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This page was generated on 2024-05-04 11:37:04 -0400 (Sat, 04 May 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_644.4.0 beta (2024-04-15 r86425) -- "Puppy Cup" 4753
palomino3Windows Server 2022 Datacenterx644.4.0 beta (2024-04-15 r86425 ucrt) -- "Puppy Cup" 4486
lconwaymacOS 12.7.1 Montereyx86_644.4.0 beta (2024-04-14 r86421) -- "Puppy Cup" 4519
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch644.4.0 beta (2024-04-15 r86425) -- "Puppy Cup" 4479
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 1745/2300HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ReUseData 1.4.0  (landing page)
Qian Liu
Snapshot Date: 2024-05-03 14:00:19 -0400 (Fri, 03 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)
nebbiolo1Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino3Windows Server 2022 Datacenter / x64... NOT SUPPORTED ...
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kunpeng2Linux (openEuler 22.03 LTS-SP1) / aarch64  OK    OK    OK  
kjohnson3macOS 13.6.5 Ventura / arm64see weekly results here

CHECK results for ReUseData on nebbiolo1


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.

raw results


Summary

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: 2024-05-04 02:54:19 -0400 (Sat, 04 May 2024)
EndedAt: 2024-05-04 02:57:19 -0400 (Sat, 04 May 2024)
EllapsedTime: 179.6 seconds
RetCode: 0
Status:   OK  
CheckDir: ReUseData.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### 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 beta (2024-04-15 r86425)
* 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 6.296  0.459   6.757
* 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.


Installation output

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)

Tests output

ReUseData.Rcheck/tests/testthat.Rout


R version 4.4.0 beta (2024-04-15 r86425) -- "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.)

}INFO Final process status is success

Updating data record...
outfile.txt added

Updating data record...
345ec93c0f619b_GRCh38.primary_assembly.genome.fa.1.bt2 added
345ec97746a31_GRCh38.primary_assembly.genome.fa.2.bt2 added
345ec956c4c46e_GRCh38.primary_assembly.genome.fa.3.bt2 added
345ec97272d7d5_GRCh38.primary_assembly.genome.fa.4.bt2 added
345ec94cd1b9ca_GRCh38.primary_assembly.genome.fa.rev.1.bt2 added
345ec959569517_GRCh38.primary_assembly.genome.fa.rev.2.bt2 added
345ec938b5fc80_outfile.txt added
345ec94ab82122_GRCh37_to_GRCh38.chain added
345ec926e4c06b_GRCh37_to_NCBI34.chain added
345ec982edfb_GRCh37_to_NCBI35.chain added
345ec94bb9f29a_GRCh37_to_NCBI36.chain added
345ec9785fcb4e_GRCh38_to_GRCh37.chain added
345ec9331c403b_GRCh38_to_NCBI34.chain added
345ec96cc876cb_GRCh38_to_NCBI35.chain added
345ec9306d44f4_GRCh38_to_NCBI36.chain added
345ec96d630de2_NCBI34_to_GRCh37.chain added
345ec9a035f39_NCBI34_to_GRCh38.chain added
345ec958117186_NCBI35_to_GRCh37.chain added
345ec9617a6bea_NCBI35_to_GRCh38.chain added
345ec9cd3db14_NCBI36_to_GRCh37.chain added
345ec939db687d_NCBI36_to_GRCh38.chain added
345ec97161ffa7_GRCm38_to_NCBIM36.chain added
345ec992632c3_GRCm38_to_NCBIM37.chain added
345ec92220dd40_NCBIM36_to_GRCm38.chain added
345ec96de7778_NCBIM37_to_GRCm38.chain added
345ec96a3aef40_1000G_omni2.5.b37.vcf.gz added
345ec96450f3c5_1000G_omni2.5.b37.vcf.gz.tbi added
345ec91dc21733_Mills_and_1000G_gold_standard.indels.b37.vcf.gz added
345ec93015efb3_Mills_and_1000G_gold_standard.indels.b37.vcf.gz.tbi added
345ec93cc743ed_1000G_omni2.5.hg38.vcf.gz added
345ec964bb7a52_1000G_omni2.5.hg38.vcf.gz.tbi added
345ec96c25514e_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz added
345ec9443bae1f_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz.tbi added
345ec93b803ec1_af-only-gnomad.raw.sites.vcf added
345ec95e982923_af-only-gnomad.raw.sites.vcf.idx added
345ec9110d67e9_Mutect2-exome-panel.vcf.idx added
345ec914d6d3d8_Mutect2-WGS-panel-b37.vcf added
345ec9174e25a4_Mutect2-WGS-panel-b37.vcf.idx added
345ec95bc5890c_small_exac_common_3.vcf added
345ec93bbb9443_small_exac_common_3.vcf.idx added
345ec917d1139f_1000g_pon.hg38.vcf.gz added
345ec9277f7ba6_1000g_pon.hg38.vcf.gz.tbi added
345ec9341b5f91_af-only-gnomad.hg38.vcf.gz added
345ec94aed53db_af-only-gnomad.hg38.vcf.gz.tbi added
345ec91447f271_small_exac_common_3.hg38.vcf.gz added
345ec96488a485_small_exac_common_3.hg38.vcf.gz.tbi added
345ec9385061bd_gencode.v41.annotation.gtf added
345ec91e4b51aa_gencode.v42.annotation.gtf added
345ec93c9a160c_gencode.vM30.annotation.gtf added
345ec919cacda7_gencode.vM31.annotation.gtf added
345ec92b1f2cbe_gencode.v41.transcripts.fa added
345ec976757e89_gencode.v41.transcripts.fa.fai added
345ec9b2ccd4f_gencode.v42.transcripts.fa added
345ec934455f81_gencode.v42.transcripts.fa.fai added
345ec918965bc9_gencode.vM30.pc_transcripts.fa added
345ec9120b44c7_gencode.vM30.pc_transcripts.fa.fai added
345ec91e804ec2_gencode.vM31.pc_transcripts.fa added
345ec97ce74f8e_gencode.vM31.pc_transcripts.fa.fai added
345ec92fcd5bfa_GRCh38.primary_assembly.genome.fa.1.ht2 added
345ec94e963e75_GRCh38.primary_assembly.genome.fa.2.ht2 added
345ec939ae937c_GRCh38.primary_assembly.genome.fa.3.ht2 added
345ec91488d64c_GRCh38.primary_assembly.genome.fa.4.ht2 added
345ec93abb8fc3_GRCh38.primary_assembly.genome.fa.5.ht2 added
345ec97dea419b_GRCh38.primary_assembly.genome.fa.6.ht2 added
345ec95009150d_GRCh38.primary_assembly.genome.fa.7.ht2 added
345ec91953b8e6_GRCh38.primary_assembly.genome.fa.8.ht2 added
345ec9ef7a984_GRCh38_full_analysis_set_plus_decoy_hla.fa.fai added
345ec964dfe8e5_GRCh38_full_analysis_set_plus_decoy_hla.fa.amb added
345ec930a1de8a_GRCh38_full_analysis_set_plus_decoy_hla.fa.ann added
345ec96abd3290_GRCh38_full_analysis_set_plus_decoy_hla.fa.bwt added
345ec9209b7d28_GRCh38_full_analysis_set_plus_decoy_hla.fa.pac added
345ec94872f22a_GRCh38_full_analysis_set_plus_decoy_hla.fa.sa added
345ec9123cae36_GRCh38_full_analysis_set_plus_decoy_hla.fa added
345ec954b6dcb9_GRCh38.primary_assembly.genome.fa.fai added
345ec913604605_GRCh38.primary_assembly.genome.fa.amb added
345ec92684a0a7_GRCh38.primary_assembly.genome.fa.ann added
345ec9393f813f_GRCh38.primary_assembly.genome.fa.bwt added
345ec94bb0a7c2_GRCh38.primary_assembly.genome.fa.pac added
345ec944cff252_GRCh38.primary_assembly.genome.fa.sa added
345ec975d9974b_GRCh38.primary_assembly.genome.fa added
345ec9657b756a_hs37d5.fa.fai added
345ec96fef1f10_hs37d5.fa.amb added
345ec96c4f15d4_hs37d5.fa.ann added
345ec970a842b9_hs37d5.fa.bwt added
345ec924347e92_hs37d5.fa.pac added
345ec94e5719d_hs37d5.fa.sa added
345ec92b38780_hs37d5.fa added
345ec942b4cd54_complete_ref_lens.bin added
345ec91ccc12c_ctable.bin added
345ec93280e37a_ctg_offsets.bin added
345ec9114b0bc9_duplicate_clusters.tsv added
345ec93b7b54a8_info.json added
345ec94709b9c6_mphf.bin added
345ec94c069b8c_pos.bin added
345ec939659643_pre_indexing.log added
345ec91712ced4_rank.bin added
345ec9655a5472_ref_indexing.log added
345ec9485d3fc7_refAccumLengths.bin added
345ec97bf2b7b9_reflengths.bin added
345ec915fc32fd_refseq.bin added
345ec9331a7258_seq.bin added
345ec91c8e34e2_versionInfo.json added
345ec95e6f2527_salmon_index added
345ec94557208e_chrLength.txt added
345ec97145119b_chrName.txt added
345ec971cf6b2c_chrNameLength.txt added
345ec96bdbc136_chrStart.txt added
345ec92a8492da_exonGeTrInfo.tab added
345ec93d8012ee_exonInfo.tab added
345ec930abb388_geneInfo.tab added
345ec9205e2a25_Genome added
345ec922fb8858_genomeParameters.txt added
345ec9209ad298_Log.out added
345ec9cad3ff9_SA added
345ec913a3cb11_SAindex added
345ec944cf512a_sjdbInfo.txt added
345ec91192b197_sjdbList.fromGTF.out.tab added
345ec916575291_sjdbList.out.tab added
345ec97841e7e_transcriptInfo.tab added
345ec9135f72c3_GRCh38.GENCODE.v42_100 added
345ec948d8360b_knownGene_hg38.sql added
345ec918cf2a47_knownGene_hg38.txt added
345ec94edac76b_refGene_hg38.sql added
345ec9fe1efd2_refGene_hg38.txt added
345ec964d5c5d3_knownGene_mm39.sql added
345ec98405dae_knownGene_mm39.txt added
345ec926f4bea6_refGene_mm39.sql added
345ec94a301a46_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/Rtmp7pxUAv/test_gcpData/outfile.txt
}INFO 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 
 20.939   1.784  23.048 

Example timings

ReUseData.Rcheck/ReUseData-Ex.timings

nameusersystemelapsed
dataHub-class6.2960.4596.757
dataSearch1.1230.0831.208
dataUpdate0.0000.0000.001
getCloudData2.9150.1883.616
getData0.0000.0010.000
meta_data0.0000.0010.001
recipeHub-class0.1330.0000.134
recipeLoad1.3280.0861.415
recipeMake000
recipeSearch0.5470.0150.562
recipeUpdate0.0010.0000.000