Qian Liu
| Snapshot Date: 2024-07-22 14:00 -0400 (Mon, 22 Jul 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 2024-07-23 11:41 -0400 (Tue, 23 Jul 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4688 |
| palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" | 4280 |
| lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4455 |
| kjohnson3 | macOS 13.6.5 Ventura | arm64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4404 |
| 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 1700/2248 | 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 | | ||||||||
| palomino8 | Windows Server 2022 Datacenter / x64 | ... NOT SUPPORTED ... | ||||||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson3 | macOS 13.6.5 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: 1.5.0 |
| 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_1.5.0.tar.gz |
| StartedAt: 2024-07-22 23:44:56 -0400 (Mon, 22 Jul 2024) |
| EndedAt: 2024-07-22 23:47:50 -0400 (Mon, 22 Jul 2024) |
| EllapsedTime: 174.0 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_1.5.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.20-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 12.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* 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 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 8.196 0.967 9.384
getCloudData 3.325 0.194 10.585
* 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-3.20-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...
a2703649f4ed_GRCh38.primary_assembly.genome.fa.1.bt2 added
a270316f0f73_GRCh38.primary_assembly.genome.fa.2.bt2 added
a270725f605f_GRCh38.primary_assembly.genome.fa.3.bt2 added
a27053b037a2_GRCh38.primary_assembly.genome.fa.4.bt2 added
a2705614979a_GRCh38.primary_assembly.genome.fa.rev.1.bt2 added
a27061ed2b9c_GRCh38.primary_assembly.genome.fa.rev.2.bt2 added
a27019ca40fe_outfile.txt added
a2702d70f0ec_GRCh37_to_GRCh38.chain added
a27051d92d42_GRCh37_to_NCBI34.chain added
a27092a7209_GRCh37_to_NCBI35.chain added
a27041a4b192_GRCh37_to_NCBI36.chain added
a270238609e9_GRCh38_to_GRCh37.chain added
a27034f4b237_GRCh38_to_NCBI34.chain added
a2702ce0540a_GRCh38_to_NCBI35.chain added
a2703bad738a_GRCh38_to_NCBI36.chain added
a270787c87a1_NCBI34_to_GRCh37.chain added
a27037ac98d3_NCBI34_to_GRCh38.chain added
a27024656133_NCBI35_to_GRCh37.chain added
a2707bd06def_NCBI35_to_GRCh38.chain added
a27030e1a56a_NCBI36_to_GRCh37.chain added
a2702e32eb38_NCBI36_to_GRCh38.chain added
a27010f0c13a_GRCm38_to_NCBIM36.chain added
a2702e1dcf86_GRCm38_to_NCBIM37.chain added
a27027237e11_NCBIM36_to_GRCm38.chain added
a270b29a22a_NCBIM37_to_GRCm38.chain added
a2705a55791f_1000G_omni2.5.b37.vcf.gz added
a2702183108e_1000G_omni2.5.b37.vcf.gz.tbi added
a27023b3ebd2_Mills_and_1000G_gold_standard.indels.b37.vcf.gz added
a270793f3a4d_Mills_and_1000G_gold_standard.indels.b37.vcf.gz.tbi added
a270260cd36b_1000G_omni2.5.hg38.vcf.gz added
a270140c2951_1000G_omni2.5.hg38.vcf.gz.tbi added
a2702a6c8f1f_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz added
a2703d2851fb_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz.tbi added
a270221e551b_af-only-gnomad.raw.sites.vcf added
a2707565711c_af-only-gnomad.raw.sites.vcf.idx added
a27056e5217a_Mutect2-exome-panel.vcf.idx added
a2705cf8fd27_Mutect2-WGS-panel-b37.vcf added
a2705eb43b20_Mutect2-WGS-panel-b37.vcf.idx added
a270a95e273_small_exac_common_3.vcf added
a2707645f172_small_exac_common_3.vcf.idx added
a27069eeb007_1000g_pon.hg38.vcf.gz added
a2703566d1e6_1000g_pon.hg38.vcf.gz.tbi added
a270715e6e6d_af-only-gnomad.hg38.vcf.gz added
a2706ea3f040_af-only-gnomad.hg38.vcf.gz.tbi added
a2704cf2327f_small_exac_common_3.hg38.vcf.gz added
a27030d15750_small_exac_common_3.hg38.vcf.gz.tbi added
a2707fbb5e39_gencode.v41.annotation.gtf added
a270662731b2_gencode.v42.annotation.gtf added
a270172fd183_gencode.vM30.annotation.gtf added
a2704463fb59_gencode.vM31.annotation.gtf added
a270ab323_gencode.v41.transcripts.fa added
a2703e76beda_gencode.v41.transcripts.fa.fai added
a27065ebfa3f_gencode.v42.transcripts.fa added
a270677a725f_gencode.v42.transcripts.fa.fai added
a27017eaf00c_gencode.vM30.pc_transcripts.fa added
a2704135b018_gencode.vM30.pc_transcripts.fa.fai added
a2702bbc191a_gencode.vM31.pc_transcripts.fa added
a2704a141064_gencode.vM31.pc_transcripts.fa.fai added
a2706b403b3a_GRCh38.primary_assembly.genome.fa.1.ht2 added
a27045f093d8_GRCh38.primary_assembly.genome.fa.2.ht2 added
a270357a6dc7_GRCh38.primary_assembly.genome.fa.3.ht2 added
a27078bd3f3e_GRCh38.primary_assembly.genome.fa.4.ht2 added
a27050833d5f_GRCh38.primary_assembly.genome.fa.5.ht2 added
a27058325144_GRCh38.primary_assembly.genome.fa.6.ht2 added
a2704f757498_GRCh38.primary_assembly.genome.fa.7.ht2 added
a2702839cfe9_GRCh38.primary_assembly.genome.fa.8.ht2 added
a2706b80dea0_GRCh38_full_analysis_set_plus_decoy_hla.fa.fai added
a27059981183_GRCh38_full_analysis_set_plus_decoy_hla.fa.amb added
a270ea5dd69_GRCh38_full_analysis_set_plus_decoy_hla.fa.ann added
a2702b6b2002_GRCh38_full_analysis_set_plus_decoy_hla.fa.bwt added
a2706027993_GRCh38_full_analysis_set_plus_decoy_hla.fa.pac added
a270c7ba4fa_GRCh38_full_analysis_set_plus_decoy_hla.fa.sa added
a27098c1f7d_GRCh38_full_analysis_set_plus_decoy_hla.fa added
a2704e674c70_GRCh38.primary_assembly.genome.fa.fai added
a2705fcb7546_GRCh38.primary_assembly.genome.fa.amb added
a270268077cc_GRCh38.primary_assembly.genome.fa.ann added
a2703c3905d3_GRCh38.primary_assembly.genome.fa.bwt added
a27043ad7e88_GRCh38.primary_assembly.genome.fa.pac added
a270334e356e_GRCh38.primary_assembly.genome.fa.sa added
a2705395e312_GRCh38.primary_assembly.genome.fa added
a270156edd9d_hs37d5.fa.fai added
a27021977969_hs37d5.fa.amb added
a2705fa3edb9_hs37d5.fa.ann added
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a27026944fc_hs37d5.fa.pac added
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a270178b331b_complete_ref_lens.bin added
a27033c83db0_ctable.bin added
a2701f4a085f_ctg_offsets.bin added
a270356ba505_duplicate_clusters.tsv added
a2702e1f06a9_info.json added
a27076ee58e6_mphf.bin added
a2701a0ea10a_pos.bin added
a270366ea4e3_pre_indexing.log added
a2701a0b4f00_rank.bin added
a2705c6f965b_ref_indexing.log added
a27021f85fc6_refAccumLengths.bin added
a2703957d196_reflengths.bin added
a2703480ec43_refseq.bin added
a2707c173da2_seq.bin added
a27059cf9653_versionInfo.json added
a2704b965135_salmon_index added
a27079ad9557_chrLength.txt added
a2707327c129_chrName.txt added
a27036faa5cf_chrNameLength.txt added
a27019bd53c_chrStart.txt added
a2701dcc56f7_exonGeTrInfo.tab added
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a2707f773ebf_geneInfo.tab added
a2706db8aef9_Genome added
a27077e795b5_genomeParameters.txt added
a270515db93_Log.out added
a2705e029280_SA added
a2707ae041b7_SAindex added
a27018fa9467_sjdbInfo.txt added
a2706b250300_sjdbList.fromGTF.out.tab added
a2704ae82bf4_sjdbList.out.tab added
a270509dc697_transcriptInfo.tab added
a27026590cda_GRCh38.GENCODE.v42_100 added
a270205acfe1_knownGene_hg38.sql added
a2702a05cd5f_knownGene_hg38.txt added
a27062ee2d86_refGene_hg38.sql added
a2702eeeb28_refGene_hg38.txt added
a27013909099_knownGene_mm39.sql added
a270780536d7_knownGene_mm39.txt added
a2701e539ad0_refGene_mm39.sql added
a2702d8dd3e_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/RtmpRXVedD/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
28.268 3.679 33.389
ReUseData.Rcheck/ReUseData-Ex.timings
| name | user | system | elapsed | |
| dataHub-class | 8.196 | 0.967 | 9.384 | |
| dataSearch | 1.527 | 0.068 | 1.610 | |
| dataUpdate | 0.000 | 0.000 | 0.001 | |
| getCloudData | 3.325 | 0.194 | 10.585 | |
| getData | 0 | 0 | 0 | |
| meta_data | 0.000 | 0.000 | 0.001 | |
| recipeHub-class | 0.165 | 0.015 | 0.185 | |
| recipeLoad | 1.859 | 0.125 | 2.018 | |
| recipeMake | 0.001 | 0.001 | 0.002 | |
| recipeSearch | 0.791 | 0.052 | 0.852 | |
| recipeUpdate | 0 | 0 | 0 | |