| Back to Multiple platform build/check report for BioC 3.17: simplified long |
|
This page was generated on 2023-10-16 11:35:41 -0400 (Mon, 16 Oct 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 22.04.2 LTS) | x86_64 | 4.3.1 (2023-06-16) -- "Beagle Scouts" | 4626 |
| palomino3 | Windows Server 2022 Datacenter | x64 | 4.3.1 (2023-06-16 ucrt) -- "Beagle Scouts" | 4379 |
| merida1 | macOS 12.6.4 Monterey | x86_64 | 4.3.1 (2023-06-16) -- "Beagle Scouts" | 4395 |
| 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 1693/2230 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| ReUseData 1.0.1 (landing page) Qian Liu
| nebbiolo1 | Linux (Ubuntu 22.04.2 LTS) / x86_64 | OK | OK | ERROR | |||||||||
| palomino3 | Windows Server 2022 Datacenter / x64 | ... NOT SUPPORTED ... | ||||||||||||
| merida1 | macOS 12.6.4 Monterey / x86_64 | OK | ERROR | skipped | skipped | |||||||||
| kjohnson2 | macOS 12.6.1 Monterey / arm64 | see weekly results here | ||||||||||||
|
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: 1.0.1 |
| Command: /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:ReUseData.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/site-library --timings ReUseData_1.0.1.tar.gz |
| StartedAt: 2023-10-16 00:22:45 -0400 (Mon, 16 Oct 2023) |
| EndedAt: 2023-10-16 00:25:15 -0400 (Mon, 16 Oct 2023) |
| EllapsedTime: 149.8 seconds |
| RetCode: 1 |
| Status: ERROR |
| CheckDir: ReUseData.Rcheck |
| Warnings: NA |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:ReUseData.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/site-library --timings ReUseData_1.0.1.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/ReUseData.Rcheck’
* using R version 4.3.1 (2023-06-16)
* using platform: x86_64-pc-linux-gnu (64-bit)
* R was compiled by
gcc (Ubuntu 11.3.0-1ubuntu1~22.04.1) 11.3.0
GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04.1) 11.3.0
* running under: Ubuntu 22.04.3 LTS
* using session charset: UTF-8
* checking for file ‘ReUseData/DESCRIPTION’ ... OK
* this is package ‘ReUseData’ version ‘1.0.1’
* 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 9.895 0.506 10.512
getCloudData 7.363 0.333 8.589
dataHub-class 6.227 0.696 6.923
* 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-3.17-bioc/meat/ReUseData.Rcheck/00check.log’
for details.
ReUseData.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL ReUseData ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.17-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 4.3.1 (2023-06-16) -- "Beagle Scouts"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: x86_64-pc-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...
2d7f6056e8cda7_GRCh38.primary_assembly.genome.fa.1.bt2 added
2d7f6019ff8810_GRCh38.primary_assembly.genome.fa.2.bt2 added
2d7f603dba6123_GRCh38.primary_assembly.genome.fa.3.bt2 added
2d7f60bb13777_GRCh38.primary_assembly.genome.fa.4.bt2 added
2d7f60222e4814_GRCh38.primary_assembly.genome.fa.rev.1.bt2 added
2d7f608d74c19_GRCh38.primary_assembly.genome.fa.rev.2.bt2 added
2d7f604014a5d2_outfile.txt added
2d7f603b68a7e9_GRCh37_to_GRCh38.chain added
2d7f604d5e94d6_GRCh37_to_NCBI34.chain added
2d7f602649417d_GRCh37_to_NCBI35.chain added
2d7f6060495842_GRCh37_to_NCBI36.chain added
2d7f603416d45f_GRCh38_to_GRCh37.chain added
2d7f607d679bc2_GRCh38_to_NCBI34.chain added
2d7f6049d7fb1d_GRCh38_to_NCBI35.chain added
2d7f60edf7ae2_GRCh38_to_NCBI36.chain added
2d7f6044279fa1_NCBI34_to_GRCh37.chain added
2d7f605a07d25_NCBI34_to_GRCh38.chain added
2d7f602324442a_NCBI35_to_GRCh37.chain added
2d7f605c7cf059_NCBI35_to_GRCh38.chain added
2d7f601063431b_NCBI36_to_GRCh37.chain added
2d7f603cd4f51e_NCBI36_to_GRCh38.chain added
2d7f6034726aa8_GRCm38_to_NCBIM36.chain added
2d7f604704a62_GRCm38_to_NCBIM37.chain added
2d7f60773c06c3_NCBIM36_to_GRCm38.chain added
2d7f6078c2604d_NCBIM37_to_GRCm38.chain added
2d7f605fbe6b36_1000G_omni2.5.b37.vcf.gz added
2d7f60704d6b83_1000G_omni2.5.b37.vcf.gz.tbi added
2d7f601aec7101_Mills_and_1000G_gold_standard.indels.b37.vcf.gz added
2d7f60344b2459_Mills_and_1000G_gold_standard.indels.b37.vcf.gz.tbi added
2d7f60635f17b9_1000G_omni2.5.hg38.vcf.gz added
2d7f60120175ae_1000G_omni2.5.hg38.vcf.gz.tbi added
2d7f60b33f200_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz added
2d7f607d5e9fca_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz.tbi added
2d7f604fbbd6d1_af-only-gnomad.raw.sites.vcf added
2d7f6016e52978_af-only-gnomad.raw.sites.vcf.idx added
2d7f601f8ce7de_Mutect2-exome-panel.vcf.idx added
2d7f60589322ea_Mutect2-WGS-panel-b37.vcf added
2d7f6056f9cf4a_Mutect2-WGS-panel-b37.vcf.idx added
2d7f605af58fc7_small_exac_common_3.vcf added
2d7f6025f1b7c0_small_exac_common_3.vcf.idx added
2d7f607d4310c7_1000g_pon.hg38.vcf.gz added
2d7f603b3ee809_1000g_pon.hg38.vcf.gz.tbi added
2d7f605a088c1f_af-only-gnomad.hg38.vcf.gz added
2d7f607aaaac89_af-only-gnomad.hg38.vcf.gz.tbi added
2d7f60516e326_small_exac_common_3.hg38.vcf.gz added
2d7f6068e80701_small_exac_common_3.hg38.vcf.gz.tbi added
2d7f603ed24c2a_gencode.v41.annotation.gtf added
2d7f60ab7604b_gencode.v42.annotation.gtf added
2d7f60c0c4b2b_gencode.vM30.annotation.gtf added
2d7f601b4f3c83_gencode.vM31.annotation.gtf added
2d7f601b1aa367_gencode.v41.transcripts.fa added
2d7f6048e14049_gencode.v41.transcripts.fa.fai added
2d7f604fc1a72b_gencode.v42.transcripts.fa added
2d7f601f8aedc9_gencode.v42.transcripts.fa.fai added
2d7f60401d470c_gencode.vM30.pc_transcripts.fa added
2d7f6048840778_gencode.vM30.pc_transcripts.fa.fai added
2d7f607f4958ff_gencode.vM31.pc_transcripts.fa added
2d7f60306ab290_gencode.vM31.pc_transcripts.fa.fai added
2d7f6063707879_GRCh38.primary_assembly.genome.fa.1.ht2 added
2d7f6033947d58_GRCh38.primary_assembly.genome.fa.2.ht2 added
2d7f6013c9ca49_GRCh38.primary_assembly.genome.fa.3.ht2 added
2d7f607571ee27_GRCh38.primary_assembly.genome.fa.4.ht2 added
2d7f603ec86f59_GRCh38.primary_assembly.genome.fa.5.ht2 added
2d7f6011286a13_GRCh38.primary_assembly.genome.fa.6.ht2 added
2d7f60452dc4f8_GRCh38.primary_assembly.genome.fa.7.ht2 added
2d7f6055ad98d1_GRCh38.primary_assembly.genome.fa.8.ht2 added
2d7f6030b551f1_GRCh38_full_analysis_set_plus_decoy_hla.fa.fai added
2d7f601dc0e7e2_GRCh38_full_analysis_set_plus_decoy_hla.fa.amb added
2d7f602ca7681b_GRCh38_full_analysis_set_plus_decoy_hla.fa.ann added
2d7f60baae1b8_GRCh38_full_analysis_set_plus_decoy_hla.fa.bwt added
2d7f6043b29fa2_GRCh38_full_analysis_set_plus_decoy_hla.fa.pac added
2d7f6029ea78e3_GRCh38_full_analysis_set_plus_decoy_hla.fa.sa added
2d7f6046e9c9c1_GRCh38_full_analysis_set_plus_decoy_hla.fa added
2d7f601dbb2bc1_GRCh38.primary_assembly.genome.fa.fai added
2d7f602495256c_GRCh38.primary_assembly.genome.fa.amb added
2d7f604c00ace7_GRCh38.primary_assembly.genome.fa.ann added
2d7f606a332c2_GRCh38.primary_assembly.genome.fa.bwt added
2d7f6063677197_GRCh38.primary_assembly.genome.fa.pac added
2d7f6056b80d33_GRCh38.primary_assembly.genome.fa.sa added
2d7f6012af7dee_GRCh38.primary_assembly.genome.fa added
2d7f607eb6ae1a_hs37d5.fa.fai added
2d7f6071d2b09a_hs37d5.fa.amb added
2d7f605b90be37_hs37d5.fa.ann added
2d7f604e785546_hs37d5.fa.bwt added
2d7f60115d9e63_hs37d5.fa.pac added
2d7f601bae0544_hs37d5.fa.sa added
2d7f6016fc5cbe_hs37d5.fa added
2d7f6010a6f763_complete_ref_lens.bin added
2d7f604c18b7d4_ctable.bin added
2d7f607a6cd538_ctg_offsets.bin added
2d7f60443b74bb_duplicate_clusters.tsv added
2d7f605fe2821d_info.json added
2d7f606fdec35f_mphf.bin added
2d7f60303e414_pos.bin added
2d7f60710aec31_pre_indexing.log added
2d7f60350c8858_rank.bin added
2d7f6058b17ce5_ref_indexing.log added
2d7f6021c03e22_refAccumLengths.bin added
2d7f6052cd703a_reflengths.bin added
2d7f60558e501_refseq.bin added
2d7f602d6b1fdb_seq.bin added
2d7f6016800fdd_versionInfo.json added
2d7f602f435de4_salmon_index added
2d7f607454e99c_chrLength.txt added
2d7f60343b3b9e_chrName.txt added
2d7f6053d88350_chrNameLength.txt added
2d7f6040559684_chrStart.txt added
2d7f603ade6e61_exonGeTrInfo.tab added
2d7f60373ff4e7_exonInfo.tab added
2d7f60170da3b7_geneInfo.tab added
2d7f604d8dec4f_Genome added
2d7f6035f6a302_genomeParameters.txt added
2d7f608e05451_Log.out added
2d7f60291eaa86_SA added
2d7f6046ef848_SAindex added
2d7f601a3df2b4_sjdbInfo.txt added
2d7f6044ccafca_sjdbList.fromGTF.out.tab added
2d7f601b6b5506_sjdbList.out.tab added
2d7f602ae4ea17_transcriptInfo.tab added
2d7f6010e5679e_GRCh38.GENCODE.v42_100 added
2d7f6015d82a3e_knownGene_hg38.sql added
2d7f606f205ed3_knownGene_hg38.txt added
2d7f6070c7e9bc_refGene_hg38.sql added
2d7f605b6ed9e_refGene_hg38.txt added
2d7f60722442e7_knownGene_mm39.sql added
2d7f6061d2d5ed_knownGene_mm39.txt added
2d7f603ac375f6_refGene_mm39.sql added
2d7f604ad5bfcd_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/Rtmp8sXA2O/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
20.863 0.983 22.557
ReUseData.Rcheck/ReUseData-Ex.timings
| name | user | system | elapsed | |
| dataHub-class | 6.227 | 0.696 | 6.923 | |
| dataSearch | 0.975 | 0.040 | 1.015 | |
| dataUpdate | 9.895 | 0.506 | 10.512 | |
| getCloudData | 7.363 | 0.333 | 8.589 | |
| getData | 3.155 | 0.096 | 3.257 | |
| meta_data | 0.006 | 0.000 | 0.006 | |
| recipeHub-class | 0.206 | 0.012 | 0.217 | |
| recipeLoad | 1.053 | 0.055 | 1.109 | |
| recipeMake | 3.015 | 0.146 | 3.161 | |
| recipeSearch | 0.483 | 0.024 | 0.508 | |
| recipeUpdate | 0.000 | 0.000 | 0.001 | |