Qian Liu
| Snapshot Date: 2024-06-26 14:00 -0400 (Wed, 26 Jun 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 2024-06-28 17:45 -0400 (Fri, 28 Jun 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4760 |
| palomino3 | Windows Server 2022 Datacenter | x64 | 4.4.0 (2024-04-24 ucrt) -- "Puppy Cup" | 4494 |
| merida1 | macOS 12.7.4 Monterey | x86_64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4508 |
| kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4466 |
| palomino7 | Windows Server 2022 Datacenter | x64 | 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" | 4362 |
| 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 | | ||||||||
| palomino3 | 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 | | ||||||||
| palomino7 | Windows Server 2022 Datacenter / x64 | ... NOT SUPPORTED ... | ||||||||||||
|
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: 2024-06-28 07:01:13 -0400 (Fri, 28 Jun 2024) |
| EndedAt: 2024-06-28 07:03:40 -0400 (Fri, 28 Jun 2024) |
| EllapsedTime: 146.7 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 4.4.0 (2024-04-24)
* 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 6.965 0.753 7.754
* 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 4.4.0 (2024-04-24) -- "Puppy Cup"
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...
161cf4222d41a_GRCh38.primary_assembly.genome.fa.1.bt2 added
161cf7c9318e1_GRCh38.primary_assembly.genome.fa.2.bt2 added
161cf1d469bac_GRCh38.primary_assembly.genome.fa.3.bt2 added
161cf6964838_GRCh38.primary_assembly.genome.fa.4.bt2 added
161cf745f57e8_GRCh38.primary_assembly.genome.fa.rev.1.bt2 added
161cf1f847c08_GRCh38.primary_assembly.genome.fa.rev.2.bt2 added
161cf32eb0162_outfile.txt added
161cf62a7e30b_GRCh37_to_GRCh38.chain added
161cf7c2b19c6_GRCh37_to_NCBI34.chain added
161cf71a955d9_GRCh37_to_NCBI35.chain added
161cf244353db_GRCh37_to_NCBI36.chain added
161cf40366176_GRCh38_to_GRCh37.chain added
161cf3238aae9_GRCh38_to_NCBI34.chain added
161cf265cc0c1_GRCh38_to_NCBI35.chain added
161cf1372d294_GRCh38_to_NCBI36.chain added
161cf575efc85_NCBI34_to_GRCh37.chain added
161cf1d14ac93_NCBI34_to_GRCh38.chain added
161cf384df5cf_NCBI35_to_GRCh37.chain added
161cf64505ea_NCBI35_to_GRCh38.chain added
161cf1d8748dd_NCBI36_to_GRCh37.chain added
161cf1cc0b450_NCBI36_to_GRCh38.chain added
161cf2f7dfeef_GRCm38_to_NCBIM36.chain added
161cf78ec1544_GRCm38_to_NCBIM37.chain added
161cf53686161_NCBIM36_to_GRCm38.chain added
161cf69d1520e_NCBIM37_to_GRCm38.chain added
161cf2d624b68_1000G_omni2.5.b37.vcf.gz added
161cf1044b01f_1000G_omni2.5.b37.vcf.gz.tbi added
161cfd86cb91_Mills_and_1000G_gold_standard.indels.b37.vcf.gz added
161cfc9ea387_Mills_and_1000G_gold_standard.indels.b37.vcf.gz.tbi added
161cf301fa8a_1000G_omni2.5.hg38.vcf.gz added
161cf76e77b90_1000G_omni2.5.hg38.vcf.gz.tbi added
161cf576167ec_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz added
161cf3bede3c5_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz.tbi added
161cf7f04b93f_af-only-gnomad.raw.sites.vcf added
161cff1e183f_af-only-gnomad.raw.sites.vcf.idx added
161cfc9d7da_Mutect2-exome-panel.vcf.idx added
161cf437a299d_Mutect2-WGS-panel-b37.vcf added
161cf9422507_Mutect2-WGS-panel-b37.vcf.idx added
161cf558cf350_small_exac_common_3.vcf added
161cf18ba3511_small_exac_common_3.vcf.idx added
161cf68f1fbc5_1000g_pon.hg38.vcf.gz added
161cf66c87856_1000g_pon.hg38.vcf.gz.tbi added
161cf73548ad1_af-only-gnomad.hg38.vcf.gz added
161cf3365da7e_af-only-gnomad.hg38.vcf.gz.tbi added
161cf63eba08e_small_exac_common_3.hg38.vcf.gz added
161cf279fde2_small_exac_common_3.hg38.vcf.gz.tbi added
161cf170b01b3_gencode.v41.annotation.gtf added
161cf539c9a96_gencode.v42.annotation.gtf added
161cf4e6918bc_gencode.vM30.annotation.gtf added
161cf55d706db_gencode.vM31.annotation.gtf added
161cf18033fe4_gencode.v41.transcripts.fa added
161cf7d579e0c_gencode.v41.transcripts.fa.fai added
161cf349661e_gencode.v42.transcripts.fa added
161cf47cf3d41_gencode.v42.transcripts.fa.fai added
161cf76be9b3b_gencode.vM30.pc_transcripts.fa added
161cf5bc17b64_gencode.vM30.pc_transcripts.fa.fai added
161cf7b8c114b_gencode.vM31.pc_transcripts.fa added
161cf28c3924b_gencode.vM31.pc_transcripts.fa.fai added
161cf3fb98ed5_GRCh38.primary_assembly.genome.fa.1.ht2 added
161cf2f5062a2_GRCh38.primary_assembly.genome.fa.2.ht2 added
161cf467b91f2_GRCh38.primary_assembly.genome.fa.3.ht2 added
161cf5aaacb04_GRCh38.primary_assembly.genome.fa.4.ht2 added
161cf2f6a21d_GRCh38.primary_assembly.genome.fa.5.ht2 added
161cfe0d1f70_GRCh38.primary_assembly.genome.fa.6.ht2 added
161cf7f8af944_GRCh38.primary_assembly.genome.fa.7.ht2 added
161cf7cf320c6_GRCh38.primary_assembly.genome.fa.8.ht2 added
161cf3dece740_GRCh38_full_analysis_set_plus_decoy_hla.fa.fai added
161cfc423a83_GRCh38_full_analysis_set_plus_decoy_hla.fa.amb added
161cf500f74be_GRCh38_full_analysis_set_plus_decoy_hla.fa.ann added
161cf26b98f02_GRCh38_full_analysis_set_plus_decoy_hla.fa.bwt added
161cf605be02a_GRCh38_full_analysis_set_plus_decoy_hla.fa.pac added
161cf2fda16d2_GRCh38_full_analysis_set_plus_decoy_hla.fa.sa added
161cf17104d89_GRCh38_full_analysis_set_plus_decoy_hla.fa added
161cf2f526933_GRCh38.primary_assembly.genome.fa.fai added
161cf4b78ab8a_GRCh38.primary_assembly.genome.fa.amb added
161cf5f4617bb_GRCh38.primary_assembly.genome.fa.ann added
161cf72c026da_GRCh38.primary_assembly.genome.fa.bwt added
161cf2536ed11_GRCh38.primary_assembly.genome.fa.pac added
161cf39060a2d_GRCh38.primary_assembly.genome.fa.sa added
161cf3b862d9a_GRCh38.primary_assembly.genome.fa added
161cf661bf7fd_hs37d5.fa.fai added
161cf3636376a_hs37d5.fa.amb added
161cf21702bf4_hs37d5.fa.ann added
161cf4b55b152_hs37d5.fa.bwt added
161cf66eca521_hs37d5.fa.pac added
161cf3a4d4e51_hs37d5.fa.sa added
161cf2950c5be_hs37d5.fa added
161cf75e65222_complete_ref_lens.bin added
161cf641a72a6_ctable.bin added
161cf45d23a2_ctg_offsets.bin added
161cf7ece62ea_duplicate_clusters.tsv added
161cf1fc031b0_info.json added
161cf2fe2a19_mphf.bin added
161cf7c7dd0d7_pos.bin added
161cf281a131b_pre_indexing.log added
161cf47dc662e_rank.bin added
161cf56b87add_ref_indexing.log added
161cf698a6fa5_refAccumLengths.bin added
161cf7fa7efc4_reflengths.bin added
161cf6a6e6e55_refseq.bin added
161cf780dc509_seq.bin added
161cf50030f72_versionInfo.json added
161cf78eb2e67_salmon_index added
161cf1833aa36_chrLength.txt added
161cf67ebcba3_chrName.txt added
161cf29866fa2_chrNameLength.txt added
161cf390b09fa_chrStart.txt added
161cf3bc1958_exonGeTrInfo.tab added
161cf3223e252_exonInfo.tab added
161cf51df8f35_geneInfo.tab added
161cf2c330a91_Genome added
161cf4afacc42_genomeParameters.txt added
161cf17782783_Log.out added
161cf516a157e_SA added
161cfba92cf4_SAindex added
161cffc64d27_sjdbInfo.txt added
161cf23f34388_sjdbList.fromGTF.out.tab added
161cf37d6a828_sjdbList.out.tab added
161cf6db9f6bb_transcriptInfo.tab added
161cf4bf5a744_GRCh38.GENCODE.v42_100 added
161cf6cb88851_knownGene_hg38.sql added
161cf46fdb59a_knownGene_hg38.txt added
161cf3a9db5df_refGene_hg38.sql added
161cf480f6189_refGene_hg38.txt added
161cf69cc8e54_knownGene_mm39.sql added
161cf7494630f_knownGene_mm39.txt added
161cf39f3a994_refGene_mm39.sql added
161cf2c025145_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/RtmpdaCqHO/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
24.309 2.975 28.873
ReUseData.Rcheck/ReUseData-Ex.timings
| name | user | system | elapsed | |
| dataHub-class | 6.965 | 0.753 | 7.754 | |
| dataSearch | 1.197 | 0.052 | 1.253 | |
| dataUpdate | 0.000 | 0.001 | 0.000 | |
| getCloudData | 2.841 | 0.153 | 4.987 | |
| getData | 0 | 0 | 0 | |
| meta_data | 0.001 | 0.000 | 0.001 | |
| recipeHub-class | 0.148 | 0.014 | 0.162 | |
| recipeLoad | 1.391 | 0.084 | 1.483 | |
| recipeMake | 0.001 | 0.000 | 0.001 | |
| recipeSearch | 0.605 | 0.038 | 0.650 | |
| recipeUpdate | 0.000 | 0.001 | 0.000 | |