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This page was generated on 2024-03-28 11:39:54 -0400 (Thu, 28 Mar 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_64R Under development (unstable) (2024-03-18 r86148) -- "Unsuffered Consequences" 4708
palomino3Windows Server 2022 Datacenterx64R Under development (unstable) (2024-03-16 r86144 ucrt) -- "Unsuffered Consequences" 4446
lconwaymacOS 12.7.1 Montereyx86_64R Under development (unstable) (2024-03-18 r86148) -- "Unsuffered Consequences" 4471
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch64R Under development (unstable) (2024-03-19 r86153) -- "Unsuffered Consequences" 4426
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 1723/2270HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ReUseData 1.3.2  (landing page)
Qian Liu
Snapshot Date: 2024-03-27 14:00:18 -0400 (Wed, 27 Mar 2024)
git_url: https://git.bioconductor.org/packages/ReUseData
git_branch: devel
git_last_commit: d45ef48
git_last_commit_date: 2023-11-22 22:25:57 -0400 (Wed, 22 Nov 2023)
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  

CHECK results for ReUseData on lconway


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: 1.3.2
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_1.3.2.tar.gz
StartedAt: 2024-03-27 23:33:22 -0400 (Wed, 27 Mar 2024)
EndedAt: 2024-03-27 23:36:08 -0400 (Wed, 27 Mar 2024)
EllapsedTime: 165.4 seconds
RetCode: 0
Status:   OK  
CheckDir: ReUseData.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### 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_1.3.2.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.19-bioc/meat/ReUseData.Rcheck’
* using R Under development (unstable) (2024-03-18 r86148)
* 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 ‘1.3.2’
* 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 8.024  0.956    9.14
* 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.


Installation output

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)

Tests output

ReUseData.Rcheck/tests/testthat.Rout


R Under development (unstable) (2024-03-18 r86148) -- "Unsuffered Consequences"
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.)

}INFO Final process status is success

Updating data record...
outfile.txt added

Updating data record...
7c4c5b965867_GRCh38.primary_assembly.genome.fa.1.bt2 added
7c4c6b86012a_GRCh38.primary_assembly.genome.fa.2.bt2 added
7c4c2ab6a38c_GRCh38.primary_assembly.genome.fa.3.bt2 added
7c4c3cab523c_GRCh38.primary_assembly.genome.fa.4.bt2 added
7c4c13a40042_GRCh38.primary_assembly.genome.fa.rev.1.bt2 added
7c4c740cf720_GRCh38.primary_assembly.genome.fa.rev.2.bt2 added
7c4c7f349165_outfile.txt added
7c4c5435bf21_GRCh37_to_GRCh38.chain added
7c4c14973ab8_GRCh37_to_NCBI34.chain added
7c4c54901097_GRCh37_to_NCBI35.chain added
7c4c3e3154e0_GRCh37_to_NCBI36.chain added
7c4c18bb5e06_GRCh38_to_GRCh37.chain added
7c4c3519e899_GRCh38_to_NCBI34.chain added
7c4c37f5b00b_GRCh38_to_NCBI35.chain added
7c4c62f8bee0_GRCh38_to_NCBI36.chain added
7c4c38bb96e3_NCBI34_to_GRCh37.chain added
7c4c23af2e2e_NCBI34_to_GRCh38.chain added
7c4c4200e04f_NCBI35_to_GRCh37.chain added
7c4c47868463_NCBI35_to_GRCh38.chain added
7c4c505da444_NCBI36_to_GRCh37.chain added
7c4c33cb9594_NCBI36_to_GRCh38.chain added
7c4c7ac9421c_GRCm38_to_NCBIM36.chain added
7c4c33137b3e_GRCm38_to_NCBIM37.chain added
7c4c44003da4_NCBIM36_to_GRCm38.chain added
7c4c6bcefcdc_NCBIM37_to_GRCm38.chain added
7c4c623b06cf_1000G_omni2.5.b37.vcf.gz added
7c4c113c326b_1000G_omni2.5.b37.vcf.gz.tbi added
7c4c71217a4_Mills_and_1000G_gold_standard.indels.b37.vcf.gz added
7c4c34ce139c_Mills_and_1000G_gold_standard.indels.b37.vcf.gz.tbi added
7c4c456981d9_1000G_omni2.5.hg38.vcf.gz added
7c4c11cbf129_1000G_omni2.5.hg38.vcf.gz.tbi added
7c4c6445c3df_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz added
7c4c203e98e7_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz.tbi added
7c4c6da8763a_af-only-gnomad.raw.sites.vcf added
7c4c4eea1214_af-only-gnomad.raw.sites.vcf.idx added
7c4c69490785_Mutect2-exome-panel.vcf.idx added
7c4c398ce2c3_Mutect2-WGS-panel-b37.vcf added
7c4c507b8db9_Mutect2-WGS-panel-b37.vcf.idx added
7c4c5f9595f6_small_exac_common_3.vcf added
7c4c55a87a80_small_exac_common_3.vcf.idx added
7c4c2802956f_1000g_pon.hg38.vcf.gz added
7c4c41a0beee_1000g_pon.hg38.vcf.gz.tbi added
7c4c20571ceb_af-only-gnomad.hg38.vcf.gz added
7c4c372b98e3_af-only-gnomad.hg38.vcf.gz.tbi added
7c4cf427b61_small_exac_common_3.hg38.vcf.gz added
7c4c55b2251a_small_exac_common_3.hg38.vcf.gz.tbi added
7c4c22a1f9ea_gencode.v41.annotation.gtf added
7c4c381e8369_gencode.v42.annotation.gtf added
7c4c5b457f47_gencode.vM30.annotation.gtf added
7c4c2fa73d21_gencode.vM31.annotation.gtf added
7c4cc9e59f8_gencode.v41.transcripts.fa added
7c4c7024af40_gencode.v41.transcripts.fa.fai added
7c4c786dcc44_gencode.v42.transcripts.fa added
7c4c707dc220_gencode.v42.transcripts.fa.fai added
7c4c5053fc92_gencode.vM30.pc_transcripts.fa added
7c4c39eafe71_gencode.vM30.pc_transcripts.fa.fai added
7c4c72e6ca6b_gencode.vM31.pc_transcripts.fa added
7c4cdf371bc_gencode.vM31.pc_transcripts.fa.fai added
7c4c69aff4cb_GRCh38.primary_assembly.genome.fa.1.ht2 added
7c4c1ef071a2_GRCh38.primary_assembly.genome.fa.2.ht2 added
7c4c3bb4528c_GRCh38.primary_assembly.genome.fa.3.ht2 added
7c4c3b9783f3_GRCh38.primary_assembly.genome.fa.4.ht2 added
7c4c5857e515_GRCh38.primary_assembly.genome.fa.5.ht2 added
7c4c7280f302_GRCh38.primary_assembly.genome.fa.6.ht2 added
7c4c6fd24308_GRCh38.primary_assembly.genome.fa.7.ht2 added
7c4c552efb92_GRCh38.primary_assembly.genome.fa.8.ht2 added
7c4c7f8659ee_GRCh38_full_analysis_set_plus_decoy_hla.fa.fai added
7c4c4d7a59aa_GRCh38_full_analysis_set_plus_decoy_hla.fa.amb added
7c4c1b94cfa3_GRCh38_full_analysis_set_plus_decoy_hla.fa.ann added
7c4c46cbe47a_GRCh38_full_analysis_set_plus_decoy_hla.fa.bwt added
7c4c740529e5_GRCh38_full_analysis_set_plus_decoy_hla.fa.pac added
7c4c7f01b4e4_GRCh38_full_analysis_set_plus_decoy_hla.fa.sa added
7c4c490b25e0_GRCh38_full_analysis_set_plus_decoy_hla.fa added
7c4c7ae3ba96_GRCh38.primary_assembly.genome.fa.fai added
7c4c7cef0ce1_GRCh38.primary_assembly.genome.fa.amb added
7c4c3236c7db_GRCh38.primary_assembly.genome.fa.ann added
7c4c2a7b149e_GRCh38.primary_assembly.genome.fa.bwt added
7c4c7686a6db_GRCh38.primary_assembly.genome.fa.pac added
7c4c234b0a8_GRCh38.primary_assembly.genome.fa.sa added
7c4c5139e6b9_GRCh38.primary_assembly.genome.fa added
7c4c305aa558_hs37d5.fa.fai added
7c4cf1d4d35_hs37d5.fa.amb added
7c4c4cb7da53_hs37d5.fa.ann added
7c4c3a5ea67e_hs37d5.fa.bwt added
7c4c1c04b822_hs37d5.fa.pac added
7c4c79d4ce8c_hs37d5.fa.sa added
7c4c24487d1_hs37d5.fa added
7c4c6130ab80_complete_ref_lens.bin added
7c4c424b9259_ctable.bin added
7c4c6f75330f_ctg_offsets.bin added
7c4c776b56f3_duplicate_clusters.tsv added
7c4c2819a8c5_info.json added
7c4c2c973214_mphf.bin added
7c4c7a58d5ea_pos.bin added
7c4c5e443466_pre_indexing.log added
7c4c4fcc44e3_rank.bin added
7c4c6bbebc02_ref_indexing.log added
7c4c37295e91_refAccumLengths.bin added
7c4c7cff9de1_reflengths.bin added
7c4c71d65ee3_refseq.bin added
7c4c30efc378_seq.bin added
7c4c4d0a1461_versionInfo.json added
7c4c50c013ca_salmon_index added
7c4c72535c30_chrLength.txt added
7c4c3ec98df3_chrName.txt added
7c4c22866cb9_chrNameLength.txt added
7c4c274bf764_chrStart.txt added
7c4c6c5eda63_exonGeTrInfo.tab added
7c4c4753d12a_exonInfo.tab added
7c4c4fc940fb_geneInfo.tab added
7c4c25c947a9_Genome added
7c4c417fbba0_genomeParameters.txt added
7c4c28f726f8_Log.out added
7c4c7a1f78ca_SA added
7c4c28335469_SAindex added
7c4c41eace1d_sjdbInfo.txt added
7c4c1e81f3ba_sjdbList.fromGTF.out.tab added
7c4c65a847fb_sjdbList.out.tab added
7c4cb0de3e1_transcriptInfo.tab added
7c4c3cebce72_GRCh38.GENCODE.v42_100 added
7c4c1d3ebd9d_knownGene_hg38.sql added
7c4c2129d6b_knownGene_hg38.txt added
7c4c141cdcdd_refGene_hg38.sql added
7c4c72e83b7b_refGene_hg38.txt added
7c4c6c99432c_knownGene_mm39.sql added
7c4c42093567_knownGene_mm39.txt added
7c4c6a911f0f_refGene_mm39.sql added
7c4c5d8e4871_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/RtmpwO4pjB/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 
 26.133   3.562  30.956 

Example timings

ReUseData.Rcheck/ReUseData-Ex.timings

nameusersystemelapsed
dataHub-class8.0240.9569.140
dataSearch1.4360.0671.518
dataUpdate0.0000.0010.001
getCloudData3.0480.1764.102
getData0.0000.0000.001
meta_data0.0010.0000.001
recipeHub-class0.1620.0150.179
recipeLoad1.6190.1111.750
recipeMake0.0000.0010.001
recipeSearch0.7230.0490.780
recipeUpdate000