Qian Liu
| Snapshot Date: 2024-06-27 14:00 -0400 (Thu, 27 Jun 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 2024-06-28 11:41 -0400 (Fri, 28 Jun 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.0 RC (2024-04-16 r86468) -- "Puppy Cup" | 4693 |
| palomino6 | Windows Server 2022 Datacenter | x64 | 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" | 4089 |
| lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.1 RC (2024-06-06 r86719) -- "Race for Your Life" | 4407 |
| kjohnson3 | macOS 13.6.5 Ventura | arm64 | 4.4.1 RC (2024-06-06 r86719) -- "Race for Your Life" | 4356 |
| 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 1695/2243 | 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 | | ||||||||
| palomino6 | 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 | | ||||||||
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | 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: 1.5.0 |
| 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: 2024-06-27 23:37:53 -0400 (Thu, 27 Jun 2024) |
| EndedAt: 2024-06-27 23:38:42 -0400 (Thu, 27 Jun 2024) |
| EllapsedTime: 48.5 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_1.5.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/ReUseData.Rcheck’
* using R version 4.4.1 RC (2024-06-06 r86719)
* 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 13.6.5
* 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
* 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-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 RC (2024-06-06 r86719) -- "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...
a21771cd659_GRCh38.primary_assembly.genome.fa.1.bt2 added
a217763c70b4_GRCh38.primary_assembly.genome.fa.2.bt2 added
a2177a0b7610_GRCh38.primary_assembly.genome.fa.3.bt2 added
a2176745309_GRCh38.primary_assembly.genome.fa.4.bt2 added
a2173ef7772e_GRCh38.primary_assembly.genome.fa.rev.1.bt2 added
a21768b18d4d_GRCh38.primary_assembly.genome.fa.rev.2.bt2 added
a21760b3efed_outfile.txt added
a217454ce234_GRCh37_to_GRCh38.chain added
a2173a96e777_GRCh37_to_NCBI34.chain added
a21793653ae_GRCh37_to_NCBI35.chain added
a2174dafc93b_GRCh37_to_NCBI36.chain added
a2174fc46855_GRCh38_to_GRCh37.chain added
a217679dcd5c_GRCh38_to_NCBI34.chain added
a21729158829_GRCh38_to_NCBI35.chain added
a217449e50d1_GRCh38_to_NCBI36.chain added
a21775cbec88_NCBI34_to_GRCh37.chain added
a2171f161123_NCBI34_to_GRCh38.chain added
a21761bf20c6_NCBI35_to_GRCh37.chain added
a2174b00d94c_NCBI35_to_GRCh38.chain added
a21724ba330c_NCBI36_to_GRCh37.chain added
a2173c6d6baa_NCBI36_to_GRCh38.chain added
a21733b784e4_GRCm38_to_NCBIM36.chain added
a2175575af42_GRCm38_to_NCBIM37.chain added
a217214541e3_NCBIM36_to_GRCm38.chain added
a21749e8af25_NCBIM37_to_GRCm38.chain added
a2174b42cc0b_1000G_omni2.5.b37.vcf.gz added
a217e620cc7_1000G_omni2.5.b37.vcf.gz.tbi added
a2174734e431_Mills_and_1000G_gold_standard.indels.b37.vcf.gz added
a2176171717c_Mills_and_1000G_gold_standard.indels.b37.vcf.gz.tbi added
a2175ed1b5de_1000G_omni2.5.hg38.vcf.gz added
a21719fb3274_1000G_omni2.5.hg38.vcf.gz.tbi added
a2173aad6aff_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz added
a2174f4ba971_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz.tbi added
a21770616262_af-only-gnomad.raw.sites.vcf added
a2179824992_af-only-gnomad.raw.sites.vcf.idx added
a21748ac151e_Mutect2-exome-panel.vcf.idx added
a217199e89d8_Mutect2-WGS-panel-b37.vcf added
a217776bd10b_Mutect2-WGS-panel-b37.vcf.idx added
a2174769666d_small_exac_common_3.vcf added
a21758c3a2bb_small_exac_common_3.vcf.idx added
a21713f0d084_1000g_pon.hg38.vcf.gz added
a21727099456_1000g_pon.hg38.vcf.gz.tbi added
a21765e9ae1f_af-only-gnomad.hg38.vcf.gz added
a21750a6a97e_af-only-gnomad.hg38.vcf.gz.tbi added
a2176dc1b88f_small_exac_common_3.hg38.vcf.gz added
a217493bec94_small_exac_common_3.hg38.vcf.gz.tbi added
a2177d290e1b_gencode.v41.annotation.gtf added
a217125d4ecf_gencode.v42.annotation.gtf added
a2172be10174_gencode.vM30.annotation.gtf added
a21741267d2d_gencode.vM31.annotation.gtf added
a21745e436c5_gencode.v41.transcripts.fa added
a2179c7e35c_gencode.v41.transcripts.fa.fai added
a217221fb208_gencode.v42.transcripts.fa added
a2174ee13cb8_gencode.v42.transcripts.fa.fai added
a21725597c7d_gencode.vM30.pc_transcripts.fa added
a21715fc05b3_gencode.vM30.pc_transcripts.fa.fai added
a21754da360b_gencode.vM31.pc_transcripts.fa added
a217421237b2_gencode.vM31.pc_transcripts.fa.fai added
a2173a06a901_GRCh38.primary_assembly.genome.fa.1.ht2 added
a217b419e6a_GRCh38.primary_assembly.genome.fa.2.ht2 added
a21710746ec_GRCh38.primary_assembly.genome.fa.3.ht2 added
a2174c1307b_GRCh38.primary_assembly.genome.fa.4.ht2 added
a2172755ddad_GRCh38.primary_assembly.genome.fa.5.ht2 added
a217764c9d07_GRCh38.primary_assembly.genome.fa.6.ht2 added
a2171fd9733e_GRCh38.primary_assembly.genome.fa.7.ht2 added
a2177d1cfbc7_GRCh38.primary_assembly.genome.fa.8.ht2 added
a21779d605fc_GRCh38_full_analysis_set_plus_decoy_hla.fa.fai added
a217522321e1_GRCh38_full_analysis_set_plus_decoy_hla.fa.amb added
a2178564e8_GRCh38_full_analysis_set_plus_decoy_hla.fa.ann added
a21735a3bb9c_GRCh38_full_analysis_set_plus_decoy_hla.fa.bwt added
a21710721a47_GRCh38_full_analysis_set_plus_decoy_hla.fa.pac added
a217331b33c0_GRCh38_full_analysis_set_plus_decoy_hla.fa.sa added
a2173ee29c76_GRCh38_full_analysis_set_plus_decoy_hla.fa added
a217f8e273b_GRCh38.primary_assembly.genome.fa.fai added
a2173db19a77_GRCh38.primary_assembly.genome.fa.amb added
a21757141a45_GRCh38.primary_assembly.genome.fa.ann added
a21768c8d4ac_GRCh38.primary_assembly.genome.fa.bwt added
a21759029df2_GRCh38.primary_assembly.genome.fa.pac added
a2173acfa885_GRCh38.primary_assembly.genome.fa.sa added
a2171740d1ed_GRCh38.primary_assembly.genome.fa added
a21720962a88_hs37d5.fa.fai added
a21762c2576e_hs37d5.fa.amb added
a21744fa2969_hs37d5.fa.ann added
a2173b4cfe0_hs37d5.fa.bwt added
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a217507bc6f9_complete_ref_lens.bin added
a2176e442eb6_ctable.bin added
a2173e56e748_ctg_offsets.bin added
a2173b6a47f1_duplicate_clusters.tsv added
a2173e993db0_info.json added
a2173ea10deb_mphf.bin added
a2173f98df6c_pos.bin added
a2174d744c12_pre_indexing.log added
a217e2e5978_rank.bin added
a2174f3dc8e_ref_indexing.log added
a2172614f12c_refAccumLengths.bin added
a21728e5933c_reflengths.bin added
a21778255d1d_refseq.bin added
a2175d04588a_seq.bin added
a2174850fbbb_versionInfo.json added
a2173cbed714_salmon_index added
a217151a8134_chrLength.txt added
a2177f1887be_chrName.txt added
a21723780c22_chrNameLength.txt added
a2171e649e5f_chrStart.txt added
a2175fd97e8f_exonGeTrInfo.tab added
a21740040f72_exonInfo.tab added
a2174a922633_geneInfo.tab added
a217410a0484_Genome added
a21778ae9777_genomeParameters.txt added
a217e5a4387_Log.out added
a21748075b6d_SA added
a2175b03760c_SAindex added
a217403b3c82_sjdbInfo.txt added
a21771019bbf_sjdbList.fromGTF.out.tab added
a2172098528f_sjdbList.out.tab added
a21770543b00_transcriptInfo.tab added
a21729edb69d_GRCh38.GENCODE.v42_100 added
a217357012ec_knownGene_hg38.sql added
a21750ea5f5c_knownGene_hg38.txt added
a2174b1aba84_refGene_hg38.sql added
a21747cb56a1_refGene_hg38.txt added
a21776a488d9_knownGene_mm39.sql added
a2172c149b69_knownGene_mm39.txt added
a2177ce7211a_refGene_mm39.sql added
a2172a2e7206_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:
/var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//Rtmps3Jh0M/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
7.226 0.890 8.718
ReUseData.Rcheck/ReUseData-Ex.timings
| name | user | system | elapsed | |
| dataHub-class | 1.848 | 0.192 | 2.044 | |
| dataSearch | 0.300 | 0.014 | 0.313 | |
| dataUpdate | 0 | 0 | 0 | |
| getCloudData | 0.765 | 0.042 | 1.498 | |
| getData | 0 | 0 | 0 | |
| meta_data | 0 | 0 | 0 | |
| recipeHub-class | 0.038 | 0.004 | 0.043 | |
| recipeLoad | 0.351 | 0.024 | 0.378 | |
| recipeMake | 0.000 | 0.000 | 0.001 | |
| recipeSearch | 0.156 | 0.010 | 0.166 | |
| recipeUpdate | 0 | 0 | 0 | |