41_gencode.v42.transcripts.fa.fai added
197cb548e9c542_gencode.vM30.pc_transcripts.fa added
197cb53e45fa63_gencode.vM30.pc_transcripts.fa.fai added
197cb5381f30c6_gencode.vM31.pc_transcripts.fa added
197cb54b6fbfee_gencode.vM31.pc_transcripts.fa.fai added
197cb555a3041d_GRCh38.primary_assembly.genome.fa.1.ht2 added
197cb55c5273ed_GRCh38.primary_assembly.genome.fa.2.ht2 added
197cb53324014d_GRCh38.primary_assembly.genome.fa.3.ht2 added
197cb567d56be9_GRCh38.primary_assembly.genome.fa.4.ht2 added
197cb572c00920_GRCh38.primary_assembly.genome.fa.5.ht2 added
197cb56104f14d_GRCh38.primary_assembly.genome.fa.6.ht2 added
197cb5175527dc_GRCh38.primary_assembly.genome.fa.7.ht2 added
197cb520fef9da_GRCh38.primary_assembly.genome.fa.8.ht2 added
197cb526fa9f36_GRCh38_full_analysis_set_plus_decoy_hla.fa.fai added
197cb525e2ed3b_GRCh38_full_analysis_set_plus_decoy_hla.fa.amb added
197cb51149464a_GRCh38_full_analysis_set_plus_decoy_hla.fa.ann added
197cb5cc19ea_GRCh38_full_analysis_set_plus_decoy_hla.fa.bwt added
197cb56fae5a1c_GRCh38_full_analysis_set_plus_decoy_hla.fa.pac added
197cb570339822_GRCh38_full_analysis_set_plus_decoy_hla.fa.sa added
197cb51551a2d9_GRCh38_full_analysis_set_plus_decoy_hla.fa added
197cb560134309_GRCh38.primary_assembly.genome.fa.fai added
197cb52c79f0ce_GRCh38.primary_assembly.genome.fa.amb added
197cb52807e339_GRCh38.primary_assembly.genome.fa.ann added
197cb562101b32_GRCh38.primary_assembly.genome.fa.bwt added
197cb537a37df1_GRCh38.primary_assembly.genome.fa.pac added
197cb5294e27a4_GRCh38.primary_assembly.genome.fa.sa added
197cb55c1e8a53_GRCh38.primary_assembly.genome.fa added
197cb548670917_hs37d5.fa.fai added
197cb51b25a6_hs37d5.fa.amb added
197cb5dc4b111_hs37d5.fa.ann added
197cb5178764a9_hs37d5.fa.bwt added
197cb586e30e7_hs37d5.fa.pac added
197cb556ae7653_hs37d5.fa.sa added
197cb555cd5f0c_hs37d5.fa added
197cb5408d61ae_complete_ref_lens.bin added
197cb5221e3641_ctable.bin added
197cb52b70632a_ctg_offsets.bin added
197cb51cdfd59b_duplicate_clusters.tsv added
197cb55542378e_info.json added
197cb51345cf13_mphf.bin added
197cb5f9fdebb_pos.bin added
197cb5364728db_pre_indexing.log added
197cb52a9af6ef_rank.bin added
197cb5309ed895_ref_indexing.log added
197cb55d41c812_refAccumLengths.bin added
197cb5507de42b_reflengths.bin added
197cb541e81ee0_refseq.bin added
197cb55e0de1fc_seq.bin added
197cb5402c3e47_versionInfo.json added
197cb5321bb702_salmon_index added
197cb5735f84d5_chrLength.txt added
197cb5203f8150_chrName.txt added
197cb55e95a7d0_chrNameLength.txt added
197cb51b67680e_chrStart.txt added
197cb524f9c83_exonGeTrInfo.tab added
197cb5163925c1_exonInfo.tab added
197cb544b58fb2_geneInfo.tab added
197cb55e6e26d6_Genome added
197cb55ea02ed8_genomeParameters.txt added
197cb544d0b558_Log.out added
197cb56c32d7e7_SA added
197cb576279382_SAindex added
197cb54d3ee640_sjdbInfo.txt added
197cb542e14e3b_sjdbList.fromGTF.out.tab added
197cb54bf4f28e_sjdbList.out.tab added
197cb5dcc47ee_transcriptInfo.tab added
197cb564ff847c_GRCh38.GENCODE.v42_100 added
197cb5776555b8_knownGene_hg38.sql added
197cb52aac1d89_knownGene_hg38.txt added
197cb53a41bc0b_refGene_hg38.sql added
197cb5aab24cc_refGene_hg38.txt added
197cb53a4bfc44_knownGene_mm39.sql added
197cb57088e4e6_knownGene_mm39.txt added
197cb535461bbb_refGene_mm39.sql added
197cb56aead4d9_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/RtmpEXbpmA/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
20.961 1.896 23.097
ReUseData.Rcheck/ReUseData-Ex.timings
| name | user | system | elapsed | |
| dataHub-class | 5.816 | 0.381 | 6.200 | |
| dataSearch | 1.105 | 0.036 | 1.142 | |
| dataUpdate | 0.001 | 0.000 | 0.000 | |
| getCloudData | 2.529 | 0.107 | 3.204 | |
| getData | 0 | 0 | 0 | |
| meta_data | 0.001 | 0.000 | 0.001 | |
| recipeHub-class | 0.122 | 0.011 | 0.135 | |
| recipeLoad | 1.262 | 0.027 | 1.290 | |
| recipeMake | 0.001 | 0.000 | 0.001 | |
| recipeSearch | 0.565 | 0.007 | 0.573 | |
| recipeUpdate | 0.000 | 0.000 | 0.001 | |