Qian Liu
| Snapshot Date: 2024-06-12 14:00 -0400 (Wed, 12 Jun 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 2024-06-14 14:37 -0400 (Fri, 14 Jun 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" | 4757 |
| palomino3 | Windows Server 2022 Datacenter | x64 | 4.4.0 (2024-04-24 ucrt) -- "Puppy Cup" | 4491 |
| 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 ... | ||||||||||||
|
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: /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:ReUseData.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings ReUseData_1.4.0.tar.gz |
| StartedAt: 2024-06-13 02:48:27 -0400 (Thu, 13 Jun 2024) |
| EndedAt: 2024-06-13 02:51:23 -0400 (Thu, 13 Jun 2024) |
| EllapsedTime: 175.4 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: ReUseData.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:ReUseData.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings ReUseData_1.4.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/ReUseData.Rcheck’
* using R version 4.4.0 (2024-04-24)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
* running under: Ubuntu 22.04.4 LTS
* using session charset: UTF-8
* 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 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 5.96 0.352 6.314
* 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-3.19-bioc/meat/ReUseData.Rcheck/00check.log’
for details.
ReUseData.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD INSTALL ReUseData ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.19-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 4.4.0 (2024-04-24) -- "Puppy Cup"
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...
1aa24917dba3bc_GRCh38.primary_assembly.genome.fa.1.bt2 added
1aa2494e8d1f8e_GRCh38.primary_assembly.genome.fa.2.bt2 added
1aa2491f1c1010_GRCh38.primary_assembly.genome.fa.3.bt2 added
1aa2492ecff139_GRCh38.primary_assembly.genome.fa.4.bt2 added
1aa24934495353_GRCh38.primary_assembly.genome.fa.rev.1.bt2 added
1aa2492ef0a514_GRCh38.primary_assembly.genome.fa.rev.2.bt2 added
1aa24930c80cf_outfile.txt added
1aa24916d005f4_GRCh37_to_GRCh38.chain added
1aa2494c23af7f_GRCh37_to_NCBI34.chain added
1aa2493a6d7ae6_GRCh37_to_NCBI35.chain added
1aa2496982f4ef_GRCh37_to_NCBI36.chain added
1aa249c79dcfc_GRCh38_to_GRCh37.chain added
1aa2493b8cbb_GRCh38_to_NCBI34.chain added
1aa2495d1348da_GRCh38_to_NCBI35.chain added
1aa24922ca38fc_GRCh38_to_NCBI36.chain added
1aa24991cc86d_NCBI34_to_GRCh37.chain added
1aa2491f0b26f0_NCBI34_to_GRCh38.chain added
1aa2494f231e5c_NCBI35_to_GRCh37.chain added
1aa24959de3dcd_NCBI35_to_GRCh38.chain added
1aa2495b952ad4_NCBI36_to_GRCh37.chain added
1aa249517b67c3_NCBI36_to_GRCh38.chain added
1aa2496f14abb_GRCm38_to_NCBIM36.chain added
1aa24979389016_GRCm38_to_NCBIM37.chain added
1aa24915da7c8_NCBIM36_to_GRCm38.chain added
1aa2494eaf35cd_NCBIM37_to_GRCm38.chain added
1aa249175a9348_1000G_omni2.5.b37.vcf.gz added
1aa249818b639_1000G_omni2.5.b37.vcf.gz.tbi added
1aa24958169f6d_Mills_and_1000G_gold_standard.indels.b37.vcf.gz added
1aa249210bc620_Mills_and_1000G_gold_standard.indels.b37.vcf.gz.tbi added
1aa24950a58ad4_1000G_omni2.5.hg38.vcf.gz added
1aa249301c2518_1000G_omni2.5.hg38.vcf.gz.tbi added
1aa24938e769dd_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz added
1aa2491f32aa62_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz.tbi added
1aa2494f383528_af-only-gnomad.raw.sites.vcf added
1aa24967b75b16_af-only-gnomad.raw.sites.vcf.idx added
1aa249537bfdb5_Mutect2-exome-panel.vcf.idx added
1aa2497e28da3d_Mutect2-WGS-panel-b37.vcf added
1aa2496ac3dbe5_Mutect2-WGS-panel-b37.vcf.idx added
1aa2496a4c03aa_small_exac_common_3.vcf added
1aa2494a4c89bc_small_exac_common_3.vcf.idx added
1aa249253156cb_1000g_pon.hg38.vcf.gz added
1aa24953cef899_1000g_pon.hg38.vcf.gz.tbi added
1aa24956c666b8_af-only-gnomad.hg38.vcf.gz added
1aa249256ce386_af-only-gnomad.hg38.vcf.gz.tbi added
1aa24930e24174_small_exac_common_3.hg38.vcf.gz added
1aa24979909fb4_small_exac_common_3.hg38.vcf.gz.tbi added
1aa2492e89abf3_gencode.v41.annotation.gtf added
1aa2494fed6864_gencode.v42.annotation.gtf added
1aa24948b3be10_gencode.vM30.annotation.gtf added
1aa249867e9c0_gencode.vM31.annotation.gtf added
1aa2492b829338_gencode.v41.transcripts.fa added
1aa2491a2f25d3_gencode.v41.transcripts.fa.fai added
1aa249f59347b_gencode.v42.transcripts.fa added
1aa24924bb234e_gencode.v42.transcripts.fa.fai added
1aa2491b8ccd9c_gencode.vM30.pc_transcripts.fa added
1aa2495e086a49_gencode.vM30.pc_transcripts.fa.fai added
1aa2493c15b697_gencode.vM31.pc_transcripts.fa added
1aa24923a583d5_gencode.vM31.pc_transcripts.fa.fai added
1aa249361f09b6_GRCh38.primary_assembly.genome.fa.1.ht2 added
1aa2495d217cb7_GRCh38.primary_assembly.genome.fa.2.ht2 added
1aa249744b0ea9_GRCh38.primary_assembly.genome.fa.3.ht2 added
1aa249663b2ece_GRCh38.primary_assembly.genome.fa.4.ht2 added
1aa2491608e694_GRCh38.primary_assembly.genome.fa.5.ht2 added
1aa249137db90b_GRCh38.primary_assembly.genome.fa.6.ht2 added
1aa249357363f7_GRCh38.primary_assembly.genome.fa.7.ht2 added
1aa2497dc041aa_GRCh38.primary_assembly.genome.fa.8.ht2 added
1aa24966f9b6c0_GRCh38_full_analysis_set_plus_decoy_hla.fa.fai added
1aa249339c3e34_GRCh38_full_analysis_set_plus_decoy_hla.fa.amb added
1aa24968841d8f_GRCh38_full_analysis_set_plus_decoy_hla.fa.ann added
1aa2495145ba6a_GRCh38_full_analysis_set_plus_decoy_hla.fa.bwt added
1aa2497de8c7f0_GRCh38_full_analysis_set_plus_decoy_hla.fa.pac added
1aa249db5745a_GRCh38_full_analysis_set_plus_decoy_hla.fa.sa added
1aa2492514b304_GRCh38_full_analysis_set_plus_decoy_hla.fa added
1aa24954af2ea8_GRCh38.primary_assembly.genome.fa.fai added
1aa249332257e0_GRCh38.primary_assembly.genome.fa.amb added
1aa24955f6f478_GRCh38.primary_assembly.genome.fa.ann added
1aa2494e3fce5c_GRCh38.primary_assembly.genome.fa.bwt added
1aa24961ac03d4_GRCh38.primary_assembly.genome.fa.pac added
1aa24925e45cdc_GRCh38.primary_assembly.genome.fa.sa added
1aa24916f38c6c_GRCh38.primary_assembly.genome.fa added
1aa2496a13ed94_hs37d5.fa.fai added
1aa2495166f014_hs37d5.fa.amb added
1aa2493122b240_hs37d5.fa.ann added
1aa249796d2210_hs37d5.fa.bwt added
1aa24976221362_hs37d5.fa.pac added
1aa2494caf7fdc_hs37d5.fa.sa added
1aa24957758c59_hs37d5.fa added
1aa2493237c9f9_complete_ref_lens.bin added
1aa249705503b1_ctable.bin added
1aa249d94960f_ctg_offsets.bin added
1aa249f5946b1_duplicate_clusters.tsv added
1aa24964a0125a_info.json added
1aa24973cfc4dd_mphf.bin added
1aa24925622d45_pos.bin added
1aa249781dcb65_pre_indexing.log added
1aa249294328d4_rank.bin added
1aa24923226ef0_ref_indexing.log added
1aa2495f178225_refAccumLengths.bin added
1aa2495cdf6708_reflengths.bin added
1aa249ba68c7f_refseq.bin added
1aa249305d3c90_seq.bin added
1aa2495ac82ef8_versionInfo.json added
1aa249195c00da_salmon_index added
1aa2495571ef94_chrLength.txt added
1aa2492f775da0_chrName.txt added
1aa2494c7e58ba_chrNameLength.txt added
1aa2492b68e40c_chrStart.txt added
1aa2497db72bfc_exonGeTrInfo.tab added
1aa2492e2a5c8e_exonInfo.tab added
1aa249514d40e8_geneInfo.tab added
1aa24914aab869_Genome added
1aa249183e4a23_genomeParameters.txt added
1aa24922b430fc_Log.out added
1aa24945cd6aa9_SA added
1aa24911ab6c33_SAindex added
1aa24918d6445e_sjdbInfo.txt added
1aa249127cea85_sjdbList.fromGTF.out.tab added
1aa2496920f88c_sjdbList.out.tab added
1aa2494b0e0e58_transcriptInfo.tab added
1aa2492d1ee36_GRCh38.GENCODE.v42_100 added
1aa24976b58e9b_knownGene_hg38.sql added
1aa2495a675509_knownGene_hg38.txt added
1aa24967720090_refGene_hg38.sql added
1aa2496a855378_refGene_hg38.txt added
1aa2497fc9824e_knownGene_mm39.sql added
1aa2495f8fcbf5_knownGene_mm39.txt added
1aa24913c87c4d_refGene_mm39.sql added
1aa24922ebf13e_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/RtmpEm9ULQ/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
19.721 1.684 21.658
ReUseData.Rcheck/ReUseData-Ex.timings
| name | user | system | elapsed | |
| dataHub-class | 5.960 | 0.352 | 6.314 | |
| dataSearch | 1.092 | 0.060 | 1.151 | |
| dataUpdate | 0.000 | 0.000 | 0.001 | |
| getCloudData | 2.637 | 0.120 | 3.260 | |
| getData | 0.000 | 0.000 | 0.001 | |
| meta_data | 0.000 | 0.000 | 0.001 | |
| recipeHub-class | 0.122 | 0.008 | 0.131 | |
| recipeLoad | 1.240 | 0.072 | 1.313 | |
| recipeMake | 0.001 | 0.000 | 0.001 | |
| recipeSearch | 0.531 | 0.008 | 0.540 | |
| recipeUpdate | 0 | 0 | 0 | |