Qian Liu
| Snapshot Date: 2024-06-09 14:00 -0400 (Sun, 09 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 2024-06-11 15:43 -0400 (Tue, 11 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" | 4679 |
| palomino4 | Windows Server 2022 Datacenter | x64 | 4.4.0 RC (2024-04-16 r86468 ucrt) -- "Puppy Cup" | 4414 |
| merida1 | macOS 12.7.4 Monterey | x86_64 | 4.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup" | 4441 |
| kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup" | 4394 |
| 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 1693/2239 | 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 | | ||||||||
| palomino4 | 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: 1.5.0 |
| 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: 2024-06-11 05:59:33 -0400 (Tue, 11 Jun 2024) |
| EndedAt: 2024-06-11 06:01:58 -0400 (Tue, 11 Jun 2024) |
| EllapsedTime: 144.3 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 4.4.0 Patched (2024-04-24 r86482)
* 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 ‘1.5.0’
* 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 6.93 0.762 7.771
* 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 4.4.0 Patched (2024-04-24 r86482) -- "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...
7e45301b436b_GRCh38.primary_assembly.genome.fa.1.bt2 added
7e454de73e79_GRCh38.primary_assembly.genome.fa.2.bt2 added
7e458b6a1e4_GRCh38.primary_assembly.genome.fa.3.bt2 added
7e45e3e8434_GRCh38.primary_assembly.genome.fa.4.bt2 added
7e452a59793a_GRCh38.primary_assembly.genome.fa.rev.1.bt2 added
7e455825e48e_GRCh38.primary_assembly.genome.fa.rev.2.bt2 added
7e451fc053d8_outfile.txt added
7e45bc09a31_GRCh37_to_GRCh38.chain added
7e4511cb0cfe_GRCh37_to_NCBI34.chain added
7e4529c200d2_GRCh37_to_NCBI35.chain added
7e457fc3f068_GRCh37_to_NCBI36.chain added
7e4518dc7d60_GRCh38_to_GRCh37.chain added
7e4533ab3660_GRCh38_to_NCBI34.chain added
7e452d7ef320_GRCh38_to_NCBI35.chain added
7e45698bd135_GRCh38_to_NCBI36.chain added
7e455a5424b5_NCBI34_to_GRCh37.chain added
7e454a361567_NCBI34_to_GRCh38.chain added
7e4524b74341_NCBI35_to_GRCh37.chain added
7e457ba0733b_NCBI35_to_GRCh38.chain added
7e4562ed65e5_NCBI36_to_GRCh37.chain added
7e454fbcd020_NCBI36_to_GRCh38.chain added
7e4575040dc5_GRCm38_to_NCBIM36.chain added
7e455d243c87_GRCm38_to_NCBIM37.chain added
7e457601f2d6_NCBIM36_to_GRCm38.chain added
7e4579edfc20_NCBIM37_to_GRCm38.chain added
7e457743d769_1000G_omni2.5.b37.vcf.gz added
7e456f36bab_1000G_omni2.5.b37.vcf.gz.tbi added
7e455721ab1d_Mills_and_1000G_gold_standard.indels.b37.vcf.gz added
7e456369299b_Mills_and_1000G_gold_standard.indels.b37.vcf.gz.tbi added
7e45d2ab21a_1000G_omni2.5.hg38.vcf.gz added
7e456e12cfb6_1000G_omni2.5.hg38.vcf.gz.tbi added
7e451502ee2f_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz added
7e4573635a6f_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz.tbi added
7e457fc66897_af-only-gnomad.raw.sites.vcf added
7e453afcd30a_af-only-gnomad.raw.sites.vcf.idx added
7e452c8353c7_Mutect2-exome-panel.vcf.idx added
7e4561f144a5_Mutect2-WGS-panel-b37.vcf added
7e4526d1dedf_Mutect2-WGS-panel-b37.vcf.idx added
7e451c7f1662_small_exac_common_3.vcf added
7e455b968a8b_small_exac_common_3.vcf.idx added
7e457861daa6_1000g_pon.hg38.vcf.gz added
7e45605a0608_1000g_pon.hg38.vcf.gz.tbi added
7e45364228a3_af-only-gnomad.hg38.vcf.gz added
7e45317a0129_af-only-gnomad.hg38.vcf.gz.tbi added
7e4540e2441f_small_exac_common_3.hg38.vcf.gz added
7e4546e67080_small_exac_common_3.hg38.vcf.gz.tbi added
7e4542e407dd_gencode.v41.annotation.gtf added
7e458c0607a_gencode.v42.annotation.gtf added
7e45dfdee13_gencode.vM30.annotation.gtf added
7e451a192892_gencode.vM31.annotation.gtf added
7e4569b696a0_gencode.v41.transcripts.fa added
7e45525b1898_gencode.v41.transcripts.fa.fai added
7e455aabcd65_gencode.v42.transcripts.fa added
7e454539d064_gencode.v42.transcripts.fa.fai added
7e4556a078bd_gencode.vM30.pc_transcripts.fa added
7e454156ecb9_gencode.vM30.pc_transcripts.fa.fai added
7e4531cf8732_gencode.vM31.pc_transcripts.fa added
7e452fb4fd2a_gencode.vM31.pc_transcripts.fa.fai added
7e451358e8de_GRCh38.primary_assembly.genome.fa.1.ht2 added
7e45322050be_GRCh38.primary_assembly.genome.fa.2.ht2 added
7e45679503a7_GRCh38.primary_assembly.genome.fa.3.ht2 added
7e456822fe11_GRCh38.primary_assembly.genome.fa.4.ht2 added
7e4551564380_GRCh38.primary_assembly.genome.fa.5.ht2 added
7e457669b237_GRCh38.primary_assembly.genome.fa.6.ht2 added
7e451533759d_GRCh38.primary_assembly.genome.fa.7.ht2 added
7e45656ea14a_GRCh38.primary_assembly.genome.fa.8.ht2 added
7e45421f354c_GRCh38_full_analysis_set_plus_decoy_hla.fa.fai added
7e45ee4327e_GRCh38_full_analysis_set_plus_decoy_hla.fa.amb added
7e4527aef5d5_GRCh38_full_analysis_set_plus_decoy_hla.fa.ann added
7e454f8d874d_GRCh38_full_analysis_set_plus_decoy_hla.fa.bwt added
7e4554adf908_GRCh38_full_analysis_set_plus_decoy_hla.fa.pac added
7e4569b8a7a6_GRCh38_full_analysis_set_plus_decoy_hla.fa.sa added
7e455a06b983_GRCh38_full_analysis_set_plus_decoy_hla.fa added
7e456f7d75a1_GRCh38.primary_assembly.genome.fa.fai added
7e4515b5d636_GRCh38.primary_assembly.genome.fa.amb added
7e4555027e5c_GRCh38.primary_assembly.genome.fa.ann added
7e4516b5f59e_GRCh38.primary_assembly.genome.fa.bwt added
7e4541063b8_GRCh38.primary_assembly.genome.fa.pac added
7e455002c71d_GRCh38.primary_assembly.genome.fa.sa added
7e45665e69f4_GRCh38.primary_assembly.genome.fa added
7e45407e46ad_hs37d5.fa.fai added
7e45225228ef_hs37d5.fa.amb added
7e453ffd7483_hs37d5.fa.ann added
7e4518ec6547_hs37d5.fa.bwt added
7e4547ed2519_hs37d5.fa.pac added
7e45221eb133_hs37d5.fa.sa added
7e45d039cc5_hs37d5.fa added
7e456829502f_complete_ref_lens.bin added
7e45704f7315_ctable.bin added
7e45700ca14d_ctg_offsets.bin added
7e454d31ffb3_duplicate_clusters.tsv added
7e45d8a685d_info.json added
7e4579c9b89c_mphf.bin added
7e452a77483b_pos.bin added
7e457d272f44_pre_indexing.log added
7e451790598d_rank.bin added
7e455e74411_ref_indexing.log added
7e451225bb1e_refAccumLengths.bin added
7e456b1fb7e0_reflengths.bin added
7e456f610a11_refseq.bin added
7e454bdc1b37_seq.bin added
7e455f7edec9_versionInfo.json added
7e452548f1a_salmon_index added
7e457d7ef527_chrLength.txt added
7e451a1113cf_chrName.txt added
7e45572b8867_chrNameLength.txt added
7e456b084ee6_chrStart.txt added
7e456e7414ef_exonGeTrInfo.tab added
7e4570a8f90_exonInfo.tab added
7e4546573a8c_geneInfo.tab added
7e458c4e168_Genome added
7e4535aa7757_genomeParameters.txt added
7e454a810c47_Log.out added
7e455e4d2f87_SA added
7e451d6b786f_SAindex added
7e457aafce7f_sjdbInfo.txt added
7e452c1e32c6_sjdbList.fromGTF.out.tab added
7e4572977bca_sjdbList.out.tab added
7e453740458c_transcriptInfo.tab added
7e455c9606aa_GRCh38.GENCODE.v42_100 added
7e457d8fb262_knownGene_hg38.sql added
7e4565088054_knownGene_hg38.txt added
7e4511213e9e_refGene_hg38.sql added
7e451d95ffdb_refGene_hg38.txt added
7e4562d09209_knownGene_mm39.sql added
7e456b23bf8d_knownGene_mm39.txt added
7e4577f4f8ee_refGene_mm39.sql added
7e4574030ec8_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/RtmpjLACWe/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
23.563 2.814 27.659
ReUseData.Rcheck/ReUseData-Ex.timings
| name | user | system | elapsed | |
| dataHub-class | 6.930 | 0.762 | 7.771 | |
| dataSearch | 1.128 | 0.045 | 1.173 | |
| dataUpdate | 0.000 | 0.001 | 0.001 | |
| getCloudData | 2.577 | 0.141 | 4.226 | |
| getData | 0 | 0 | 0 | |
| meta_data | 0.001 | 0.000 | 0.001 | |
| recipeHub-class | 0.150 | 0.012 | 0.162 | |
| recipeLoad | 1.384 | 0.084 | 1.474 | |
| recipeMake | 0.000 | 0.001 | 0.001 | |
| recipeSearch | 0.576 | 0.032 | 0.607 | |
| recipeUpdate | 0.000 | 0.001 | 0.000 | |