| Back to Multiple platform build/check report for BioC 3.17 |
|
This page was generated on 2023-04-12 10:55:30 -0400 (Wed, 12 Apr 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 22.04.1 LTS) | x86_64 | 4.3.0 alpha (2023-04-03 r84154) | 4547 |
| nebbiolo2 | Linux (Ubuntu 20.04.5 LTS) | x86_64 | R Under development (unstable) (2023-02-14 r83833) -- "Unsuffered Consequences" | 4333 |
| 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 1676/2207 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| ReUseData 0.99.38 (landing page) Qian Liu
| nebbiolo1 | Linux (Ubuntu 22.04.1 LTS) / x86_64 | OK | OK | ERROR | |||||||||
| nebbiolo2 | Linux (Ubuntu 20.04.5 LTS) / x86_64 | OK | OK | ERROR | ||||||||||
| Package: ReUseData |
| Version: 0.99.38 |
| 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_0.99.38.tar.gz |
| StartedAt: 2023-04-11 22:57:18 -0400 (Tue, 11 Apr 2023) |
| EndedAt: 2023-04-11 22:59:51 -0400 (Tue, 11 Apr 2023) |
| EllapsedTime: 152.8 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_0.99.38.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/ReUseData.Rcheck’
* using R version 4.3.0 alpha (2023-04-03 r84154)
* using platform: x86_64-pc-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 ‘0.99.38’
* 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 10.211 0.425 10.642
getCloudData 7.788 0.412 9.093
dataHub-class 6.309 0.395 6.706
* 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 4.3.0 alpha (2023-04-03 r84154)
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...
8415e353e0505_GRCh38.primary_assembly.genome.fa.1.bt2 added
8415e1697d89_GRCh38.primary_assembly.genome.fa.2.bt2 added
8415e315e05fc_GRCh38.primary_assembly.genome.fa.3.bt2 added
8415e4cca56ee_GRCh38.primary_assembly.genome.fa.4.bt2 added
8415e524bc624_GRCh38.primary_assembly.genome.fa.rev.1.bt2 added
8415e1ffb3fb1_GRCh38.primary_assembly.genome.fa.rev.2.bt2 added
8415e5b63104_outfile.txt added
8415e1e084439_GRCh37_to_GRCh38.chain added
8415e7c61d588_GRCh37_to_NCBI34.chain added
8415e713e80e2_GRCh37_to_NCBI35.chain added
8415e64b6602e_GRCh37_to_NCBI36.chain added
8415e3e072b14_GRCh38_to_GRCh37.chain added
8415e60a47625_GRCh38_to_NCBI34.chain added
8415eaf8d1b9_GRCh38_to_NCBI35.chain added
8415e19485d23_GRCh38_to_NCBI36.chain added
8415e65edadd8_NCBI34_to_GRCh37.chain added
8415e71f8450c_NCBI34_to_GRCh38.chain added
8415e43f8b557_NCBI35_to_GRCh37.chain added
8415e11cade77_NCBI35_to_GRCh38.chain added
8415e508159fc_NCBI36_to_GRCh37.chain added
8415e7fef5201_NCBI36_to_GRCh38.chain added
8415e51c7e0a9_GRCm38_to_NCBIM36.chain added
8415e44c65db9_GRCm38_to_NCBIM37.chain added
8415e6e4ef1e6_NCBIM36_to_GRCm38.chain added
8415e7561b58a_NCBIM37_to_GRCm38.chain added
8415e1ca1f88c_1000G_omni2.5.b37.vcf.gz added
8415e7641ae9d_1000G_omni2.5.b37.vcf.gz.tbi added
8415e4a6c9b24_Mills_and_1000G_gold_standard.indels.b37.vcf.gz added
8415e7d20bc1b_Mills_and_1000G_gold_standard.indels.b37.vcf.gz.tbi added
8415e490cd277_1000G_omni2.5.hg38.vcf.gz added
8415e74ebe9f2_1000G_omni2.5.hg38.vcf.gz.tbi added
8415e325ec121_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz added
8415e4a765001_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz.tbi added
8415e2649efee_af-only-gnomad.raw.sites.vcf added
8415e7f29180f_af-only-gnomad.raw.sites.vcf.idx added
8415e1cc21625_Mutect2-exome-panel.vcf.idx added
8415e46452f9f_Mutect2-WGS-panel-b37.vcf added
8415e4df4913_Mutect2-WGS-panel-b37.vcf.idx added
8415e3aca5a5e_small_exac_common_3.vcf added
8415e42a70527_small_exac_common_3.vcf.idx added
8415e761dc9f5_1000g_pon.hg38.vcf.gz added
8415e1f80ba8c_1000g_pon.hg38.vcf.gz.tbi added
8415eae303b_af-only-gnomad.hg38.vcf.gz added
8415e56c2401a_af-only-gnomad.hg38.vcf.gz.tbi added
8415e2a798c45_small_exac_common_3.hg38.vcf.gz added
8415e19f68d5e_small_exac_common_3.hg38.vcf.gz.tbi added
8415e3cafedf2_gencode.v41.annotation.gtf added
8415e1c71d152_gencode.v42.annotation.gtf added
8415e5def42b6_gencode.vM30.annotation.gtf added
8415e4e7acc69_gencode.vM31.annotation.gtf added
8415e6cf32b4e_gencode.v41.transcripts.fa added
8415e5dde94b7_gencode.v41.transcripts.fa.fai added
8415e2042ad13_gencode.v42.transcripts.fa added
8415e31b98907_gencode.v42.transcripts.fa.fai added
8415e4c2d869e_gencode.vM30.pc_transcripts.fa added
8415e15a4629d_gencode.vM30.pc_transcripts.fa.fai added
8415e4e5b8194_gencode.vM31.pc_transcripts.fa added
8415e426f353b_gencode.vM31.pc_transcripts.fa.fai added
8415e6010fdc2_GRCh38.primary_assembly.genome.fa.1.ht2 added
8415e4b7c3daf_GRCh38.primary_assembly.genome.fa.2.ht2 added
8415eb7c07b3_GRCh38.primary_assembly.genome.fa.3.ht2 added
8415e54fce7b4_GRCh38.primary_assembly.genome.fa.4.ht2 added
8415e7ddafed0_GRCh38.primary_assembly.genome.fa.5.ht2 added
8415e55f257b4_GRCh38.primary_assembly.genome.fa.6.ht2 added
8415e7b46d7a2_GRCh38.primary_assembly.genome.fa.7.ht2 added
8415e7d0416df_GRCh38.primary_assembly.genome.fa.8.ht2 added
8415e72b46dd9_GRCh38_full_analysis_set_plus_decoy_hla.fa.fai added
8415e418c0742_GRCh38_full_analysis_set_plus_decoy_hla.fa.amb added
8415e1e35ff2_GRCh38_full_analysis_set_plus_decoy_hla.fa.ann added
8415e2d7ec837_GRCh38_full_analysis_set_plus_decoy_hla.fa.bwt added
8415e4330c69_GRCh38_full_analysis_set_plus_decoy_hla.fa.pac added
8415e780129e7_GRCh38_full_analysis_set_plus_decoy_hla.fa.sa added
8415e4cff82c4_GRCh38_full_analysis_set_plus_decoy_hla.fa added
8415e4e13ca5_GRCh38.primary_assembly.genome.fa.fai added
8415e4ec36a02_GRCh38.primary_assembly.genome.fa.amb added
8415e77790f09_GRCh38.primary_assembly.genome.fa.ann added
8415e1ed7ca03_GRCh38.primary_assembly.genome.fa.bwt added
8415eb7357f4_GRCh38.primary_assembly.genome.fa.pac added
8415e13eae05b_GRCh38.primary_assembly.genome.fa.sa added
8415e7cc70cb9_GRCh38.primary_assembly.genome.fa added
8415e59ee245e_hs37d5.fa.fai added
8415ede0ba9_hs37d5.fa.amb added
8415e5aa5a171_hs37d5.fa.ann added
8415e7a30d171_hs37d5.fa.bwt added
8415e329794b1_hs37d5.fa.pac added
8415e26d3280f_hs37d5.fa.sa added
8415efd5340e_hs37d5.fa added
8415ef31645_complete_ref_lens.bin added
8415e69425d4a_ctable.bin added
8415e6fe631d0_ctg_offsets.bin added
8415e4c6f53f4_duplicate_clusters.tsv added
8415e74be64fd_info.json added
8415e44e31984_mphf.bin added
8415e4a4a52c5_pos.bin added
8415e4ab0bcb1_pre_indexing.log added
8415e4029f127_rank.bin added
8415e474e69a4_ref_indexing.log added
8415e3d652a8a_refAccumLengths.bin added
8415e1b5f869_reflengths.bin added
8415e4931c997_refseq.bin added
8415e6ae3f2c2_seq.bin added
8415e5e904d2_versionInfo.json added
8415e4132f37e_salmon_index added
8415e37e37586_chrLength.txt added
8415eaca4177_chrName.txt added
8415eff65d80_chrNameLength.txt added
8415e2f5c848f_chrStart.txt added
8415e29a20b7b_exonGeTrInfo.tab added
8415e1b69b575_exonInfo.tab added
8415e434764eb_geneInfo.tab added
8415e26691834_Genome added
8415e7557d9d3_genomeParameters.txt added
8415e44257094_Log.out added
8415e10eb9a5_SA added
8415e6f88ab44_SAindex added
8415e76bd0545_sjdbInfo.txt added
8415e27e1e1b4_sjdbList.fromGTF.out.tab added
8415e7f5ddf52_sjdbList.out.tab added
8415e77b01b8a_transcriptInfo.tab added
8415e11243eff_GRCh38.GENCODE.v42_100 added
8415e6f441123_knownGene_hg38.sql added
8415e441f6f7f_knownGene_hg38.txt added
8415e5e2a3fc_refGene_hg38.sql added
8415e34272aa7_refGene_hg38.txt added
8415ee69c244_knownGene_mm39.sql added
8415e509360ae_knownGene_mm39.txt added
8415e74511bce_refGene_mm39.sql added
8415e55b82be8_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/RtmpRrtVL9/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
21.923 1.653 23.959
ReUseData.Rcheck/ReUseData-Ex.timings
| name | user | system | elapsed | |
| dataHub-class | 6.309 | 0.395 | 6.706 | |
| dataSearch | 1.026 | 0.037 | 1.061 | |
| dataUpdate | 10.211 | 0.425 | 10.642 | |
| getCloudData | 7.788 | 0.412 | 9.093 | |
| getData | 3.08 | 0.16 | 3.24 | |
| meta_data | 0.006 | 0.000 | 0.007 | |
| recipeHub-class | 0.213 | 0.028 | 0.241 | |
| recipeLoad | 1.059 | 0.071 | 1.132 | |
| recipeMake | 2.963 | 0.087 | 3.051 | |
| recipeSearch | 0.531 | 0.020 | 0.552 | |
| recipeUpdate | 0 | 0 | 0 | |