| Back to Multiple platform build/check report for BioC 3.17 |
|
This page was generated on 2023-04-12 10:55:40 -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: 2023-04-12 08:47:09 -0400 (Wed, 12 Apr 2023) |
| EndedAt: 2023-04-12 08:50:32 -0400 (Wed, 12 Apr 2023) |
| EllapsedTime: 203.6 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 Under development (unstable) (2023-02-14 r83833)
* using platform: x86_64-pc-linux-gnu (64-bit)
* R was compiled by
gcc (Ubuntu 9.4.0-1ubuntu1~20.04.1) 9.4.0
GNU Fortran (Ubuntu 9.4.0-1ubuntu1~20.04.1) 9.4.0
* running under: Ubuntu 20.04.6 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 13.774 0.445 14.223
getCloudData 11.205 0.336 12.411
dataHub-class 9.482 0.407 9.894
* 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 Under development (unstable) (2023-02-14 r83833) -- "Unsuffered Consequences"
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...
f92b12003c58_GRCh38.primary_assembly.genome.fa.1.bt2 added
f92b7aab50bb_GRCh38.primary_assembly.genome.fa.2.bt2 added
f92b5d74092e_GRCh38.primary_assembly.genome.fa.3.bt2 added
f92b6441402c_GRCh38.primary_assembly.genome.fa.4.bt2 added
f92b339a42d4_GRCh38.primary_assembly.genome.fa.rev.1.bt2 added
f92b2d767901_GRCh38.primary_assembly.genome.fa.rev.2.bt2 added
f92bc62b09b_outfile.txt added
f92b4f46693d_GRCh37_to_GRCh38.chain added
f92b396fbbc2_GRCh37_to_NCBI34.chain added
f92b13ef4e74_GRCh37_to_NCBI35.chain added
f92b54272ee1_GRCh37_to_NCBI36.chain added
f92b32669475_GRCh38_to_GRCh37.chain added
f92b1f498510_GRCh38_to_NCBI34.chain added
f92b5240007b_GRCh38_to_NCBI35.chain added
f92b1c90bbd7_GRCh38_to_NCBI36.chain added
f92b44e57b6_NCBI34_to_GRCh37.chain added
f92b356700a9_NCBI34_to_GRCh38.chain added
f92b660e3241_NCBI35_to_GRCh37.chain added
f92b7c64d6e4_NCBI35_to_GRCh38.chain added
f92b6ad2716d_NCBI36_to_GRCh37.chain added
f92b5f7e19b_NCBI36_to_GRCh38.chain added
f92b10ea1450_GRCm38_to_NCBIM36.chain added
f92b73b8f984_GRCm38_to_NCBIM37.chain added
f92b7d8e07c0_NCBIM36_to_GRCm38.chain added
f92b7ddbda01_NCBIM37_to_GRCm38.chain added
f92b28a5c84c_1000G_omni2.5.b37.vcf.gz added
f92b7aa05768_1000G_omni2.5.b37.vcf.gz.tbi added
f92b61ac7adf_Mills_and_1000G_gold_standard.indels.b37.vcf.gz added
f92b56e952c5_Mills_and_1000G_gold_standard.indels.b37.vcf.gz.tbi added
f92b1304ea53_1000G_omni2.5.hg38.vcf.gz added
f92b44c04987_1000G_omni2.5.hg38.vcf.gz.tbi added
f92b68e98f1d_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz added
f92bdb03b0e_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz.tbi added
f92b223452b6_af-only-gnomad.raw.sites.vcf added
f92b4d2acf49_af-only-gnomad.raw.sites.vcf.idx added
f92b414a7de2_Mutect2-exome-panel.vcf.idx added
f92b4faacbb7_Mutect2-WGS-panel-b37.vcf added
f92b598d7fe4_Mutect2-WGS-panel-b37.vcf.idx added
f92b1090e720_small_exac_common_3.vcf added
f92b91a877a_small_exac_common_3.vcf.idx added
f92b6d7cce58_1000g_pon.hg38.vcf.gz added
f92b64b81601_1000g_pon.hg38.vcf.gz.tbi added
f92b3b811bef_af-only-gnomad.hg38.vcf.gz added
f92bcc65369_af-only-gnomad.hg38.vcf.gz.tbi added
f92b36f8167c_small_exac_common_3.hg38.vcf.gz added
f92b5811d7c6_small_exac_common_3.hg38.vcf.gz.tbi added
f92b1114ab1f_gencode.v41.annotation.gtf added
f92b6c5f1726_gencode.v42.annotation.gtf added
f92b3e200a07_gencode.vM30.annotation.gtf added
f92bd798203_gencode.vM31.annotation.gtf added
f92b57318893_gencode.v41.transcripts.fa added
f92b4417eba2_gencode.v41.transcripts.fa.fai added
f92b1e639654_gencode.v42.transcripts.fa added
f92b4aea8217_gencode.v42.transcripts.fa.fai added
f92b41a5f363_gencode.vM30.pc_transcripts.fa added
f92b1c3f7055_gencode.vM30.pc_transcripts.fa.fai added
f92b73904a63_gencode.vM31.pc_transcripts.fa added
f92b3c464acb_gencode.vM31.pc_transcripts.fa.fai added
f92b7debeb34_GRCh38.primary_assembly.genome.fa.1.ht2 added
f92b4a799d28_GRCh38.primary_assembly.genome.fa.2.ht2 added
f92b4f4b351e_GRCh38.primary_assembly.genome.fa.3.ht2 added
f92b42ac34bc_GRCh38.primary_assembly.genome.fa.4.ht2 added
f92b33632c45_GRCh38.primary_assembly.genome.fa.5.ht2 added
f92b5cfb702c_GRCh38.primary_assembly.genome.fa.6.ht2 added
f92b64e08772_GRCh38.primary_assembly.genome.fa.7.ht2 added
f92b8dfb8e_GRCh38.primary_assembly.genome.fa.8.ht2 added
f92b1e45ee0e_GRCh38_full_analysis_set_plus_decoy_hla.fa.fai added
f92b348b5329_GRCh38_full_analysis_set_plus_decoy_hla.fa.amb added
f92b5a1b7b73_GRCh38_full_analysis_set_plus_decoy_hla.fa.ann added
f92b2ed6d52e_GRCh38_full_analysis_set_plus_decoy_hla.fa.bwt added
f92b3da5daa3_GRCh38_full_analysis_set_plus_decoy_hla.fa.pac added
f92b479849cb_GRCh38_full_analysis_set_plus_decoy_hla.fa.sa added
f92b138eeb2f_GRCh38_full_analysis_set_plus_decoy_hla.fa added
f92b7926f692_GRCh38.primary_assembly.genome.fa.fai added
f92b545e9d34_GRCh38.primary_assembly.genome.fa.amb added
f92b4a8701ac_GRCh38.primary_assembly.genome.fa.ann added
f92b5138ce58_GRCh38.primary_assembly.genome.fa.bwt added
f92b65734853_GRCh38.primary_assembly.genome.fa.pac added
f92b36e618d2_GRCh38.primary_assembly.genome.fa.sa added
f92bf58d85f_GRCh38.primary_assembly.genome.fa added
f92b72ecca57_hs37d5.fa.fai added
f92be17a165_hs37d5.fa.amb added
f92b5370c402_hs37d5.fa.ann added
f92b115060ab_hs37d5.fa.bwt added
f92b5902237c_hs37d5.fa.pac added
f92b1516b765_hs37d5.fa.sa added
f92b2d8fd100_hs37d5.fa added
f92b4c926ddf_complete_ref_lens.bin added
f92b515d0230_ctable.bin added
f92b2b7bbc34_ctg_offsets.bin added
f92b170c0b08_duplicate_clusters.tsv added
f92b20a8374e_info.json added
f92b6e27f0f0_mphf.bin added
f92b4a6f374d_pos.bin added
f92b7da3a77a_pre_indexing.log added
f92b53087862_rank.bin added
f92b4afd32dc_ref_indexing.log added
f92b1be99588_refAccumLengths.bin added
f92b793cb8c_reflengths.bin added
f92b2518ae4f_refseq.bin added
f92b4ac06ab7_seq.bin added
f92b4539a62f_versionInfo.json added
f92b6cb0f81a_salmon_index added
f92b5e4f55e6_chrLength.txt added
f92b3e609cc2_chrName.txt added
f92b410f954f_chrNameLength.txt added
f92b28d65792_chrStart.txt added
f92bf996b1a_exonGeTrInfo.tab added
f92b2682dda2_exonInfo.tab added
f92b5fbc7064_geneInfo.tab added
f92b1ef2437a_Genome added
f92b196fa7f9_genomeParameters.txt added
f92b6dd411c9_Log.out added
f92b7263077c_SA added
f92b2ac008a4_SAindex added
f92b46d63545_sjdbInfo.txt added
f92b779bee1_sjdbList.fromGTF.out.tab added
f92b584fd9a4_sjdbList.out.tab added
f92b1368a325_transcriptInfo.tab added
f92b58d6c111_GRCh38.GENCODE.v42_100 added
f92b3cb95d9_knownGene_hg38.sql added
f92b2a74ae2d_knownGene_hg38.txt added
f92b797ef85f_refGene_hg38.sql added
f92b71f386c9_refGene_hg38.txt added
f92b74e3e57a_knownGene_mm39.sql added
f92b77229fd9_knownGene_mm39.txt added
f92b44fbff2c_refGene_mm39.sql added
f92b3fe11856_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/RtmpRF0luu/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
28.702 1.540 30.655
ReUseData.Rcheck/ReUseData-Ex.timings
| name | user | system | elapsed | |
| dataHub-class | 9.482 | 0.407 | 9.894 | |
| dataSearch | 1.639 | 0.020 | 1.660 | |
| dataUpdate | 13.774 | 0.445 | 14.223 | |
| getCloudData | 11.205 | 0.336 | 12.411 | |
| getData | 3.236 | 0.190 | 3.420 | |
| meta_data | 0.007 | 0.000 | 0.008 | |
| recipeHub-class | 0.291 | 0.004 | 0.294 | |
| recipeLoad | 1.620 | 0.140 | 1.763 | |
| recipeMake | 2.976 | 0.214 | 3.187 | |
| recipeSearch | 0.563 | 0.032 | 0.594 | |
| recipeUpdate | 0 | 0 | 0 | |