Qian Liu
| Snapshot Date: 2024-07-07 14:00 -0400 (Sun, 07 Jul 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 2024-07-09 17:42 -0400 (Tue, 09 Jul 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4709 |
| palomino7 | Windows Server 2022 Datacenter | x64 | 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" | 4483 |
| merida1 | macOS 12.7.4 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4512 |
| kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4461 |
| 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 | | ||||||||
| palomino7 | 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 | 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: 2024-07-08 10:26:00 -0400 (Mon, 08 Jul 2024) |
| EndedAt: 2024-07-08 10:31:13 -0400 (Mon, 08 Jul 2024) |
| EllapsedTime: 312.4 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 4.4.1 (2024-06-14)
* 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 12.7.4
* 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 13.582 1.316 16.331
getCloudData 5.011 0.220 6.778
* 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 4.4.1 (2024-06-14) -- "Race for Your Life"
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...
c50555db0627_GRCh38.primary_assembly.genome.fa.1.bt2 added
c5051e71167a_GRCh38.primary_assembly.genome.fa.2.bt2 added
c505127ab333_GRCh38.primary_assembly.genome.fa.3.bt2 added
c505358ae2bf_GRCh38.primary_assembly.genome.fa.4.bt2 added
c505312c850f_GRCh38.primary_assembly.genome.fa.rev.1.bt2 added
c50561d3b501_GRCh38.primary_assembly.genome.fa.rev.2.bt2 added
c505121086d4_outfile.txt added
c5057b03d18f_GRCh37_to_GRCh38.chain added
c50537b34261_GRCh37_to_NCBI34.chain added
c50559cb0ad8_GRCh37_to_NCBI35.chain added
c505213518f6_GRCh37_to_NCBI36.chain added
c50524f9cf82_GRCh38_to_GRCh37.chain added
c505ca672c5_GRCh38_to_NCBI34.chain added
c5053b8ea00_GRCh38_to_NCBI35.chain added
c505610aa7e8_GRCh38_to_NCBI36.chain added
c505295a21e_NCBI34_to_GRCh37.chain added
c5052dc660e5_NCBI34_to_GRCh38.chain added
c5053b0371dd_NCBI35_to_GRCh37.chain added
c5055f28826f_NCBI35_to_GRCh38.chain added
c5055c8b7637_NCBI36_to_GRCh37.chain added
c50547fe4458_NCBI36_to_GRCh38.chain added
c5056391255_GRCm38_to_NCBIM36.chain added
c505ce28da4_GRCm38_to_NCBIM37.chain added
c5056dc11097_NCBIM36_to_GRCm38.chain added
c5051e2861cc_NCBIM37_to_GRCm38.chain added
c5056d2ca78b_1000G_omni2.5.b37.vcf.gz added
c505eabceac_1000G_omni2.5.b37.vcf.gz.tbi added
c505318d85ba_Mills_and_1000G_gold_standard.indels.b37.vcf.gz added
c50542468fc0_Mills_and_1000G_gold_standard.indels.b37.vcf.gz.tbi added
c5052687a83e_1000G_omni2.5.hg38.vcf.gz added
c50514369235_1000G_omni2.5.hg38.vcf.gz.tbi added
c505ab8dff1_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz added
c5056f764cb6_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz.tbi added
c5053fa679e5_af-only-gnomad.raw.sites.vcf added
c5054a8cca08_af-only-gnomad.raw.sites.vcf.idx added
c5056123f974_Mutect2-exome-panel.vcf.idx added
c505ce607f_Mutect2-WGS-panel-b37.vcf added
c5056d213242_Mutect2-WGS-panel-b37.vcf.idx added
c5051e6ac307_small_exac_common_3.vcf added
c505732a102a_small_exac_common_3.vcf.idx added
c5054e8b7077_1000g_pon.hg38.vcf.gz added
c5052484bcea_1000g_pon.hg38.vcf.gz.tbi added
c50568eb961_af-only-gnomad.hg38.vcf.gz added
c50542c92a4_af-only-gnomad.hg38.vcf.gz.tbi added
c505a4f4f20_small_exac_common_3.hg38.vcf.gz added
c5055cd3c329_small_exac_common_3.hg38.vcf.gz.tbi added
c50552b1e85b_gencode.v41.annotation.gtf added
c5051e0dd8c7_gencode.v42.annotation.gtf added
c5051f13003b_gencode.vM30.annotation.gtf added
c5051874316d_gencode.vM31.annotation.gtf added
c5057458f7a5_gencode.v41.transcripts.fa added
c5057ceaad4f_gencode.v41.transcripts.fa.fai added
c50513185d9b_gencode.v42.transcripts.fa added
c50524a974e8_gencode.v42.transcripts.fa.fai added
c505713a3e25_gencode.vM30.pc_transcripts.fa added
c50526c62936_gencode.vM30.pc_transcripts.fa.fai added
c5051bbbac1d_gencode.vM31.pc_transcripts.fa added
c5053e20b224_gencode.vM31.pc_transcripts.fa.fai added
c505548f7959_GRCh38.primary_assembly.genome.fa.1.ht2 added
c5051767ed6e_GRCh38.primary_assembly.genome.fa.2.ht2 added
c5052814dcc3_GRCh38.primary_assembly.genome.fa.3.ht2 added
c50571a99ac3_GRCh38.primary_assembly.genome.fa.4.ht2 added
c50535efb281_GRCh38.primary_assembly.genome.fa.5.ht2 added
c505bb04ed1_GRCh38.primary_assembly.genome.fa.6.ht2 added
c50564068155_GRCh38.primary_assembly.genome.fa.7.ht2 added
c505671526c0_GRCh38.primary_assembly.genome.fa.8.ht2 added
c5051da33c1f_GRCh38_full_analysis_set_plus_decoy_hla.fa.fai added
c50547c0266c_GRCh38_full_analysis_set_plus_decoy_hla.fa.amb added
c505181aa141_GRCh38_full_analysis_set_plus_decoy_hla.fa.ann added
c5057c50bec3_GRCh38_full_analysis_set_plus_decoy_hla.fa.bwt added
c505191c33f8_GRCh38_full_analysis_set_plus_decoy_hla.fa.pac added
c505a97eba9_GRCh38_full_analysis_set_plus_decoy_hla.fa.sa added
c5057bf0a9ad_GRCh38_full_analysis_set_plus_decoy_hla.fa added
c5057513dc6c_GRCh38.primary_assembly.genome.fa.fai added
c5056aec7280_GRCh38.primary_assembly.genome.fa.amb added
c50549516857_GRCh38.primary_assembly.genome.fa.ann added
c5057f994d5b_GRCh38.primary_assembly.genome.fa.bwt added
c50529a5d2cf_GRCh38.primary_assembly.genome.fa.pac added
c50545b32965_GRCh38.primary_assembly.genome.fa.sa added
c5057562c9a2_GRCh38.primary_assembly.genome.fa added
c50528a3e6e3_hs37d5.fa.fai added
c505208b55ed_hs37d5.fa.amb added
c5051bb64b4c_hs37d5.fa.ann added
c5055d0978ca_hs37d5.fa.bwt added
c50518d9457e_hs37d5.fa.pac added
c50560615ff0_hs37d5.fa.sa added
c50518e1b6ff_hs37d5.fa added
c505ab52c1c_complete_ref_lens.bin added
c5057c62e7c1_ctable.bin added
c505415d6fb3_ctg_offsets.bin added
c5055d50724b_duplicate_clusters.tsv added
c5054c7fc9c9_info.json added
c5055998d25b_mphf.bin added
c505401a8251_pos.bin added
c505c61b4b8_pre_indexing.log added
c505629fa261_rank.bin added
c5055e5dc0dc_ref_indexing.log added
c5055d20dbea_refAccumLengths.bin added
c50518460f6a_reflengths.bin added
c5051f9e0499_refseq.bin added
c5053f3fe906_seq.bin added
c5057cdba95a_versionInfo.json added
c505394b93c0_salmon_index added
c50510d13fa3_chrLength.txt added
c50519a8eef5_chrName.txt added
c50521e023fc_chrNameLength.txt added
c50525a86c4_chrStart.txt added
c505545af11_exonGeTrInfo.tab added
c50521e887cb_exonInfo.tab added
c505292b31d1_geneInfo.tab added
c50552d3a574_Genome added
c50545138d27_genomeParameters.txt added
c5056981edf_Log.out added
c5056d12c5da_SA added
c5056b7ba327_SAindex added
c5052148c92_sjdbInfo.txt added
c5051318c64f_sjdbList.fromGTF.out.tab added
c5053f837654_sjdbList.out.tab added
c5054fcda55f_transcriptInfo.tab added
c505462428e7_GRCh38.GENCODE.v42_100 added
c5056ff979aa_knownGene_hg38.sql added
c50563a2c154_knownGene_hg38.txt added
c5055242a4e6_refGene_hg38.sql added
c5051558223b_refGene_hg38.txt added
c5054d2f5a6f_knownGene_mm39.sql added
c5055fda54ff_knownGene_mm39.txt added
c50577026282_refGene_mm39.sql added
c5053d9181d8_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/RtmpvF6Na9/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
45.395 5.641 61.372
ReUseData.Rcheck/ReUseData-Ex.timings
| name | user | system | elapsed | |
| dataHub-class | 13.582 | 1.316 | 16.331 | |
| dataSearch | 2.689 | 0.085 | 3.252 | |
| dataUpdate | 0.001 | 0.002 | 0.002 | |
| getCloudData | 5.011 | 0.220 | 6.778 | |
| getData | 0.000 | 0.001 | 0.004 | |
| meta_data | 0.002 | 0.000 | 0.002 | |
| recipeHub-class | 0.290 | 0.021 | 0.365 | |
| recipeLoad | 3.021 | 0.152 | 3.630 | |
| recipeMake | 0.001 | 0.002 | 0.002 | |
| recipeSearch | 1.245 | 0.056 | 1.469 | |
| recipeUpdate | 0.000 | 0.001 | 0.000 | |