Qian Liu
| Snapshot Date: 2024-05-15 14:00:14 -0400 (Wed, 15 May 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 2024-05-16 11:38:28 -0400 (Thu, 16 May 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" | 4751 |
| palomino3 | Windows Server 2022 Datacenter | x64 | 4.4.0 (2024-04-24 ucrt) -- "Puppy Cup" | 4485 |
| lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4515 |
| 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 ... | ||||||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson3 | macOS 13.6.5 Ventura / arm64 | 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: 1.4.0 |
| 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: 2024-05-15 23:19:31 -0400 (Wed, 15 May 2024) |
| EndedAt: 2024-05-15 23:22:13 -0400 (Wed, 15 May 2024) |
| EllapsedTime: 162.4 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: x86_64-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 Monterey 12.7.1
* 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 8.212 0.973 9.424
* 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-x86_64/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: x86_64-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...
d8fc1096f493_GRCh38.primary_assembly.genome.fa.1.bt2 added
d8fc2692e767_GRCh38.primary_assembly.genome.fa.2.bt2 added
d8fc76962ef9_GRCh38.primary_assembly.genome.fa.3.bt2 added
d8fc7de61a41_GRCh38.primary_assembly.genome.fa.4.bt2 added
d8fcdc5e1fa_GRCh38.primary_assembly.genome.fa.rev.1.bt2 added
d8fc3a76eb26_GRCh38.primary_assembly.genome.fa.rev.2.bt2 added
d8fc554829c6_outfile.txt added
d8fc74aeb1e7_GRCh37_to_GRCh38.chain added
d8fc7921f089_GRCh37_to_NCBI34.chain added
d8fc2336f080_GRCh37_to_NCBI35.chain added
d8fc6be7758f_GRCh37_to_NCBI36.chain added
d8fc28d736a1_GRCh38_to_GRCh37.chain added
d8fc494398f9_GRCh38_to_NCBI34.chain added
d8fc74f02902_GRCh38_to_NCBI35.chain added
d8fc43147e48_GRCh38_to_NCBI36.chain added
d8fc766ecb5f_NCBI34_to_GRCh37.chain added
d8fc63ea06b7_NCBI34_to_GRCh38.chain added
d8fc195f0ba0_NCBI35_to_GRCh37.chain added
d8fc2ef44263_NCBI35_to_GRCh38.chain added
d8fc263289aa_NCBI36_to_GRCh37.chain added
d8fc3fec0b7d_NCBI36_to_GRCh38.chain added
d8fc21e65c54_GRCm38_to_NCBIM36.chain added
d8fc1ab7a02f_GRCm38_to_NCBIM37.chain added
d8fcd757b5d_NCBIM36_to_GRCm38.chain added
d8fc1bf61d92_NCBIM37_to_GRCm38.chain added
d8fc3b0f6a95_1000G_omni2.5.b37.vcf.gz added
d8fc711e7a7d_1000G_omni2.5.b37.vcf.gz.tbi added
d8fc7fbde90_Mills_and_1000G_gold_standard.indels.b37.vcf.gz added
d8fc28d0c408_Mills_and_1000G_gold_standard.indels.b37.vcf.gz.tbi added
d8fc21f5fe27_1000G_omni2.5.hg38.vcf.gz added
d8fc1d00c3dc_1000G_omni2.5.hg38.vcf.gz.tbi added
d8fc1d3aaf64_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz added
d8fc77d0dd39_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz.tbi added
d8fc316c06a3_af-only-gnomad.raw.sites.vcf added
d8fc2b27d0ae_af-only-gnomad.raw.sites.vcf.idx added
d8fc42f565a4_Mutect2-exome-panel.vcf.idx added
d8fc7ce41453_Mutect2-WGS-panel-b37.vcf added
d8fc61f29533_Mutect2-WGS-panel-b37.vcf.idx added
d8fc7d217981_small_exac_common_3.vcf added
d8fc20b04455_small_exac_common_3.vcf.idx added
d8fc14563937_1000g_pon.hg38.vcf.gz added
d8fc28c6544f_1000g_pon.hg38.vcf.gz.tbi added
d8fc74c92372_af-only-gnomad.hg38.vcf.gz added
d8fc41364d44_af-only-gnomad.hg38.vcf.gz.tbi added
d8fc540accce_small_exac_common_3.hg38.vcf.gz added
d8fc110c137d_small_exac_common_3.hg38.vcf.gz.tbi added
d8fc2fd37c49_gencode.v41.annotation.gtf added
d8fc6584b526_gencode.v42.annotation.gtf added
d8fc6b9105db_gencode.vM30.annotation.gtf added
d8fc7e17a408_gencode.vM31.annotation.gtf added
d8fc421249e4_gencode.v41.transcripts.fa added
d8fc3eb1399f_gencode.v41.transcripts.fa.fai added
d8fc653e15e0_gencode.v42.transcripts.fa added
d8fc4f0e590d_gencode.v42.transcripts.fa.fai added
d8fc36f88d07_gencode.vM30.pc_transcripts.fa added
d8fc77f2e2c2_gencode.vM30.pc_transcripts.fa.fai added
d8fc6b056c13_gencode.vM31.pc_transcripts.fa added
d8fc30fa8a49_gencode.vM31.pc_transcripts.fa.fai added
d8fc108cd7be_GRCh38.primary_assembly.genome.fa.1.ht2 added
d8fcea8036f_GRCh38.primary_assembly.genome.fa.2.ht2 added
d8fc387973ed_GRCh38.primary_assembly.genome.fa.3.ht2 added
d8fc2da9e992_GRCh38.primary_assembly.genome.fa.4.ht2 added
d8fc6e2587a9_GRCh38.primary_assembly.genome.fa.5.ht2 added
d8fc61eda0bd_GRCh38.primary_assembly.genome.fa.6.ht2 added
d8fc37d40a85_GRCh38.primary_assembly.genome.fa.7.ht2 added
d8fc41febe65_GRCh38.primary_assembly.genome.fa.8.ht2 added
d8fc3b85fabc_GRCh38_full_analysis_set_plus_decoy_hla.fa.fai added
d8fc59106b2b_GRCh38_full_analysis_set_plus_decoy_hla.fa.amb added
d8fc44ec01bb_GRCh38_full_analysis_set_plus_decoy_hla.fa.ann added
d8fc6265bf56_GRCh38_full_analysis_set_plus_decoy_hla.fa.bwt added
d8fc5f4d992_GRCh38_full_analysis_set_plus_decoy_hla.fa.pac added
d8fcdf8034c_GRCh38_full_analysis_set_plus_decoy_hla.fa.sa added
d8fc15a079be_GRCh38_full_analysis_set_plus_decoy_hla.fa added
d8fc5a98b409_GRCh38.primary_assembly.genome.fa.fai added
d8fc5f53e956_GRCh38.primary_assembly.genome.fa.amb added
d8fc7dfc3dfe_GRCh38.primary_assembly.genome.fa.ann added
d8fc3b4a2f50_GRCh38.primary_assembly.genome.fa.bwt added
d8fc3684b99_GRCh38.primary_assembly.genome.fa.pac added
d8fc343b2b8e_GRCh38.primary_assembly.genome.fa.sa added
d8fc18a8926c_GRCh38.primary_assembly.genome.fa added
d8fc6324fd19_hs37d5.fa.fai added
d8fc1164a729_hs37d5.fa.amb added
d8fc671a7daa_hs37d5.fa.ann added
d8fc7c3058c7_hs37d5.fa.bwt added
d8fc4a14b083_hs37d5.fa.pac added
d8fc14508e74_hs37d5.fa.sa added
d8fc34b86c17_hs37d5.fa added
d8fc37c0750b_complete_ref_lens.bin added
d8fc3c4441c5_ctable.bin added
d8fc253a0b6c_ctg_offsets.bin added
d8fc5c3f28c_duplicate_clusters.tsv added
d8fc368c849_info.json added
d8fc5435325e_mphf.bin added
d8fc707de482_pos.bin added
d8fc59254c80_pre_indexing.log added
d8fc1fc19539_rank.bin added
d8fc5e2be178_ref_indexing.log added
d8fc12dfbd95_refAccumLengths.bin added
d8fc1f178ae1_reflengths.bin added
d8fc429ec9b9_refseq.bin added
d8fc46cdb2da_seq.bin added
d8fc6a992a86_versionInfo.json added
d8fc6db6fa16_salmon_index added
d8fc7dcf2a0_chrLength.txt added
d8fc3abcea68_chrName.txt added
d8fc48c16ff8_chrNameLength.txt added
d8fc139e2819_chrStart.txt added
d8fc745a8b5e_exonGeTrInfo.tab added
d8fc647403ff_exonInfo.tab added
d8fc7cb28dde_geneInfo.tab added
d8fc2e8029c7_Genome added
d8fc6036dfaa_genomeParameters.txt added
d8fc3296433f_Log.out added
d8fc2718f70b_SA added
d8fc5803073a_SAindex added
d8fc2ecf9dfa_sjdbInfo.txt added
d8fc408ca018_sjdbList.fromGTF.out.tab added
d8fc5062a8c3_sjdbList.out.tab added
d8fc7d35c36f_transcriptInfo.tab added
d8fc54b1eca1_GRCh38.GENCODE.v42_100 added
d8fc6d266977_knownGene_hg38.sql added
d8fc74d63b9c_knownGene_hg38.txt added
d8fc1ce3bab1_refGene_hg38.sql added
d8fc2af5c948_refGene_hg38.txt added
d8fc6e71ac00_knownGene_mm39.sql added
d8fc68d36ca5_knownGene_mm39.txt added
d8fc1081fa67_refGene_mm39.sql added
d8fc455e88a8_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/Rtmp5qlLeE/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
25.896 3.551 30.799
ReUseData.Rcheck/ReUseData-Ex.timings
| name | user | system | elapsed | |
| dataHub-class | 8.212 | 0.973 | 9.424 | |
| dataSearch | 1.707 | 0.084 | 1.819 | |
| dataUpdate | 0.000 | 0.001 | 0.000 | |
| getCloudData | 3.032 | 0.177 | 4.030 | |
| getData | 0.000 | 0.000 | 0.001 | |
| meta_data | 0.001 | 0.000 | 0.001 | |
| recipeHub-class | 0.160 | 0.016 | 0.178 | |
| recipeLoad | 1.727 | 0.120 | 1.872 | |
| recipeMake | 0.000 | 0.000 | 0.001 | |
| recipeSearch | 0.715 | 0.048 | 0.772 | |
| recipeUpdate | 0 | 0 | 0 | |