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This page was generated on 2023-05-31 05:44:42 -0000 (Wed, 31 May 2023).

HostnameOSArch (*)R versionInstalled pkgs
kunpeng1Linux (Ubuntu 22.04.1 LTS)aarch644.3.0 (2023-04-21) -- "Already Tomorrow" 4219
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CHECK results for ReUseData on kunpeng1


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.

Note: If "R CMD check" recently failed on the Linux builder over a missing dependency, add the missing dependency to "Suggests" in your DESCRIPTION file. See the Renviron.bioc for details.

raw results

Package 1665/2197HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ReUseData 1.1.0  (landing page)
Qian Liu
Snapshot Date: 2023-05-29 10:19:22 -0000 (Mon, 29 May 2023)
git_url: https://git.bioconductor.org/packages/ReUseData
git_branch: devel
git_last_commit: 3a1df6c
git_last_commit_date: 2023-04-25 15:42:19 -0000 (Tue, 25 Apr 2023)
kunpeng1Linux (Ubuntu 22.04.1 LTS) / aarch64  OK    OK    ERROR  

Summary

Package: ReUseData
Version: 1.1.0
Command: /home/biocbuild/R/R-4.3.0/bin/R CMD check --install=check:ReUseData.install-out.txt --library=/home/biocbuild/R/R-4.3.0/site-library --timings ReUseData_1.1.0.tar.gz
StartedAt: 2023-05-30 16:49:38 -0000 (Tue, 30 May 2023)
EndedAt: 2023-05-30 16:53:01 -0000 (Tue, 30 May 2023)
EllapsedTime: 202.3 seconds
RetCode: 1
Status:   ERROR  
CheckDir: ReUseData.Rcheck
Warnings: NA

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R-4.3.0/bin/R CMD check --install=check:ReUseData.install-out.txt --library=/home/biocbuild/R/R-4.3.0/site-library --timings ReUseData_1.1.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.18-bioc/meat/ReUseData.Rcheck’
* using R version 4.3.0 (2023-04-21)
* using platform: aarch64-unknown-linux-gnu (64-bit)
* R was compiled by
    gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
    GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
* running under: Ubuntu 22.04.2 LTS
* using session charset: UTF-8
* checking for file ‘ReUseData/DESCRIPTION’ ... OK
* this is package ‘ReUseData’ version ‘1.1.0’
* 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 R 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
dataUpdate    16.082  1.219  17.300
getCloudData  10.719  0.616  14.994
dataHub-class  8.726  0.551   9.283
getData        4.837  0.342   5.173
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ...
  ‘ReUseData_data.Rmd’ using ‘UTF-8’... OK
  ‘ReUseData_quickStart.Rmd’ using ‘UTF-8’... OK
  ‘ReUseData_recipe.Rmd’ using ‘UTF-8’... OK
 NONE
* checking re-building of vignette outputs ... ERROR
Error(s) in re-building vignettes:
  ...
--- re-building ‘ReUseData_data.Rmd’ using rmarkdown
Error: processing vignette 'ReUseData_data.Rmd' failed with diagnostics:
there is no package called ‘BiocStyle’
--- failed re-building ‘ReUseData_data.Rmd’

--- re-building ‘ReUseData_quickStart.Rmd’ using rmarkdown
Error: processing vignette 'ReUseData_quickStart.Rmd' failed with diagnostics:
there is no package called ‘BiocStyle’
--- failed re-building ‘ReUseData_quickStart.Rmd’

--- re-building ‘ReUseData_recipe.Rmd’ using rmarkdown
Error: processing vignette 'ReUseData_recipe.Rmd' failed with diagnostics:
there is no package called ‘BiocStyle’
--- failed re-building ‘ReUseData_recipe.Rmd’

SUMMARY: processing the following files failed:
  ‘ReUseData_data.Rmd’ ‘ReUseData_quickStart.Rmd’
  ‘ReUseData_recipe.Rmd’

Error: Vignette re-building failed.
Execution halted

* checking PDF version of manual ... OK
* DONE

Status: 1 ERROR, 1 NOTE
See
  ‘/home/biocbuild/bbs-3.18-bioc/meat/ReUseData.Rcheck/00check.log’
for details.


Installation output

ReUseData.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R-4.3.0/bin/R CMD INSTALL ReUseData
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/R/R-4.3.0/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 4.3.0 (2023-04-21) -- "Already Tomorrow"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: aarch64-unknown-linux-gnu (64-bit)

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...
2cb14b3f3e9a90_GRCh38.primary_assembly.genome.fa.1.bt2 added
2cb14b4acef023_GRCh38.primary_assembly.genome.fa.2.bt2 added
2cb14b44b0d5d9_GRCh38.primary_assembly.genome.fa.3.bt2 added
2cb14b383a314b_GRCh38.primary_assembly.genome.fa.4.bt2 added
2cb14b6d565ad9_GRCh38.primary_assembly.genome.fa.rev.1.bt2 added
2cb14b73030d88_GRCh38.primary_assembly.genome.fa.rev.2.bt2 added
2cb14b21f1330f_outfile.txt added
2cb14b1e4209b1_GRCh37_to_GRCh38.chain added
2cb14b78c457ea_GRCh37_to_NCBI34.chain added
2cb14b76c56ad2_GRCh37_to_NCBI35.chain added
2cb14b41ad4a81_GRCh37_to_NCBI36.chain added
2cb14b7e9bfc69_GRCh38_to_GRCh37.chain added
2cb14b4343010a_GRCh38_to_NCBI34.chain added
2cb14b3759e0b5_GRCh38_to_NCBI35.chain added
2cb14b3b08db53_GRCh38_to_NCBI36.chain added
2cb14b79b05f17_NCBI34_to_GRCh37.chain added
2cb14b7eb6ce6b_NCBI34_to_GRCh38.chain added
2cb14b6695a59c_NCBI35_to_GRCh37.chain added
2cb14b2b92bb4_NCBI35_to_GRCh38.chain added
2cb14b4d75fd8f_NCBI36_to_GRCh37.chain added
2cb14b5bc3416a_NCBI36_to_GRCh38.chain added
2cb14b42a66ec2_GRCm38_to_NCBIM36.chain added
2cb14b4de8e201_GRCm38_to_NCBIM37.chain added
2cb14b634a45c5_NCBIM36_to_GRCm38.chain added
2cb14b75406247_NCBIM37_to_GRCm38.chain added
2cb14b3b7033a6_1000G_omni2.5.b37.vcf.gz added
2cb14b4ebfa019_1000G_omni2.5.b37.vcf.gz.tbi added
2cb14b4b59ff2c_Mills_and_1000G_gold_standard.indels.b37.vcf.gz added
2cb14b4844378a_Mills_and_1000G_gold_standard.indels.b37.vcf.gz.tbi added
2cb14b254ad5f6_1000G_omni2.5.hg38.vcf.gz added
2cb14b3af86ec7_1000G_omni2.5.hg38.vcf.gz.tbi added
2cb14b782d21a_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz added
2cb14b7019c619_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz.tbi added
2cb14b7fa944a0_af-only-gnomad.raw.sites.vcf added
2cb14b3fbd0366_af-only-gnomad.raw.sites.vcf.idx added
2cb14b5d7020f2_Mutect2-exome-panel.vcf.idx added
2cb14b72ac5229_Mutect2-WGS-panel-b37.vcf added
2cb14b61ae3675_Mutect2-WGS-panel-b37.vcf.idx added
2cb14b7bb22aa4_small_exac_common_3.vcf added
2cb14b6b70aa13_small_exac_common_3.vcf.idx added
2cb14b5873a148_1000g_pon.hg38.vcf.gz added
2cb14b3d5f7525_1000g_pon.hg38.vcf.gz.tbi added
2cb14b6a0ca67c_af-only-gnomad.hg38.vcf.gz added
2cb14b1bb6a252_af-only-gnomad.hg38.vcf.gz.tbi added
2cb14b74b955db_small_exac_common_3.hg38.vcf.gz added
2cb14b251581cf_small_exac_common_3.hg38.vcf.gz.tbi added
2cb14b15670169_gencode.v41.annotation.gtf added
2cb14b73702446_gencode.v42.annotation.gtf added
2cb14bbab276c_gencode.vM30.annotation.gtf added
2cb14b18202d1e_gencode.vM31.annotation.gtf added
2cb14b40e621d6_gencode.v41.transcripts.fa added
2cb14b676e68d6_gencode.v41.transcripts.fa.fai added
2cb14b5ac69be0_gencode.v42.transcripts.fa added
2cb14becf03d7_gencode.v42.transcripts.fa.fai added
2cb14b4ab8ae9b_gencode.vM30.pc_transcripts.fa added
2cb14b5006fe28_gencode.vM30.pc_transcripts.fa.fai added
2cb14b4a3f377d_gencode.vM31.pc_transcripts.fa added
2cb14b19784eb5_gencode.vM31.pc_transcripts.fa.fai added
2cb14b1b60fd54_GRCh38.primary_assembly.genome.fa.1.ht2 added
2cb14b12836f07_GRCh38.primary_assembly.genome.fa.2.ht2 added
2cb14b3ec324ab_GRCh38.primary_assembly.genome.fa.3.ht2 added
2cb14b56596c1b_GRCh38.primary_assembly.genome.fa.4.ht2 added
2cb14b1a064121_GRCh38.primary_assembly.genome.fa.5.ht2 added
2cb14b2edceac4_GRCh38.primary_assembly.genome.fa.6.ht2 added
2cb14b5602b0bc_GRCh38.primary_assembly.genome.fa.7.ht2 added
2cb14b59c34487_GRCh38.primary_assembly.genome.fa.8.ht2 added
2cb14bc4d0bb6_GRCh38_full_analysis_set_plus_decoy_hla.fa.fai added
2cb14b48af02e5_GRCh38_full_analysis_set_plus_decoy_hla.fa.amb added
2cb14b3b717afd_GRCh38_full_analysis_set_plus_decoy_hla.fa.ann added
2cb14b7ff365a_GRCh38_full_analysis_set_plus_decoy_hla.fa.bwt added
2cb14b341facf8_GRCh38_full_analysis_set_plus_decoy_hla.fa.pac added
2cb14b13e51c45_GRCh38_full_analysis_set_plus_decoy_hla.fa.sa added
2cb14b455eab80_GRCh38_full_analysis_set_plus_decoy_hla.fa added
2cb14b1e2c5375_GRCh38.primary_assembly.genome.fa.fai added
2cb14b2f9bbe97_GRCh38.primary_assembly.genome.fa.amb added
2cb14b3a18015b_GRCh38.primary_assembly.genome.fa.ann added
2cb14b4341d544_GRCh38.primary_assembly.genome.fa.bwt added
2cb14b4502c000_GRCh38.primary_assembly.genome.fa.pac added
2cb14b2d8825a1_GRCh38.primary_assembly.genome.fa.sa added
2cb14b4eecfcb0_GRCh38.primary_assembly.genome.fa added
2cb14b5d22ed1e_hs37d5.fa.fai added
2cb14b6e6e4777_hs37d5.fa.amb added
2cb14b365b6587_hs37d5.fa.ann added
2cb14b37e988ff_hs37d5.fa.bwt added
2cb14b7d3d4b4e_hs37d5.fa.pac added
2cb14b1141422_hs37d5.fa.sa added
2cb14b7f08727_hs37d5.fa added
2cb14b477c82cb_complete_ref_lens.bin added
2cb14b1a8c62d7_ctable.bin added
2cb14b2351847b_ctg_offsets.bin added
2cb14b59fff1d2_duplicate_clusters.tsv added
2cb14b594f8782_info.json added
2cb14b79aaf096_mphf.bin added
2cb14b740632f4_pos.bin added
2cb14b82c7246_pre_indexing.log added
2cb14b4fada152_rank.bin added
2cb14b4dc9777b_ref_indexing.log added
2cb14b14797dfd_refAccumLengths.bin added
2cb14b185ca437_reflengths.bin added
2cb14b93af278_refseq.bin added
2cb14b1c78b457_seq.bin added
2cb14b4c7c5130_versionInfo.json added
2cb14b1d200ebd_salmon_index added
2cb14b61d75fd7_chrLength.txt added
2cb14b6aa8a4a5_chrName.txt added
2cb14b4cbbcd54_chrNameLength.txt added
2cb14b1bef6132_chrStart.txt added
2cb14b2dea79e9_exonGeTrInfo.tab added
2cb14b11be8d55_exonInfo.tab added
2cb14b497786d4_geneInfo.tab added
2cb14b7cd7769a_Genome added
2cb14b6ee17a73_genomeParameters.txt added
2cb14b37e5ce4b_Log.out added
2cb14b3332dc21_SA added
2cb14b26cb0372_SAindex added
2cb14b3523199a_sjdbInfo.txt added
2cb14b3446f043_sjdbList.fromGTF.out.tab added
2cb14b2ebb8a99_sjdbList.out.tab added
2cb14b7c9f9c65_transcriptInfo.tab added
2cb14b4ed3531b_GRCh38.GENCODE.v42_100 added
2cb14b520d0f14_knownGene_hg38.sql added
2cb14b569f8e38_knownGene_hg38.txt added
2cb14b2822da9d_refGene_hg38.sql added
2cb14b4bb7ffab_refGene_hg38.txt added
2cb14b4aa5c12c_knownGene_mm39.sql added
2cb14b304f4ce4_knownGene_mm39.txt added
2cb14b1b65a0fd_refGene_mm39.sql added
2cb14b186f38a7_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/RtmphXM5jv/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 ]
> 
> proc.time()
   user  system elapsed 
 32.164   2.433  36.213 

Example timings

ReUseData.Rcheck/ReUseData-Ex.timings

nameusersystemelapsed
dataHub-class8.7260.5519.283
dataSearch1.3940.0591.454
dataUpdate16.082 1.21917.300
getCloudData10.719 0.61614.994
getData4.8370.3425.173
meta_data0.0120.0010.013
recipeHub-class0.2660.0240.290
recipeLoad1.5780.0921.673
recipeMake4.5570.2554.808
recipeSearch0.7450.0040.748
recipeUpdate0.0020.0000.002