Qian Liu
| Snapshot Date: 2024-07-10 14:00 -0400 (Wed, 10 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 2024-07-12 17:42 -0400 (Fri, 12 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" | 4741 |
| 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: 2024-07-12 06:33:04 -0400 (Fri, 12 Jul 2024) |
| EndedAt: 2024-07-12 06:35:30 -0400 (Fri, 12 Jul 2024) |
| EllapsedTime: 146.2 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: aarch64-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 Ventura 13.6.6
* 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 7.003 0.757 7.786
* 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-arm64/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: aarch64-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...
63243969effb_GRCh38.primary_assembly.genome.fa.1.bt2 added
63245a0a652f_GRCh38.primary_assembly.genome.fa.2.bt2 added
632460791ed7_GRCh38.primary_assembly.genome.fa.3.bt2 added
63242fd7e6bc_GRCh38.primary_assembly.genome.fa.4.bt2 added
632476d592e_GRCh38.primary_assembly.genome.fa.rev.1.bt2 added
63241bf9ded1_GRCh38.primary_assembly.genome.fa.rev.2.bt2 added
6324319379b0_outfile.txt added
6324491a2b3d_GRCh37_to_GRCh38.chain added
6324550cd749_GRCh37_to_NCBI34.chain added
63243e0a253e_GRCh37_to_NCBI35.chain added
6324c132944_GRCh37_to_NCBI36.chain added
63243dfa358d_GRCh38_to_GRCh37.chain added
632475d1dbc4_GRCh38_to_NCBI34.chain added
632424b35d4a_GRCh38_to_NCBI35.chain added
63247bb1b818_GRCh38_to_NCBI36.chain added
632450ad6f19_NCBI34_to_GRCh37.chain added
63242a58fbb0_NCBI34_to_GRCh38.chain added
632437f3f588_NCBI35_to_GRCh37.chain added
6324717cd06a_NCBI35_to_GRCh38.chain added
63243957195b_NCBI36_to_GRCh37.chain added
6324541c2c6_NCBI36_to_GRCh38.chain added
6324205a57dc_GRCm38_to_NCBIM36.chain added
6324b3e3d1c_GRCm38_to_NCBIM37.chain added
6324231dff08_NCBIM36_to_GRCm38.chain added
6324652783b_NCBIM37_to_GRCm38.chain added
632410536cbb_1000G_omni2.5.b37.vcf.gz added
63245507715c_1000G_omni2.5.b37.vcf.gz.tbi added
63245ba37aa0_Mills_and_1000G_gold_standard.indels.b37.vcf.gz added
632449c7cd60_Mills_and_1000G_gold_standard.indels.b37.vcf.gz.tbi added
63245c7c7f77_1000G_omni2.5.hg38.vcf.gz added
632471948d10_1000G_omni2.5.hg38.vcf.gz.tbi added
63244fb94fb1_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz added
6324f1f165b_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz.tbi added
632441f4b81e_af-only-gnomad.raw.sites.vcf added
63242963db66_af-only-gnomad.raw.sites.vcf.idx added
63245ad91ac4_Mutect2-exome-panel.vcf.idx added
6324636c6874_Mutect2-WGS-panel-b37.vcf added
6324623dcaaa_Mutect2-WGS-panel-b37.vcf.idx added
632446c49149_small_exac_common_3.vcf added
6324131e73eb_small_exac_common_3.vcf.idx added
6324344c531b_1000g_pon.hg38.vcf.gz added
63247ee42c6f_1000g_pon.hg38.vcf.gz.tbi added
632436216c7e_af-only-gnomad.hg38.vcf.gz added
63244c59dff5_af-only-gnomad.hg38.vcf.gz.tbi added
6324207e74fc_small_exac_common_3.hg38.vcf.gz added
63244e325d0e_small_exac_common_3.hg38.vcf.gz.tbi added
63244c7b6a3d_gencode.v41.annotation.gtf added
63243a7bf205_gencode.v42.annotation.gtf added
63241f4e4442_gencode.vM30.annotation.gtf added
63244b63591c_gencode.vM31.annotation.gtf added
6324676f63ee_gencode.v41.transcripts.fa added
63244209d34f_gencode.v41.transcripts.fa.fai added
632413100968_gencode.v42.transcripts.fa added
63241d9949f_gencode.v42.transcripts.fa.fai added
632473ac53ab_gencode.vM30.pc_transcripts.fa added
632436a93ae1_gencode.vM30.pc_transcripts.fa.fai added
63242058a5d0_gencode.vM31.pc_transcripts.fa added
63241bee0b47_gencode.vM31.pc_transcripts.fa.fai added
6324292670a4_GRCh38.primary_assembly.genome.fa.1.ht2 added
63241aad3417_GRCh38.primary_assembly.genome.fa.2.ht2 added
63246136dfaf_GRCh38.primary_assembly.genome.fa.3.ht2 added
632459978c05_GRCh38.primary_assembly.genome.fa.4.ht2 added
63246c69ca36_GRCh38.primary_assembly.genome.fa.5.ht2 added
6324155ad6d5_GRCh38.primary_assembly.genome.fa.6.ht2 added
63247ece44e6_GRCh38.primary_assembly.genome.fa.7.ht2 added
6324180d9914_GRCh38.primary_assembly.genome.fa.8.ht2 added
632424bcfc62_GRCh38_full_analysis_set_plus_decoy_hla.fa.fai added
6324735d98c5_GRCh38_full_analysis_set_plus_decoy_hla.fa.amb added
63245d8e8af_GRCh38_full_analysis_set_plus_decoy_hla.fa.ann added
632463943c28_GRCh38_full_analysis_set_plus_decoy_hla.fa.bwt added
632418f9992b_GRCh38_full_analysis_set_plus_decoy_hla.fa.pac added
63242ab6e2dc_GRCh38_full_analysis_set_plus_decoy_hla.fa.sa added
63244ce7ef6c_GRCh38_full_analysis_set_plus_decoy_hla.fa added
6324f17c2e6_GRCh38.primary_assembly.genome.fa.fai added
632460fc91c7_GRCh38.primary_assembly.genome.fa.amb added
632465c6d18f_GRCh38.primary_assembly.genome.fa.ann added
63245fe8377c_GRCh38.primary_assembly.genome.fa.bwt added
6324692df15_GRCh38.primary_assembly.genome.fa.pac added
63241473df12_GRCh38.primary_assembly.genome.fa.sa added
6324433a213b_GRCh38.primary_assembly.genome.fa added
63241d5bcaf8_hs37d5.fa.fai added
6324756a6ed6_hs37d5.fa.amb added
63241e92dfd3_hs37d5.fa.ann added
63243ca4a553_hs37d5.fa.bwt added
63245d620b3f_hs37d5.fa.pac added
63244fd084fe_hs37d5.fa.sa added
63242cb68a2_hs37d5.fa added
63247842651c_complete_ref_lens.bin added
63244efc4ef2_ctable.bin added
632416a31a61_ctg_offsets.bin added
63242e18e1e3_duplicate_clusters.tsv added
6324639615b9_info.json added
6324126c57c3_mphf.bin added
63246f5cca8_pos.bin added
6324734f2d29_pre_indexing.log added
6324531e19e3_rank.bin added
63245d35b0b6_ref_indexing.log added
63246fe4ac88_refAccumLengths.bin added
6324dfb4e1c_reflengths.bin added
63246dc5176f_refseq.bin added
63242685b0b6_seq.bin added
63241314907c_versionInfo.json added
63242b19c6ad_salmon_index added
632429429df6_chrLength.txt added
6324549096a3_chrName.txt added
63246091d2b4_chrNameLength.txt added
63245a058f4_chrStart.txt added
6324622ffe0e_exonGeTrInfo.tab added
63243cd07b7e_exonInfo.tab added
63241b5bac63_geneInfo.tab added
63241f92a59d_Genome added
632454b6f69c_genomeParameters.txt added
632437f8a737_Log.out added
632425aa2896_SA added
6324464ea32b_SAindex added
632454ba801c_sjdbInfo.txt added
63242030d9b9_sjdbList.fromGTF.out.tab added
632467261131_sjdbList.out.tab added
63247432dcde_transcriptInfo.tab added
63243742ae6b_GRCh38.GENCODE.v42_100 added
63247ac90f24_knownGene_hg38.sql added
632426014376_knownGene_hg38.txt added
63241cf40b78_refGene_hg38.sql added
63245a1d0221_refGene_hg38.txt added
63242676f2bf_knownGene_mm39.sql added
63244b3aed53_knownGene_mm39.txt added
63249b30abb_refGene_mm39.sql added
632449857ff6_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/RtmpLe5lKe/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
23.948 2.895 28.392
ReUseData.Rcheck/ReUseData-Ex.timings
| name | user | system | elapsed | |
| dataHub-class | 7.003 | 0.757 | 7.786 | |
| dataSearch | 1.239 | 0.052 | 1.293 | |
| dataUpdate | 0 | 0 | 0 | |
| getCloudData | 2.710 | 0.142 | 4.571 | |
| getData | 0.001 | 0.001 | 0.000 | |
| meta_data | 0.001 | 0.000 | 0.001 | |
| recipeHub-class | 0.134 | 0.014 | 0.148 | |
| recipeLoad | 1.392 | 0.083 | 1.482 | |
| recipeMake | 0.001 | 0.001 | 0.001 | |
| recipeSearch | 0.589 | 0.035 | 0.634 | |
| recipeUpdate | 0.001 | 0.000 | 0.001 | |