Qian Liu
| Snapshot Date: 2024-11-28 13:00 -0500 (Thu, 28 Nov 2024) |
| 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 2024-12-02 12:04 -0500 (Mon, 02 Dec 2024).
| 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" | 4739 |
| palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" | 4482 |
| merida1 | macOS 12.7.5 Monterey | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4510 |
| kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4462 |
| 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 | | ||||||||
|
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: /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:ReUseData.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings ReUseData_1.6.0.tar.gz |
| StartedAt: 2024-11-29 05:22:22 -0500 (Fri, 29 Nov 2024) |
| EndedAt: 2024-11-29 05:28:42 -0500 (Fri, 29 Nov 2024) |
| EllapsedTime: 379.2 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: ReUseData.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:ReUseData.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings ReUseData_1.6.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/ReUseData.Rcheck’
* using R version 4.4.2 (2024-10-31)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0
GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0
* running under: Ubuntu 24.04.1 LTS
* using session charset: UTF-8
* 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 ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
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 loading without being on the library search path ... 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 5.678 0.299 5.979
* 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 re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE
Status: 1 NOTE
See
‘/home/biocbuild/bbs-3.20-bioc/meat/ReUseData.Rcheck/00check.log’
for details.
ReUseData.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD INSTALL ReUseData ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.20-bioc/R/site-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: x86_64-pc-linux-gnu
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...
e59c020e91e_GRCh38.primary_assembly.genome.fa.1.bt2 added
e59c05d561d15_GRCh38.primary_assembly.genome.fa.2.bt2 added
e59c048833952_GRCh38.primary_assembly.genome.fa.3.bt2 added
e59c05062d999_GRCh38.primary_assembly.genome.fa.4.bt2 added
e59c0399f89e_GRCh38.primary_assembly.genome.fa.rev.1.bt2 added
e59c03ba1cdb2_GRCh38.primary_assembly.genome.fa.rev.2.bt2 added
e59c06dceb158_outfile.txt added
e59c05b4ad787_GRCh37_to_GRCh38.chain added
e59c0ce43770_GRCh37_to_NCBI34.chain added
e59c0375089f7_GRCh37_to_NCBI35.chain added
e59c03b7920a5_GRCh37_to_NCBI36.chain added
e59c04745537_GRCh38_to_GRCh37.chain added
e59c0b24334b_GRCh38_to_NCBI34.chain added
e59c06f22c1e0_GRCh38_to_NCBI35.chain added
e59c03123d18a_GRCh38_to_NCBI36.chain added
e59c01dbdf1b4_NCBI34_to_GRCh37.chain added
e59c069811c67_NCBI34_to_GRCh38.chain added
e59c023ca5b22_NCBI35_to_GRCh37.chain added
e59c04b1d7a7_NCBI35_to_GRCh38.chain added
e59c04da7bda4_NCBI36_to_GRCh37.chain added
e59c05c26a138_NCBI36_to_GRCh38.chain added
e59c055f7e3ce_GRCm38_to_NCBIM36.chain added
e59c07e318db_GRCm38_to_NCBIM37.chain added
e59c03375a5e7_NCBIM36_to_GRCm38.chain added
e59c063e6becf_NCBIM37_to_GRCm38.chain added
e59c03095e38d_1000G_omni2.5.b37.vcf.gz added
e59c02650a4e_1000G_omni2.5.b37.vcf.gz.tbi added
e59c02ceed2c7_Mills_and_1000G_gold_standard.indels.b37.vcf.gz added
e59c013e87b12_Mills_and_1000G_gold_standard.indels.b37.vcf.gz.tbi added
e59c01ce581dc_1000G_omni2.5.hg38.vcf.gz added
e59c04c6ddaf3_1000G_omni2.5.hg38.vcf.gz.tbi added
e59c014096430_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz added
e59c07a3b9ef2_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz.tbi added
e59c014f11445_af-only-gnomad.raw.sites.vcf added
e59c0646c3dca_af-only-gnomad.raw.sites.vcf.idx added
e59c07dd59790_Mutect2-exome-panel.vcf.idx added
e59c05092e1f7_Mutect2-WGS-panel-b37.vcf added
e59c0523aef22_Mutect2-WGS-panel-b37.vcf.idx added
e59c059206f18_small_exac_common_3.vcf added
e59c05d771967_small_exac_common_3.vcf.idx added
e59c098b7919_1000g_pon.hg38.vcf.gz added
e59c014998fbd_1000g_pon.hg38.vcf.gz.tbi added
e59c061eb6e9f_af-only-gnomad.hg38.vcf.gz added
e59c014afac65_af-only-gnomad.hg38.vcf.gz.tbi added
e59c03bc519d_small_exac_common_3.hg38.vcf.gz added
e59c0130f4029_small_exac_common_3.hg38.vcf.gz.tbi added
e59c0326d9e19_gencode.v41.annotation.gtf added
e59c06d3d6e05_gencode.v42.annotation.gtf added
e59c036d99b4c_gencode.vM30.annotation.gtf added
e59c0371f75c0_gencode.vM31.annotation.gtf added
e59c03ae52ba9_gencode.v41.transcripts.fa added
e59c013003c84_gencode.v41.transcripts.fa.fai added
e59c0d17598f_gencode.v42.transcripts.fa added
e59c042c84485_gencode.v42.transcripts.fa.fai added
e59c04675e26b_gencode.vM30.pc_transcripts.fa added
e59c070fe185e_gencode.vM30.pc_transcripts.fa.fai added
e59c0735e2812_gencode.vM31.pc_transcripts.fa added
e59c048daecba_gencode.vM31.pc_transcripts.fa.fai added
e59c01deceb26_GRCh38.primary_assembly.genome.fa.1.ht2 added
e59c0746a324_GRCh38.primary_assembly.genome.fa.2.ht2 added
e59c065c06e96_GRCh38.primary_assembly.genome.fa.3.ht2 added
e59c06a5ac619_GRCh38.primary_assembly.genome.fa.4.ht2 added
e59c01b500754_GRCh38.primary_assembly.genome.fa.5.ht2 added
e59c05ffc0d88_GRCh38.primary_assembly.genome.fa.6.ht2 added
e59c07f4bda5e_GRCh38.primary_assembly.genome.fa.7.ht2 added
e59c07fbc451e_GRCh38.primary_assembly.genome.fa.8.ht2 added
e59c05dd1a519_GRCh38_full_analysis_set_plus_decoy_hla.fa.fai added
e59c04fdebc55_GRCh38_full_analysis_set_plus_decoy_hla.fa.amb added
e59c051f73440_GRCh38_full_analysis_set_plus_decoy_hla.fa.ann added
e59c036f21431_GRCh38_full_analysis_set_plus_decoy_hla.fa.bwt added
e59c02d55d5bc_GRCh38_full_analysis_set_plus_decoy_hla.fa.pac added
e59c05b82ad5a_GRCh38_full_analysis_set_plus_decoy_hla.fa.sa added
e59c04b8ba3ee_GRCh38_full_analysis_set_plus_decoy_hla.fa added
e59c0f41445b_GRCh38.primary_assembly.genome.fa.fai added
e59c0703259bf_GRCh38.primary_assembly.genome.fa.amb added
e59c04f47f58c_GRCh38.primary_assembly.genome.fa.ann added
e59c022508485_GRCh38.primary_assembly.genome.fa.bwt added
e59c0229ff7d8_GRCh38.primary_assembly.genome.fa.pac added
e59c03c856391_GRCh38.primary_assembly.genome.fa.sa added
e59c0592a1fd1_GRCh38.primary_assembly.genome.fa added
e59c059bf6d98_hs37d5.fa.fai added
e59c0776a8f3a_hs37d5.fa.amb added
e59c06c2a5c55_hs37d5.fa.ann added
e59c066d6c727_hs37d5.fa.bwt added
e59c03a32d3bf_hs37d5.fa.pac added
e59c032a03ec1_hs37d5.fa.sa added
e59c057d4df86_hs37d5.fa added
e59c02d90fbd1_complete_ref_lens.bin added
e59c07b7b2b7b_ctable.bin added
e59c075c1caac_ctg_offsets.bin added
e59c034d79ef5_duplicate_clusters.tsv added
e59c0613b9a11_info.json added
e59c0601c90c5_mphf.bin added
e59c05027a64a_pos.bin added
e59c04137a79a_pre_indexing.log added
e59c05f686b23_rank.bin added
e59c04fe3eb68_ref_indexing.log added
e59c01f094cb3_refAccumLengths.bin added
e59c02f472778_reflengths.bin added
e59c021db1fa9_refseq.bin added
e59c055fb60e4_seq.bin added
e59c05c9cfd34_versionInfo.json added
e59c07d5dcd03_salmon_index added
e59c0218704d2_chrLength.txt added
e59c06bde4190_chrName.txt added
e59c06d9026c2_chrNameLength.txt added
e59c070cefa5e_chrStart.txt added
e59c0e2ec615_exonGeTrInfo.tab added
e59c010301e9a_exonInfo.tab added
e59c02d545def_geneInfo.tab added
e59c06758e5e6_Genome added
e59c069ef8c32_genomeParameters.txt added
e59c024beed2a_Log.out added
e59c05383423b_SA added
e59c050c6535a_SAindex added
e59c05ef1c0e9_sjdbInfo.txt added
e59c062380fc_sjdbList.fromGTF.out.tab added
e59c0289b32e0_sjdbList.out.tab added
e59c0c82bcbb_transcriptInfo.tab added
e59c019eac77_GRCh38.GENCODE.v42_100 added
e59c01e5cfd8c_knownGene_hg38.sql added
e59c0415a5bb0_knownGene_hg38.txt added
e59c062da4689_refGene_hg38.sql added
e59c07e798e51_refGene_hg38.txt added
e59c0118201fa_knownGene_mm39.sql added
e59c02411ee23_knownGene_mm39.txt added
e59c05de1f974_refGene_mm39.sql added
e59c06165ed63_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:
/home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpzTIBOC/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
18.164 1.117 19.726
ReUseData.Rcheck/ReUseData-Ex.timings
| name | user | system | elapsed | |
| dataHub-class | 5.678 | 0.299 | 5.979 | |
| dataSearch | 1.068 | 0.007 | 1.074 | |
| dataUpdate | 0 | 0 | 0 | |
| getCloudData | 2.501 | 0.146 | 3.414 | |
| getData | 0.000 | 0.001 | 0.000 | |
| meta_data | 0.001 | 0.000 | 0.001 | |
| recipeHub-class | 0.130 | 0.005 | 0.135 | |
| recipeLoad | 1.215 | 0.040 | 1.256 | |
| recipeMake | 0 | 0 | 0 | |
| recipeSearch | 0.542 | 0.027 | 0.570 | |
| recipeUpdate | 0 | 0 | 0 | |