Qian Liu
| Snapshot Date: 2024-04-15 14:05:01 -0400 (Mon, 15 Apr 2024) |
| git_url: https://git.bioconductor.org/packages/ReUseData |
| git_branch: RELEASE_3_18 |
| git_last_commit: 836e03f |
| git_last_commit_date: 2023-12-08 16:02:19 -0400 (Fri, 08 Dec 2023) |
| Back to Multiple platform build/check report for BioC 3.18: simplified long |
|
This page was generated on 2024-04-17 11:38:08 -0400 (Wed, 17 Apr 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.3.3 (2024-02-29) -- "Angel Food Cake" | 4676 |
| palomino4 | Windows Server 2022 Datacenter | x64 | 4.3.3 (2024-02-29 ucrt) -- "Angel Food Cake" | 4414 |
| merida1 | macOS 12.7.1 Monterey | x86_64 | 4.3.3 (2024-02-29) -- "Angel Food Cake" | 4437 |
| 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 1725/2266 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| ReUseData 1.2.2 (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 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson1 | macOS 13.6.1 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: 1.2.2 |
| 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_1.2.2.tar.gz |
| StartedAt: 2024-04-16 07:42:06 -0400 (Tue, 16 Apr 2024) |
| EndedAt: 2024-04-16 07:46:31 -0400 (Tue, 16 Apr 2024) |
| EllapsedTime: 265.5 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_1.2.2.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.18-bioc/meat/ReUseData.Rcheck’
* using R version 4.3.3 (2024-02-29)
* using platform: x86_64-apple-darwin20 (64-bit)
* 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 ‘1.2.2’
* 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 R 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 11.979 1.258 14.338
getCloudData 4.379 0.201 5.694
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’
OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... 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-3.18-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/4.3-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 4.3.3 (2024-02-29) -- "Angel Food Cake"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20 (64-bit)
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...
c501740c7957_GRCh38.primary_assembly.genome.fa.1.bt2 added
c5015ef27a46_GRCh38.primary_assembly.genome.fa.2.bt2 added
c501139ba5d_GRCh38.primary_assembly.genome.fa.3.bt2 added
c50174fa304b_GRCh38.primary_assembly.genome.fa.4.bt2 added
c5015578c7ec_GRCh38.primary_assembly.genome.fa.rev.1.bt2 added
c5016c8d82ca_GRCh38.primary_assembly.genome.fa.rev.2.bt2 added
c5013e85d373_outfile.txt added
c50143fd4316_GRCh37_to_GRCh38.chain added
c501283f7c39_GRCh37_to_NCBI34.chain added
c5015ff496d3_GRCh37_to_NCBI35.chain added
c50132da27dc_GRCh37_to_NCBI36.chain added
c501106ef699_GRCh38_to_GRCh37.chain added
c50164ffbf3c_GRCh38_to_NCBI34.chain added
c50152642ff1_GRCh38_to_NCBI35.chain added
c5012f87a179_GRCh38_to_NCBI36.chain added
c501717a274f_NCBI34_to_GRCh37.chain added
c501aaaedbd_NCBI34_to_GRCh38.chain added
c5015bde18c3_NCBI35_to_GRCh37.chain added
c501522bd953_NCBI35_to_GRCh38.chain added
c5013cc9024a_NCBI36_to_GRCh37.chain added
c50130b56773_NCBI36_to_GRCh38.chain added
c501559ac800_GRCm38_to_NCBIM36.chain added
c50124c0a3e8_GRCm38_to_NCBIM37.chain added
c5016348e731_NCBIM36_to_GRCm38.chain added
c501474274e3_NCBIM37_to_GRCm38.chain added
c5015c0807a1_1000G_omni2.5.b37.vcf.gz added
c501132d0a3b_1000G_omni2.5.b37.vcf.gz.tbi added
c50171fab152_Mills_and_1000G_gold_standard.indels.b37.vcf.gz added
c50118fb8f4_Mills_and_1000G_gold_standard.indels.b37.vcf.gz.tbi added
c5012b79bf9_1000G_omni2.5.hg38.vcf.gz added
c5016460f9d3_1000G_omni2.5.hg38.vcf.gz.tbi added
c5011ab1bf21_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz added
c501b7b1d38_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz.tbi added
c5013fbb4d6b_af-only-gnomad.raw.sites.vcf added
c50121d7cc7d_af-only-gnomad.raw.sites.vcf.idx added
c5015eb233e6_Mutect2-exome-panel.vcf.idx added
c50156d719c_Mutect2-WGS-panel-b37.vcf added
c501543dbb8c_Mutect2-WGS-panel-b37.vcf.idx added
c50120e40f89_small_exac_common_3.vcf added
c5015cb7fc3d_small_exac_common_3.vcf.idx added
c50133113859_1000g_pon.hg38.vcf.gz added
c5012f8a7540_1000g_pon.hg38.vcf.gz.tbi added
c5012b17d522_af-only-gnomad.hg38.vcf.gz added
c50129a9c148_af-only-gnomad.hg38.vcf.gz.tbi added
c50147d07356_small_exac_common_3.hg38.vcf.gz added
c501464437ef_small_exac_common_3.hg38.vcf.gz.tbi added
c50128b44ff3_gencode.v41.annotation.gtf added
c50155ecef65_gencode.v42.annotation.gtf added
c5013658fbf5_gencode.vM30.annotation.gtf added
c501c05adb3_gencode.vM31.annotation.gtf added
c50148cec8ef_gencode.v41.transcripts.fa added
c5017fe9e840_gencode.v41.transcripts.fa.fai added
c501558f035b_gencode.v42.transcripts.fa added
c5012025773f_gencode.v42.transcripts.fa.fai added
c5017bb7d995_gencode.vM30.pc_transcripts.fa added
c501632e04a7_gencode.vM30.pc_transcripts.fa.fai added
c5016233a2cf_gencode.vM31.pc_transcripts.fa added
c5012c05f667_gencode.vM31.pc_transcripts.fa.fai added
c5013b73fac5_GRCh38.primary_assembly.genome.fa.1.ht2 added
c5013b54ba01_GRCh38.primary_assembly.genome.fa.2.ht2 added
c501377fb615_GRCh38.primary_assembly.genome.fa.3.ht2 added
c501218b392a_GRCh38.primary_assembly.genome.fa.4.ht2 added
c5013b56059a_GRCh38.primary_assembly.genome.fa.5.ht2 added
c501c89dfe5_GRCh38.primary_assembly.genome.fa.6.ht2 added
c5012fca39d1_GRCh38.primary_assembly.genome.fa.7.ht2 added
c501599e0da_GRCh38.primary_assembly.genome.fa.8.ht2 added
c50139790b15_GRCh38_full_analysis_set_plus_decoy_hla.fa.fai added
c50139c6ad2d_GRCh38_full_analysis_set_plus_decoy_hla.fa.amb added
c501229382fd_GRCh38_full_analysis_set_plus_decoy_hla.fa.ann added
c50127cc1c7_GRCh38_full_analysis_set_plus_decoy_hla.fa.bwt added
c5014c95f117_GRCh38_full_analysis_set_plus_decoy_hla.fa.pac added
c5018074449_GRCh38_full_analysis_set_plus_decoy_hla.fa.sa added
c501151418bd_GRCh38_full_analysis_set_plus_decoy_hla.fa added
c5015a642b1a_GRCh38.primary_assembly.genome.fa.fai added
c5016649e652_GRCh38.primary_assembly.genome.fa.amb added
c5017db045f4_GRCh38.primary_assembly.genome.fa.ann added
c5013fc0d6a3_GRCh38.primary_assembly.genome.fa.bwt added
c501d4b8808_GRCh38.primary_assembly.genome.fa.pac added
c50159cfcc09_GRCh38.primary_assembly.genome.fa.sa added
c501595c90ef_GRCh38.primary_assembly.genome.fa added
c5014c2f68be_hs37d5.fa.fai added
c5013c85b905_hs37d5.fa.amb added
c5016f36164d_hs37d5.fa.ann added
c50147f25245_hs37d5.fa.bwt added
c50175f754e9_hs37d5.fa.pac added
c50140e7c980_hs37d5.fa.sa added
c501315e13ca_hs37d5.fa added
c50117654c18_complete_ref_lens.bin added
c5017b66c7a7_ctable.bin added
c50118bde43c_ctg_offsets.bin added
c5015ad32bd4_duplicate_clusters.tsv added
c5015de299e1_info.json added
c50147e4b2ee_mphf.bin added
c501779f4c21_pos.bin added
c5017b3f47e1_pre_indexing.log added
c501778843fd_rank.bin added
c5011327d45a_ref_indexing.log added
c5011be66a89_refAccumLengths.bin added
c501345c56ae_reflengths.bin added
c5011a3ed45d_refseq.bin added
c50112e83321_seq.bin added
c5014a74c539_versionInfo.json added
c5013840475f_salmon_index added
c50140dcad3_chrLength.txt added
c501257ee4b9_chrName.txt added
c5012dda40ea_chrNameLength.txt added
c50153dbda2a_chrStart.txt added
c5016d02669_exonGeTrInfo.tab added
c5014b89bafd_exonInfo.tab added
c5013f535ec9_geneInfo.tab added
c5017a73fe99_Genome added
c50155502d9d_genomeParameters.txt added
c5012e2ca2d_Log.out added
c501774751d5_SA added
c5016b4db420_SAindex added
c5013a6cd7e9_sjdbInfo.txt added
c5013fd31ff6_sjdbList.fromGTF.out.tab added
c5013dd77036_sjdbList.out.tab added
c501b0808f2_transcriptInfo.tab added
c5013c834d86_GRCh38.GENCODE.v42_100 added
c5015056b773_knownGene_hg38.sql added
c5016d260839_knownGene_hg38.txt added
c5015be60e2a_refGene_hg38.sql added
c5015cac1688_refGene_hg38.txt added
c50125fb6a40_knownGene_mm39.sql added
c5011cfca33b_knownGene_mm39.txt added
c501e40855b_refGene_mm39.sql added
c5012df320ac_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/RtmpbPSQli/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
41.735 5.029 49.618
ReUseData.Rcheck/ReUseData-Ex.timings
| name | user | system | elapsed | |
| dataHub-class | 11.979 | 1.258 | 14.338 | |
| dataSearch | 2.361 | 0.080 | 2.682 | |
| dataUpdate | 0.000 | 0.001 | 0.002 | |
| getCloudData | 4.379 | 0.201 | 5.694 | |
| getData | 0.000 | 0.001 | 0.001 | |
| meta_data | 0.002 | 0.000 | 0.002 | |
| recipeHub-class | 0.244 | 0.020 | 0.267 | |
| recipeLoad | 2.675 | 0.152 | 2.926 | |
| recipeMake | 0.000 | 0.001 | 0.001 | |
| recipeSearch | 1.172 | 0.068 | 1.256 | |
| recipeUpdate | 0.001 | 0.000 | 0.001 | |