Qian Liu
| Snapshot Date: 2025-01-02 13:00 -0500 (Thu, 02 Jan 2025) |
| git_url: https://git.bioconductor.org/packages/ReUseData |
| git_branch: RELEASE_3_20 |
| git_last_commit: 5d8c0ee |
| git_last_commit_date: 2024-10-29 11:17:22 -0500 (Tue, 29 Oct 2024) |
| Back to Multiple platform build/check report for BioC 3.20: simplified long |
|
This page was generated on 2025-01-09 12:10 -0500 (Thu, 09 Jan 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4744 |
| palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" | 4487 |
| merida1 | macOS 12.7.5 Monterey | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4515 |
| kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4467 |
| taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4358 |
| 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 1727/2289 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| ReUseData 1.6.0 (landing page) Qian Liu
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino8 | Windows Server 2022 Datacenter / x64 | ... NOT SUPPORTED ... | ||||||||||||
| merida1 | macOS 12.7.5 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | OK | OK | OK | | ||||||||
| taishan | Linux (openEuler 24.03 LTS) / aarch64 | OK | ERROR | skipped | ||||||||||
|
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: 1.6.0 |
| 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_1.6.0.tar.gz |
| StartedAt: 2025-01-04 06:15:43 -0500 (Sat, 04 Jan 2025) |
| EndedAt: 2025-01-04 06:18:08 -0500 (Sat, 04 Jan 2025) |
| EllapsedTime: 145.1 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_1.6.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/ReUseData.Rcheck’
* using R version 4.4.2 (2024-10-31)
* 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 13.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘ReUseData/DESCRIPTION’ ... OK
* this is package ‘ReUseData’ version ‘1.6.0’
* 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 6.645 0.741 7.501
* 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 4.4.2 (2024-10-31) -- "Pile of Leaves"
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...
1781e74bcc96e_GRCh38.primary_assembly.genome.fa.1.bt2 added
1781e164c90a2_GRCh38.primary_assembly.genome.fa.2.bt2 added
1781e7cab871d_GRCh38.primary_assembly.genome.fa.3.bt2 added
1781e6133c0dc_GRCh38.primary_assembly.genome.fa.4.bt2 added
1781ecbadd5f_GRCh38.primary_assembly.genome.fa.rev.1.bt2 added
1781e401b8e80_GRCh38.primary_assembly.genome.fa.rev.2.bt2 added
1781e51289661_outfile.txt added
1781e3fa8e3e7_GRCh37_to_GRCh38.chain added
1781e690a7357_GRCh37_to_NCBI34.chain added
1781e2d1a8aa1_GRCh37_to_NCBI35.chain added
1781e29836729_GRCh37_to_NCBI36.chain added
1781e71e9ca09_GRCh38_to_GRCh37.chain added
1781e2bcf4f4c_GRCh38_to_NCBI34.chain added
1781e375f1d0c_GRCh38_to_NCBI35.chain added
1781e456c1b3a_GRCh38_to_NCBI36.chain added
1781e3c6fa071_NCBI34_to_GRCh37.chain added
1781e448e79b6_NCBI34_to_GRCh38.chain added
1781e65d8bee3_NCBI35_to_GRCh37.chain added
1781e78dc5d51_NCBI35_to_GRCh38.chain added
1781e4b72aed4_NCBI36_to_GRCh37.chain added
1781e563406fe_NCBI36_to_GRCh38.chain added
1781e71b739e8_GRCm38_to_NCBIM36.chain added
1781e343ae8ab_GRCm38_to_NCBIM37.chain added
1781e7814d57_NCBIM36_to_GRCm38.chain added
1781e39fc8e9a_NCBIM37_to_GRCm38.chain added
1781e73f63e33_1000G_omni2.5.b37.vcf.gz added
1781e2b6dc1bf_1000G_omni2.5.b37.vcf.gz.tbi added
1781e32caf8df_Mills_and_1000G_gold_standard.indels.b37.vcf.gz added
1781e2b991286_Mills_and_1000G_gold_standard.indels.b37.vcf.gz.tbi added
1781e4e8f31c6_1000G_omni2.5.hg38.vcf.gz added
1781e1b0ce675_1000G_omni2.5.hg38.vcf.gz.tbi added
1781e6bee1932_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz added
1781e5cb858f9_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz.tbi added
1781e4ad972fd_af-only-gnomad.raw.sites.vcf added
1781ea0c666f_af-only-gnomad.raw.sites.vcf.idx added
1781e34190690_Mutect2-exome-panel.vcf.idx added
1781e56fdf2a8_Mutect2-WGS-panel-b37.vcf added
1781e3a462036_Mutect2-WGS-panel-b37.vcf.idx added
1781e51ecd71d_small_exac_common_3.vcf added
1781e141edaf0_small_exac_common_3.vcf.idx added
1781e75b7cce1_1000g_pon.hg38.vcf.gz added
1781e75ec0427_1000g_pon.hg38.vcf.gz.tbi added
1781e5a04d8ec_af-only-gnomad.hg38.vcf.gz added
1781e743d9c1f_af-only-gnomad.hg38.vcf.gz.tbi added
1781e78d4f2d7_small_exac_common_3.hg38.vcf.gz added
1781e64933f3a_small_exac_common_3.hg38.vcf.gz.tbi added
1781e7f1c2c6b_gencode.v41.annotation.gtf added
1781e12a865ff_gencode.v42.annotation.gtf added
1781e6dc051ea_gencode.vM30.annotation.gtf added
1781e6d4211f0_gencode.vM31.annotation.gtf added
1781eca7db9a_gencode.v41.transcripts.fa added
1781e604261f3_gencode.v41.transcripts.fa.fai added
1781e262cc9e4_gencode.v42.transcripts.fa added
1781e467aab50_gencode.v42.transcripts.fa.fai added
1781e1f853556_gencode.vM30.pc_transcripts.fa added
1781e6270b144_gencode.vM30.pc_transcripts.fa.fai added
1781e548619d9_gencode.vM31.pc_transcripts.fa added
1781e300b20e9_gencode.vM31.pc_transcripts.fa.fai added
1781e2a9db9a3_GRCh38.primary_assembly.genome.fa.1.ht2 added
1781e59069230_GRCh38.primary_assembly.genome.fa.2.ht2 added
1781e3e67baf9_GRCh38.primary_assembly.genome.fa.3.ht2 added
1781ec245171_GRCh38.primary_assembly.genome.fa.4.ht2 added
1781e245ed7f1_GRCh38.primary_assembly.genome.fa.5.ht2 added
1781e4eb321de_GRCh38.primary_assembly.genome.fa.6.ht2 added
1781e52749e2f_GRCh38.primary_assembly.genome.fa.7.ht2 added
1781e663d49f3_GRCh38.primary_assembly.genome.fa.8.ht2 added
1781e41c224f5_GRCh38_full_analysis_set_plus_decoy_hla.fa.fai added
1781e3108728d_GRCh38_full_analysis_set_plus_decoy_hla.fa.amb added
1781e2198a021_GRCh38_full_analysis_set_plus_decoy_hla.fa.ann added
1781e2b38e7c2_GRCh38_full_analysis_set_plus_decoy_hla.fa.bwt added
1781e24f787b9_GRCh38_full_analysis_set_plus_decoy_hla.fa.pac added
1781e76ef95a4_GRCh38_full_analysis_set_plus_decoy_hla.fa.sa added
1781e6b497efc_GRCh38_full_analysis_set_plus_decoy_hla.fa added
1781e2630096b_GRCh38.primary_assembly.genome.fa.fai added
1781e1bba6363_GRCh38.primary_assembly.genome.fa.amb added
1781e69d306cd_GRCh38.primary_assembly.genome.fa.ann added
1781e1d63b302_GRCh38.primary_assembly.genome.fa.bwt added
1781e7c7d5760_GRCh38.primary_assembly.genome.fa.pac added
1781e8f39f7a_GRCh38.primary_assembly.genome.fa.sa added
1781e326b072d_GRCh38.primary_assembly.genome.fa added
1781e10a43537_hs37d5.fa.fai added
1781eca1b66a_hs37d5.fa.amb added
1781e4cceefa0_hs37d5.fa.ann added
1781e25d618c5_hs37d5.fa.bwt added
1781eaf440eb_hs37d5.fa.pac added
1781e29d209eb_hs37d5.fa.sa added
1781e1c8938c0_hs37d5.fa added
1781e74ecd3e2_complete_ref_lens.bin added
1781e684ad666_ctable.bin added
1781e941f808_ctg_offsets.bin added
1781e4a02d9f7_duplicate_clusters.tsv added
1781e1340d17_info.json added
1781e47619f_mphf.bin added
1781e4e5a0ddd_pos.bin added
1781e7a44505a_pre_indexing.log added
1781e1af7836c_rank.bin added
1781e6fd53548_ref_indexing.log added
1781e169d4354_refAccumLengths.bin added
1781e2eaf4b65_reflengths.bin added
1781e767eebd4_refseq.bin added
1781e6ace813_seq.bin added
1781e41b83ad1_versionInfo.json added
1781e261d910c_salmon_index added
1781e5f1dbe60_chrLength.txt added
1781e19bdc169_chrName.txt added
1781e78e4e1b2_chrNameLength.txt added
1781e7a9dab1f_chrStart.txt added
1781e54dbf1d_exonGeTrInfo.tab added
1781e333e0ba3_exonInfo.tab added
1781e2e6e149d_geneInfo.tab added
1781e3d0b673b_Genome added
1781e37a671cc_genomeParameters.txt added
1781e1079249f_Log.out added
1781e1534b2c_SA added
1781e36c3662_SAindex added
1781e35665daf_sjdbInfo.txt added
1781e5390a78c_sjdbList.fromGTF.out.tab added
1781e3de80330_sjdbList.out.tab added
1781e4b296410_transcriptInfo.tab added
1781ea687cfd_GRCh38.GENCODE.v42_100 added
1781e51e5cb61_knownGene_hg38.sql added
1781e458b7748_knownGene_hg38.txt added
1781e47443ba3_refGene_hg38.sql added
1781e50a76ee2_refGene_hg38.txt added
1781e2060e0cc_knownGene_mm39.sql added
1781e384681af_knownGene_mm39.txt added
1781e1cec2506_refGene_mm39.sql added
1781e5372bbbf_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/RtmpTNqPY0/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
23.346 2.765 27.276
ReUseData.Rcheck/ReUseData-Ex.timings
| name | user | system | elapsed | |
| dataHub-class | 6.645 | 0.741 | 7.501 | |
| dataSearch | 1.226 | 0.058 | 1.288 | |
| dataUpdate | 0.001 | 0.000 | 0.001 | |
| getCloudData | 2.722 | 0.145 | 4.514 | |
| getData | 0 | 0 | 0 | |
| meta_data | 0.001 | 0.001 | 0.001 | |
| recipeHub-class | 0.147 | 0.012 | 0.161 | |
| recipeLoad | 1.471 | 0.107 | 1.585 | |
| recipeMake | 0.000 | 0.000 | 0.001 | |
| recipeSearch | 0.616 | 0.038 | 0.655 | |
| recipeUpdate | 0 | 0 | 0 | |