| Back to Build/check report for BioC 3.18: simplified long |
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This page was generated on 2023-06-06 11:00:40 -0000 (Tue, 06 Jun 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | 4.3.0 (2023-04-21) -- "Already Tomorrow" | 4366 |
| 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 | ||||
|
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. |
| Package 1667/2199 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| ReUseData 1.1.0 (landing page) Qian Liu
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | ERROR | |||||||||
| 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: 2023-06-06 05:14:11 -0000 (Tue, 06 Jun 2023) |
| EndedAt: 2023-06-06 05:17:35 -0000 (Tue, 06 Jun 2023) |
| EllapsedTime: 203.3 seconds |
| RetCode: 1 |
| Status: ERROR |
| CheckDir: ReUseData.Rcheck |
| Warnings: NA |
##############################################################################
##############################################################################
###
### 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 (GCC) 10.3.1
GNU Fortran (GCC) 10.3.1
* running under: openEuler 22.03 (LTS-SP1)
* 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 16.421 0.764 17.220
getCloudData 9.928 0.267 15.628
dataHub-class 8.907 0.339 9.268
getData 4.866 0.156 5.025
* 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.
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)
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.)
}[1;30mINFO[0m Final process status is success
Updating data record...
outfile.txt added
Updating data record...
c6e4b468ca95b_GRCh38.primary_assembly.genome.fa.1.bt2 added
c6e4b3e4e22ed_GRCh38.primary_assembly.genome.fa.2.bt2 added
c6e4b656dde0d_GRCh38.primary_assembly.genome.fa.3.bt2 added
c6e4b33607daa_GRCh38.primary_assembly.genome.fa.4.bt2 added
c6e4b75b244c_GRCh38.primary_assembly.genome.fa.rev.1.bt2 added
c6e4b555cbf88_GRCh38.primary_assembly.genome.fa.rev.2.bt2 added
c6e4b64d2d31f_outfile.txt added
c6e4b452c439a_GRCh37_to_GRCh38.chain added
c6e4b2a859869_GRCh37_to_NCBI34.chain added
c6e4b55aaa415_GRCh37_to_NCBI35.chain added
c6e4b130084c4_GRCh37_to_NCBI36.chain added
c6e4b523e9ffc_GRCh38_to_GRCh37.chain added
c6e4bba92ed4_GRCh38_to_NCBI34.chain added
c6e4b19ba0cbc_GRCh38_to_NCBI35.chain added
c6e4b1299a50c_GRCh38_to_NCBI36.chain added
c6e4b4db40e6_NCBI34_to_GRCh37.chain added
c6e4b391fdadc_NCBI34_to_GRCh38.chain added
c6e4b52c1c150_NCBI35_to_GRCh37.chain added
c6e4b87b70a1_NCBI35_to_GRCh38.chain added
c6e4b710ba99d_NCBI36_to_GRCh37.chain added
c6e4b61681fb7_NCBI36_to_GRCh38.chain added
c6e4b7b174ea3_GRCm38_to_NCBIM36.chain added
c6e4b62b3d01_GRCm38_to_NCBIM37.chain added
c6e4b4a7955b_NCBIM36_to_GRCm38.chain added
c6e4b7c85481e_NCBIM37_to_GRCm38.chain added
c6e4b52ab016e_1000G_omni2.5.b37.vcf.gz added
c6e4b58f624d4_1000G_omni2.5.b37.vcf.gz.tbi added
c6e4b64673adc_Mills_and_1000G_gold_standard.indels.b37.vcf.gz added
c6e4b3922bb94_Mills_and_1000G_gold_standard.indels.b37.vcf.gz.tbi added
c6e4b1bddf15_1000G_omni2.5.hg38.vcf.gz added
c6e4b3586669f_1000G_omni2.5.hg38.vcf.gz.tbi added
c6e4b7faf64ef_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz added
c6e4b400c0202_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz.tbi added
c6e4b1af444ac_af-only-gnomad.raw.sites.vcf added
c6e4b330fe29a_af-only-gnomad.raw.sites.vcf.idx added
c6e4b4767264e_Mutect2-exome-panel.vcf.idx added
c6e4b70510435_Mutect2-WGS-panel-b37.vcf added
c6e4b17e2b5b9_Mutect2-WGS-panel-b37.vcf.idx added
c6e4bc9369e9_small_exac_common_3.vcf added
c6e4b1ad69c9e_small_exac_common_3.vcf.idx added
c6e4b6d8d59ce_1000g_pon.hg38.vcf.gz added
c6e4b1f93eead_1000g_pon.hg38.vcf.gz.tbi added
c6e4b6d153c9b_af-only-gnomad.hg38.vcf.gz added
c6e4b793688a2_af-only-gnomad.hg38.vcf.gz.tbi added
c6e4b394dfb6a_small_exac_common_3.hg38.vcf.gz added
c6e4b7faee1a7_small_exac_common_3.hg38.vcf.gz.tbi added
c6e4b7e11c988_gencode.v41.annotation.gtf added
c6e4b726dd646_gencode.v42.annotation.gtf added
c6e4b5270a2f7_gencode.vM30.annotation.gtf added
c6e4b68d3a29_gencode.vM31.annotation.gtf added
c6e4b63797fe3_gencode.v41.transcripts.fa added
c6e4b33d8c2ae_gencode.v41.transcripts.fa.fai added
c6e4b1a488cc_gencode.v42.transcripts.fa added
c6e4b69a4bce5_gencode.v42.transcripts.fa.fai added
c6e4b38805809_gencode.vM30.pc_transcripts.fa added
c6e4b7e29d0ea_gencode.vM30.pc_transcripts.fa.fai added
c6e4b3c4fbe53_gencode.vM31.pc_transcripts.fa added
c6e4b11767cdd_gencode.vM31.pc_transcripts.fa.fai added
c6e4b62910bc7_GRCh38.primary_assembly.genome.fa.1.ht2 added
c6e4b757279e7_GRCh38.primary_assembly.genome.fa.2.ht2 added
c6e4b13345bf3_GRCh38.primary_assembly.genome.fa.3.ht2 added
c6e4b18177266_GRCh38.primary_assembly.genome.fa.4.ht2 added
c6e4b7521ded7_GRCh38.primary_assembly.genome.fa.5.ht2 added
c6e4b53405df5_GRCh38.primary_assembly.genome.fa.6.ht2 added
c6e4b330bb713_GRCh38.primary_assembly.genome.fa.7.ht2 added
c6e4b2831c171_GRCh38.primary_assembly.genome.fa.8.ht2 added
c6e4b1aa78444_GRCh38_full_analysis_set_plus_decoy_hla.fa.fai added
c6e4b235cbb48_GRCh38_full_analysis_set_plus_decoy_hla.fa.amb added
c6e4b4014772a_GRCh38_full_analysis_set_plus_decoy_hla.fa.ann added
c6e4b273aee2d_GRCh38_full_analysis_set_plus_decoy_hla.fa.bwt added
c6e4b3e3357e6_GRCh38_full_analysis_set_plus_decoy_hla.fa.pac added
c6e4b2da1d0f8_GRCh38_full_analysis_set_plus_decoy_hla.fa.sa added
c6e4b46cedcda_GRCh38_full_analysis_set_plus_decoy_hla.fa added
c6e4b2b489481_GRCh38.primary_assembly.genome.fa.fai added
c6e4b26d8599a_GRCh38.primary_assembly.genome.fa.amb added
c6e4b1cd844_GRCh38.primary_assembly.genome.fa.ann added
c6e4b2af77628_GRCh38.primary_assembly.genome.fa.bwt added
c6e4b24ea2322_GRCh38.primary_assembly.genome.fa.pac added
c6e4b728aae8a_GRCh38.primary_assembly.genome.fa.sa added
c6e4b7d68191f_GRCh38.primary_assembly.genome.fa added
c6e4b2b775d4c_hs37d5.fa.fai added
c6e4b56042e6e_hs37d5.fa.amb added
c6e4b3140dbce_hs37d5.fa.ann added
c6e4b2d1be618_hs37d5.fa.bwt added
c6e4b3fa8eb53_hs37d5.fa.pac added
c6e4b69c133d7_hs37d5.fa.sa added
c6e4b2b45b703_hs37d5.fa added
c6e4b7bf8a9a6_complete_ref_lens.bin added
c6e4b7b37b0b5_ctable.bin added
c6e4bdd6c2ca_ctg_offsets.bin added
c6e4b716b238e_duplicate_clusters.tsv added
c6e4be6c0ca8_info.json added
c6e4b25ee3530_mphf.bin added
c6e4b668d0265_pos.bin added
c6e4b61ac6a9d_pre_indexing.log added
c6e4b58f9ec43_rank.bin added
c6e4bebec3d6_ref_indexing.log added
c6e4b7c53eee1_refAccumLengths.bin added
c6e4b7c56a78b_reflengths.bin added
c6e4b4ed33b00_refseq.bin added
c6e4b238edd0e_seq.bin added
c6e4b3a89ff72_versionInfo.json added
c6e4b7c750bf8_salmon_index added
c6e4b6a5db9e9_chrLength.txt added
c6e4b65d293f3_chrName.txt added
c6e4b234d6592_chrNameLength.txt added
c6e4b6a7a922d_chrStart.txt added
c6e4b10ca0a1c_exonGeTrInfo.tab added
c6e4b483788b4_exonInfo.tab added
c6e4b5d0540b8_geneInfo.tab added
c6e4be32233b_Genome added
c6e4b73aee600_genomeParameters.txt added
c6e4b33096f26_Log.out added
c6e4b3f72ff09_SA added
c6e4b20cacc19_SAindex added
c6e4b72b25a79_sjdbInfo.txt added
c6e4b293432e1_sjdbList.fromGTF.out.tab added
c6e4b4c10831c_sjdbList.out.tab added
c6e4b6eab041f_transcriptInfo.tab added
c6e4b246be396_GRCh38.GENCODE.v42_100 added
c6e4b59e745e6_knownGene_hg38.sql added
c6e4b601627ad_knownGene_hg38.txt added
c6e4b32d7f03e_refGene_hg38.sql added
c6e4b7fd57b16_refGene_hg38.txt added
c6e4b46a32a12_knownGene_mm39.sql added
c6e4b14845adb_knownGene_mm39.txt added
c6e4b58cf675a_refGene_mm39.sql added
c6e4b5561ede8_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/RtmpA3sjxN/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 ]
>
> proc.time()
user system elapsed
30.472 1.628 36.943
ReUseData.Rcheck/ReUseData-Ex.timings
| name | user | system | elapsed | |
| dataHub-class | 8.907 | 0.339 | 9.268 | |
| dataSearch | 1.387 | 0.012 | 1.401 | |
| dataUpdate | 16.421 | 0.764 | 17.220 | |
| getCloudData | 9.928 | 0.267 | 15.628 | |
| getData | 4.866 | 0.156 | 5.025 | |
| meta_data | 0.01 | 0.00 | 0.01 | |
| recipeHub-class | 0.235 | 0.000 | 0.236 | |
| recipeLoad | 1.502 | 0.004 | 1.511 | |
| recipeMake | 4.575 | 0.201 | 4.777 | |
| recipeSearch | 0.678 | 0.031 | 0.711 | |
| recipeUpdate | 0.000 | 0.002 | 0.002 | |