Qian Liu
| Snapshot Date: 2024-05-20 14:05:07 -0400 (Mon, 20 May 2024) |
| git_url: https://git.bioconductor.org/packages/ReUseData |
| git_branch: devel |
| git_last_commit: cbe4e73 |
| git_last_commit_date: 2024-04-30 11:46:52 -0400 (Tue, 30 Apr 2024) |
| Back to Multiple platform build/check report for BioC 3.20: simplified long |
|
This page was generated on 2024-05-22 11:36:20 -0400 (Wed, 22 May 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.0 RC (2024-04-16 r86468) -- "Puppy Cup" | 4665 |
| palomino4 | Windows Server 2022 Datacenter | x64 | 4.4.0 RC (2024-04-16 r86468 ucrt) -- "Puppy Cup" | 4400 |
| merida1 | macOS 12.7.4 Monterey | x86_64 | 4.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup" | 4427 |
| 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 1688/2233 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| ReUseData 1.5.0 (landing page) Qian Liu
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino4 | Windows Server 2022 Datacenter / x64 | ... NOT SUPPORTED ... | ||||||||||||
| merida1 | macOS 12.7.4 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson1 | macOS 13.6.6 Ventura / arm64 | see weekly results here | ||||||||||||
|
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: 1.5.0 |
| Command: /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:ReUseData.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings ReUseData_1.5.0.tar.gz |
| StartedAt: 2024-05-21 02:01:16 -0400 (Tue, 21 May 2024) |
| EndedAt: 2024-05-21 02:06:17 -0400 (Tue, 21 May 2024) |
| EllapsedTime: 300.4 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: ReUseData.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:ReUseData.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings ReUseData_1.5.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/ReUseData.Rcheck’
* using R version 4.4.0 RC (2024-04-16 r86468)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
* running under: Ubuntu 22.04.4 LTS
* using session charset: UTF-8
* checking for file ‘ReUseData/DESCRIPTION’ ... OK
* this is package ‘ReUseData’ version ‘1.5.0’
* 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 10.629 0.347 11.071
getCloudData 4.624 0.234 5.984
* 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-3.20-bioc/meat/ReUseData.Rcheck/00check.log’
for details.
ReUseData.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD INSTALL ReUseData ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.20-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 version 4.4.0 RC (2024-04-16 r86468) -- "Puppy Cup"
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...
30f12833ba4bb6_GRCh38.primary_assembly.genome.fa.1.bt2 added
30f12827ebb245_GRCh38.primary_assembly.genome.fa.2.bt2 added
30f12813ea26a_GRCh38.primary_assembly.genome.fa.3.bt2 added
30f1287f48ac07_GRCh38.primary_assembly.genome.fa.4.bt2 added
30f1284978c4d4_GRCh38.primary_assembly.genome.fa.rev.1.bt2 added
30f1285580258f_GRCh38.primary_assembly.genome.fa.rev.2.bt2 added
30f128229fa445_outfile.txt added
30f1285460cd85_GRCh37_to_GRCh38.chain added
30f128456c66d_GRCh37_to_NCBI34.chain added
30f12832d38d5e_GRCh37_to_NCBI35.chain added
30f12858387d8_GRCh37_to_NCBI36.chain added
30f1285582343e_GRCh38_to_GRCh37.chain added
30f128143fa30_GRCh38_to_NCBI34.chain added
30f128691d31fa_GRCh38_to_NCBI35.chain added
30f1282c44ec3d_GRCh38_to_NCBI36.chain added
30f1281dfc74cf_NCBI34_to_GRCh37.chain added
30f12842d8baf_NCBI34_to_GRCh38.chain added
30f128b8608d5_NCBI35_to_GRCh37.chain added
30f1286b916fbe_NCBI35_to_GRCh38.chain added
30f1282adde36f_NCBI36_to_GRCh37.chain added
30f1286e58ecb9_NCBI36_to_GRCh38.chain added
30f1284caf85dc_GRCm38_to_NCBIM36.chain added
30f12831ef7e23_GRCm38_to_NCBIM37.chain added
30f1281d5e418a_NCBIM36_to_GRCm38.chain added
30f1283be624dd_NCBIM37_to_GRCm38.chain added
30f12852f144a8_1000G_omni2.5.b37.vcf.gz added
30f128190027ef_1000G_omni2.5.b37.vcf.gz.tbi added
30f12859576ec_Mills_and_1000G_gold_standard.indels.b37.vcf.gz added
30f12874cf1d97_Mills_and_1000G_gold_standard.indels.b37.vcf.gz.tbi added
30f1286cea232f_1000G_omni2.5.hg38.vcf.gz added
30f1283c801d7b_1000G_omni2.5.hg38.vcf.gz.tbi added
30f1282889694d_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz added
30f12814d5d574_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz.tbi added
30f1283dbebfe6_af-only-gnomad.raw.sites.vcf added
30f12827d21554_af-only-gnomad.raw.sites.vcf.idx added
30f1285e4e9a48_Mutect2-exome-panel.vcf.idx added
30f128133ee575_Mutect2-WGS-panel-b37.vcf added
30f1284a71b999_Mutect2-WGS-panel-b37.vcf.idx added
30f12832af67cd_small_exac_common_3.vcf added
30f1281795abe2_small_exac_common_3.vcf.idx added
30f1287d4546f8_1000g_pon.hg38.vcf.gz added
30f1283832efa6_1000g_pon.hg38.vcf.gz.tbi added
30f1286d17e020_af-only-gnomad.hg38.vcf.gz added
30f1287e894128_af-only-gnomad.hg38.vcf.gz.tbi added
30f128215021a0_small_exac_common_3.hg38.vcf.gz added
30f128195ccc5d_small_exac_common_3.hg38.vcf.gz.tbi added
30f1281c85b5f7_gencode.v41.annotation.gtf added
30f128257dad4f_gencode.v42.annotation.gtf added
30f12824e2d533_gencode.vM30.annotation.gtf added
30f12881725b5_gencode.vM31.annotation.gtf added
30f128505b90be_gencode.v41.transcripts.fa added
30f128133bc1ec_gencode.v41.transcripts.fa.fai added
30f12854c6ab92_gencode.v42.transcripts.fa added
30f12824b0ee2_gencode.v42.transcripts.fa.fai added
30f128309a0376_gencode.vM30.pc_transcripts.fa added
30f12810acd06f_gencode.vM30.pc_transcripts.fa.fai added
30f128553c538a_gencode.vM31.pc_transcripts.fa added
30f128499a2b65_gencode.vM31.pc_transcripts.fa.fai added
30f1281642475c_GRCh38.primary_assembly.genome.fa.1.ht2 added
30f1284a0b7121_GRCh38.primary_assembly.genome.fa.2.ht2 added
30f12836844e94_GRCh38.primary_assembly.genome.fa.3.ht2 added
30f12852c264d7_GRCh38.primary_assembly.genome.fa.4.ht2 added
30f1287294da6e_GRCh38.primary_assembly.genome.fa.5.ht2 added
30f1284b5a2409_GRCh38.primary_assembly.genome.fa.6.ht2 added
30f128108124bd_GRCh38.primary_assembly.genome.fa.7.ht2 added
30f1281a66efc2_GRCh38.primary_assembly.genome.fa.8.ht2 added
30f12829a8be51_GRCh38_full_analysis_set_plus_decoy_hla.fa.fai added
30f12823c00a32_GRCh38_full_analysis_set_plus_decoy_hla.fa.amb added
30f12864d8a95c_GRCh38_full_analysis_set_plus_decoy_hla.fa.ann added
30f1285c58261f_GRCh38_full_analysis_set_plus_decoy_hla.fa.bwt added
30f1283b55b615_GRCh38_full_analysis_set_plus_decoy_hla.fa.pac added
30f128621df054_GRCh38_full_analysis_set_plus_decoy_hla.fa.sa added
30f128148b15c5_GRCh38_full_analysis_set_plus_decoy_hla.fa added
30f128286d9635_GRCh38.primary_assembly.genome.fa.fai added
30f12860a7317c_GRCh38.primary_assembly.genome.fa.amb added
30f12835db3765_GRCh38.primary_assembly.genome.fa.ann added
30f12841ca6293_GRCh38.primary_assembly.genome.fa.bwt added
30f1287d2ce773_GRCh38.primary_assembly.genome.fa.pac added
30f1285b58e4b5_GRCh38.primary_assembly.genome.fa.sa added
30f12866ad37c6_GRCh38.primary_assembly.genome.fa added
30f1285440d28_hs37d5.fa.fai added
30f1282bb47573_hs37d5.fa.amb added
30f12879e8f9b2_hs37d5.fa.ann added
30f1285a0ab8ba_hs37d5.fa.bwt added
30f1282dff8455_hs37d5.fa.pac added
30f1282a82fd28_hs37d5.fa.sa added
30f1286ab7892a_hs37d5.fa added
30f12833bd7e0_complete_ref_lens.bin added
30f128741d288d_ctable.bin added
30f128f9d086_ctg_offsets.bin added
30f1284d474901_duplicate_clusters.tsv added
30f1282aa17721_info.json added
30f12853bc355d_mphf.bin added
30f1283fdc2370_pos.bin added
30f12875fb9b2a_pre_indexing.log added
30f128643d5a1b_rank.bin added
30f1285a431332_ref_indexing.log added
30f1281fa4597c_refAccumLengths.bin added
30f1287fd644d_reflengths.bin added
30f1283f1bbc8e_refseq.bin added
30f1287bfc7f9b_seq.bin added
30f12843531a62_versionInfo.json added
30f1282139ace2_salmon_index added
30f12810879560_chrLength.txt added
30f1286bc0b098_chrName.txt added
30f1281e0de5e_chrNameLength.txt added
30f1284662ccc5_chrStart.txt added
30f1282d8b132b_exonGeTrInfo.tab added
30f1287f0dc5d1_exonInfo.tab added
30f12821bbb17a_geneInfo.tab added
30f12814384af1_Genome added
30f128451d2fa_genomeParameters.txt added
30f1284d7026ee_Log.out added
30f128e2144a3_SA added
30f1285e5c8bb4_SAindex added
30f1287b6fab43_sjdbInfo.txt added
30f12838a441cb_sjdbList.fromGTF.out.tab added
30f128491414de_sjdbList.out.tab added
30f1287eab8323_transcriptInfo.tab added
30f1282cc16a58_GRCh38.GENCODE.v42_100 added
30f1284a0de564_knownGene_hg38.sql added
30f1284bf2cc25_knownGene_hg38.txt added
30f1285762e179_refGene_hg38.sql added
30f1281dca1ac2_refGene_hg38.txt added
30f128bceef95_knownGene_mm39.sql added
30f1284d5e7ca4_knownGene_mm39.txt added
30f12820774dd_refGene_mm39.sql added
30f128661202c7_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/Rtmp3Rw23J/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
34.370 2.228 38.083
ReUseData.Rcheck/ReUseData-Ex.timings
| name | user | system | elapsed | |
| dataHub-class | 10.629 | 0.347 | 11.071 | |
| dataSearch | 1.993 | 0.031 | 2.025 | |
| dataUpdate | 0 | 0 | 0 | |
| getCloudData | 4.624 | 0.234 | 5.984 | |
| getData | 0 | 0 | 0 | |
| meta_data | 0.001 | 0.001 | 0.002 | |
| recipeHub-class | 0.245 | 0.000 | 0.246 | |
| recipeLoad | 2.506 | 0.183 | 2.691 | |
| recipeMake | 0.001 | 0.000 | 0.000 | |
| recipeSearch | 0.959 | 0.040 | 1.015 | |
| recipeUpdate | 0.001 | 0.000 | 0.000 | |